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

In Silico Subtractive Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pneumoniae Strain D39

Streptococcus pneumoniae is a notorious Gram-positive pathogen present asymptomatically in the nasophayrnx of humans. According to the World Health Organization (W.H.O), pneumococcus causes approximately one million deaths yearly. Antibiotic resistance in S. pneumoniae is raising considerable concern around the world. There is an immediate need to address the major issues that have arisen as a result of persistent infections caused by S. pneumoniae. In the present study, subtractive proteomics was used in which the entire proteome of the pathogen consisting of 1947 proteins is effectively decreased to a finite number of possible targets. Various kinds of bioinformatics tools and software were applied for the discovery of novel inhibitors. The CD-HIT analysis revealed 1887 non-redundant sequences from the entire proteome. These non-redundant proteins were submitted to the BLASTp against the human proteome and 1423 proteins were screened as non-homologous. Further, databases of essential genes (DEGG) and J browser identified almost 171 essential proteins. Moreover, non-homologous, essential proteins were subjected in KEGG Pathway Database which shortlisted six unique proteins. In addition, the subcellular localization of these unique proteins was checked and cytoplasmic proteins were chosen for the druggability analysis, which resulted in three proteins, namely DNA binding response regulator (SPD_1085), UDP-N-acetylmuramate-L-alanine Ligase (SPD_1349) and RNA polymerase sigma factor (SPD_0958), which can act as a promising potent drug candidate to limit the toxicity caused by S. pneumoniae. The 3D structures of these proteins were predicted by Swiss Model, utilizing the homology modeling approach. Later, molecular docking by PyRx software 0.8 version was used to screen a library of phytochemicals retrieved from PubChem and ZINC databases and already approved drugs from DrugBank database against novel druggable targets to check their binding affinity with receptor proteins. The top two molecules from each receptor protein were selected based on the binding affinity, RMSD value, and the highest conformation. Finally, the absorption, distribution, metabolism, excretion, and toxicity (ADMET) analyses were carried out by utilizing the SWISS ADME and Protox tools. This research supported the discovery of cost-effective drugs against S. pneumoniae. However, more in vivo/in vitro research should be conducted on these targets to investigate their pharmacological efficacy and their function as efficient inhibitors.

Evaluation of N 10 -substituted acridone-based derivatives as AKT inhibitors against breast cancer cells: in vitro and molecular docking studies

A series of N 10 -substituted acridone-2-carboxamide derivatives were synthesized and evaluated for their potent anti-cancer agents targeting AKT kinase. In vitro cytotoxicity activity of the target compounds was tested against breast cancer cell lines (MCF-7 and MDA-MB-231). Among the tested compounds, four compounds (7f, 8d, 8e, and 8f) exhibited promising anti-cancer activity against both cancer cell lines. Notably, compound 8f demonstrated the highest activity against MCF-7 and MDA-MB-231 at IC50 values of 4.72 and 5.53 μM, respectively. In vitro AKT kinase activity revealed that compounds 7f and 8f were the most potent AKT inhibitors with IC50 values of 5.38 and 6.90 μM, respectively. In addition, the quantitative ELISA method of testing confirmed that compound 8f effectively inhibited cell proliferation by suppressing the activation of p-AKT Ser473. Furthermore, molecular docking studies revealed that compound 8f can bind well to the active site of the AKT enzyme. The in silico ADME studies suggested that all synthesized molecules showed good oral bioavailability with a low-toxicity profile and can be used for further optimization as AKT kinase inhibitors in the treatment of breast cancer.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03524-z.

Multi-dimensional structural footprint identification for the design of potential scaffolds targeting METTL3 in cancer treatment from natural compounds

CONTEXT

[Formula: see text]-adenosine-methyltransferase (METTL3) is the catalytic domain of the 'writer' proteins which is involved in the post modifications of [Formula: see text]-methyladinosine ([Formula: see text]). Though its activities are essential in many biological processes, it has been implicated in several types of cancer. Thus, drug developers and researchers are relentlessly in search of small molecule inhibitors that can ameliorate the oncogenic activities of METTL3. Currently, STM2457 is a potent, highly selective inhibitor of METTL3 but is yet to be approved.

METHODS

In this study, we employed structure-based virtual screening through consensus docking by using AutoDock Vina in PyRx interface and Glide virtual screening workflow of Schrodinger Glide. Thermodynamics via MM-PBSA calculations was further used to rank the compounds based on their total free binding energies. All atom molecular dynamics simulations were performed using AMBER 18 package. FF14SB force fields and Antechamber were used to parameterize the protein and compounds respectively. Post analysis of generated trajectories was analyzed with CPPTRAJ and PTRAJ modules incorporated in the AMBER package while Discovery studio and UCSF Chimera were used for visualization, and origin data tool used to plot all graphs.

RESULTS

Three compounds with total free binding energies higher than STM2457 were selected for extended molecular dynamics simulations. The compounds, SANCDB0370, SANCDB0867, and SANCDB1033, exhibited stability and deeper penetration into the hydrophobic core of the protein. They engaged in relatively stronger intermolecular interactions involving hydrogen bonds with resultant increase in stability, reduced flexibility, and decrease in the surface area of the protein available for solvent interactions suggesting an induced folding of the catalytic domain. Furthermore, in silico pharmacokinetics and physicochemical analysis of the compounds revealed good properties suggesting these compounds could serve as promising MEETL3 entry inhibitors upon modifications and optimizations as presented by natural compounds. Further biochemical testing and experimentations would aid in the discovery of effective inhibitors against the berserk activities of METTL3.

Computational Approaches for Identification of Potential Plant Bioactives as Novel G6PD Inhibitors Using Advanced Tools and Databases

In glucose metabolism, the pentose phosphate pathway (PPP) is the major metabolic pathway that plays a crucial role in cancer growth and metastasis. Although it has been pointed out that blockade of the PPP is a promising approach against cancer, in the clinical setting, effective anti-PPP agents are still not available. Dysfunction of the G6PD enzyme in this pathway leads to cancer development as this enzyme possesses oncogenic activity. In the present study, an attempt was made to identify bioactive compounds that can be developed as potential G6PD inhibitors. In the present study, 11 natural compounds and a controlled drug were taken. The physicochemical and toxicity properties of the compounds were determined via ADMET and ProTox-II analysis. In the present study, the findings of docking studies revealed that staurosporine was the most effective compound with the highest binding energy of −9.2 kcal/mol when docked against G6PD. Homology modeling revealed that 97.56% of the residues were occupied in the Ramachandran-favored region. The modeled protein gave a quality Z-score of −10.13 by ProSA tool. iMODS server provided significant insights into the mobility, stability and flexibility of the G6PD protein that described the collective functional protein motion. In the present study, the physical and functional interactions between proteins were determined by STRING. CASTp server determined the topological and geometric properties of the G6PD protein. The findings of the present study revealed that staurosporine could be developed as a potential G6PD inhibitor; however, further in vivo and in vitro studies are needed for further validation of these results.

Synthesis, anti-angiogenic activity and prediction toxicity of (E)-3-(3-methoxyphenyl) propenoic acid

Background: Anti-angiogenic medications, one of cancer chemo preventive mechanism were permitted for different cancers. Nevertheless, major primary and secondary resistance obstruct efficacy in several tumor types. Moreover, the improvement of safe and effective NSAIDs for angiogenesis inhibition is complicated, because of their serious toxicity. So, we require improving clinically appropriate strategies to boost efficacy of anti-angiogenic drugs with low risk of toxicity. Objectives: The present study aimed to synthesize the (E)-3- (3-methoxyphenyl)propenoic acid (3MPCA), to determine the anti-angiogenic activity and predict its toxicity. Methods: 3MPCA was obtained by Knoevenagel reaction using microwave irradiation at 400 Watt. The anti-angiogenesis experimental was performed using chorioallantois membrane of embryonated chicken eggs induced by b-FGF. The potency of 3MPCA was verified at dosage 30 and 60 ng and compared with celecoxib 60 ng. Toxicity prediction of 3MPCA was performed by ProTox II online program. Results: The results showed that 3MPCA was achieved in good yield (89%). Anti angogenic activity was showed by endothelial cells growth in neovascular capillaries of new blood vessel of chorioallantois membrane of embryonated chicken eggs. The endothelial cells growth decreased until 41.7-83%. The prediction LD50 was 1772mg/kg. Conclusion: (E)-3-(3-methoxyphenyl)propenoic acid can be obtained through Knovenagel reaction using microwave irradiation and it has potential as anti-angiogenesis inhibitor with low toxicity.

DFT analysis and in silico exploration of drug-likeness, toxicity prediction, bioactivity score, and chemical reactivity properties of the urolithins

Urolithins (Uro) are human microflora-derived metabolites of ellagic acid and ellagitannins. It has been shown to be a powerful modulator of oxidative stress, agents with potential anti-inflammatory, antiproliferative, and antiaging properties. The present study aimed to explore the drug-likeness, toxicity, and bioactivity score of urolithins that were required to be considered oral drug-active using the web-based softwares, Molinspiration, and protox_II. In addition, the chemical reactivity descriptors of the urolithins (Uro A, Uro B, Uro, C, Uro D) were also determined through density functional (DFT) calculations. Furthermore, electrostatic potential (MEP), natural bonds orbitals (NBO), HOMO-LUMO energies, chemical reactivity descriptors, dipole moment, and Fukui functions of all the urolithins were investigated by resorting the conceptual of DFT at the M06-2X/6-311++G (d, p) basis set as a tool to analyse and comprehend the molecular interaction. The results showed that all the urolithins comply with the Lipinski's rule of five and have biological activity. According to the toxicity predictions, Uro A, Uro C, and Uro D belong to class 4 while Uro B belongs to class 6. The chemical reactivity and stability features of the investigated compounds were evaluated using global chemical reactivity descriptors calculated from the Frontier Molecular Orbitals (FMOs) energies gap, which revealed that the stability order of the molecules was Uro B > Uro C > Uro D > Uro A. The present findings indicate that the urolithins could be a promising candidate for development into a therapeutic medication.Communicated by Ramaswamy H. Sarma.

Anticancer and antimicrobial activity of new copper (II) complexes

In this study, three new organic ligands N'-(benzylidene)-6-chloropyrazine-2-carbohydrazonamide (L₁), 6-chloro-N'-(4-nitrobenzylidene)picolinohydrazonamide(L₂), and N'-(benzylidene)-4-chloropicolinohydrazonamide (L₃) and three copper coordination compounds (Cu(L₁)Cl₂, Cu(L₂)Cl₂ and Cu(L₃)Cl₂) based on them were synthesized. All obtained compounds were characterized using appropriate analytical techniques: elemental analysis (EA), thermogravimetric analysis (TG-DTG), Fourier transform infrared spectroscopy (FTIR) and flame-atomic absorption spectrometry (F-AAS). These methods of physicochemical analyses helped to assume that the complexation in three cases proceeds in a bidentate manner. The X-ray investigation confirmed the synthesis pathway and molecular structures for L₁ and L₃ ligands. The antimicrobial activity of the obtained compounds was then comprehensively investigated, where Cu(L₃)Cl₂ showed the strongest antibacterial properties against all tested bacteria (Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli). LN229 human glioma cells and BJ human normal fibroblasts cells were treated with tested compounds and their cytotoxicity was evaluated with MTT test. The effect of complexing on antitumor activity has been investigated. The ligand L₁ and its complex showed similar activity against normal cells while complexation increases toxicity against cancer cells in concentrations of 50 and 100 μM. For the one pair of ligand/complex compounds the apoptosis detection, cell cycle analysis and gene expression analysis (qRT-PCR) were performed. Cu(L₁)Cl₂ showed the stronger toxic effect in comparison with L₁ due to the population of early apoptotic cells which revealed metabolic activity in MTT assay.

Anti-Tuberculosis Mur Inhibitors: Structural Insights and the Way Ahead for Development of Novel Agents

Mur enzymes serve as critical molecular devices for the synthesis of UDP-MurNAc-pentapeptide, the main building block of bacterial peptidoglycan polymer. These enzymes have been extensively studied for bacterial pathogens such as Escherichia coli and Staphylococcus aureus. Various selective and mixed Mur inhibitors have been designed and synthesized in the past few years. However, this class of enzymes remains relatively unexplored for Mycobacterium tuberculosis (Mtb), and thus offers a promising approach for drug design to overcome the challenges of battling this global pandemic. This review aims to explore the potential of Mur enzymes of Mtb by systematically scrutinizing the structural aspects of various reported bacterial inhibitors and implications concerning their activity. Diverse chemical scaffolds such as thiazolidinones, pyrazole, thiazole, etc., as well as natural compounds and repurposed compounds, have been reviewed to understand their in silico interactions with the receptor or their enzyme inhibition potential. The structural diversity and wide array of substituents indicate the scope of the research into developing varied analogs and providing valuable information for the purpose of modifying reported inhibitors of other multidrug-resistant microorganisms. Therefore, this provides an opportunity to expand the arsenal against Mtb and overcome multidrug-resistant tuberculosis.

Molecular Design and In-Silico Analysis of Trisubstituted Benzimidazole Derivatives as Ftsz Inhibitor

Tuberculosis (TB) is the fastest spreading infectious disease and one of the top ten diseases that kill millions of people annually. The rapid spread of a multidrug-resistant strain of Mycobacterium tuberculosis leads to multidrug-resistance tuberculosis (MDR-TB), which is very difficult to treat. Filament temperature-sensitive protein ring-Z (Ftsz) protein could be the best target to inhibit bacterial cytokinesis. This research is conducted to predict the antitubercular activity of trisubstituted benzimidazole derivatives targeting FtsZ protein by an in-silico approach (molecular docking, pharmacokinetic parameter, drug likeliness, toxicity prediction, and biological activity prediction). Amine and aldehyde substitutions are used as primary scaffolds to design 20 trisubstituted benzimidazole derivatives for molecular docking. AutoDock vina v.1.2.0 software was used to predict the binding interaction between ligand and receptor (FtsZ, PDB ID : 1RQ7). The drug-likeliness properties and toxicity of ligands were predicted from SwissADMET and ToxiM web servers, respectively. Compound A15 (2,3,5,6-tetrafluoro-N1-{6-fluoro-5-[4-(1H-imidazole-1-yl) phenoxy]-1H-1,3-benzodiazol-2-yl} benzene-1,4-diamine) showed the best binding energy (ΔG = −10.2 kcal/mol/) along with four hydrogen bond interactions (GLY107, PHE180, ASP 184). Similarly, compounds A19 and A20 have the best binding score of −9.8 kcal/mol, with excellent pharmacokinetic parameters. It is found that the binding energy of all ligands (ΔG = −8.0 to −10.2 kcal/mol) is better than the reference compound Moxifloxacin (ΔG = −7.7 kcal/mol). None of the ligands violate Lipinski’s rule, but all ligands’ toxicity is slightly high (>0.8 score). It is reported that the amine-substituted benzimidazole derivatives have better binding energy than the aldehyde substitution. Therefore, it is concluded that compounds A19 and A20 can be the best candidate as Ftsz protein inhibitors but an in-vitro animal study and toxicity study are necessary to validate these data.

Investigating the binding affinity of andrographolide against human SARS-CoV-2 spike receptor-binding domain through docking and molecular dynamics simulations

SARS-CoV-2 is a positive-sense single-stranded RNA virus that causes a deadly coronavirus disease (COVID-19) in humans. The infection of SARS-CoV-2 in humans involves a viral surface spike glycoprotein containing the receptor-binding domain (RBD). The interactions of SARS-CoV-2 with the host angiotensin-converting enzyme 2 (ACE2) receptor are mediated by RBD. It binds to the host ACE2 and influences viral replication and disease pathogenesis. Therefore, targeting the RBD to prevent SARS-CoV-2 infections is of utmost importance. In this study, we used docking and molecular dynamics simulations to understand the binding effect of andrographolide on the SARS-CoV-2 spike protein. During docking, a strong binding affinity was observed between the ligand and the target receptor protein. MD results demonstrated higher conformational fluctuations in the ligand-free protein compared to the bound form. Several residues in the active sites make conformational rearrangements for the S protein to interact with the ligand. While RBD experiences conformational transition to gain more stability upon binding with the ligand. This binding is strengthened via several non-covalent interactions that make the complex structure more stable with higher binding affinity. Overall findings of the study may shed some valuable insights concerning the development of potential therapeutics in the strategies for COVID-19 prevention.

Sub-chronic toxicity of the aqueous leaf extract of Ocimum lamiifolium Hochst. ex Benth on biochemical parameters and histopathology of liver and kidney in rats: in vivo and in- silico toxicity studies

BACKGROUND

The aerial part of Ocimum lamiifolium is commonly used in Ethiopian traditional medicine. Although this plant is mostly used in traditional medicine, its safety profile has not been documented yet. The aim of this study was to assess the sub-chronic toxicity of O. lamiifolium aqueous extract in rats and to determine the toxicity profile of GC-MS identified bioactive compounds obtained from essential oil of O. lamiifolium using in silico toxicity methods.

METHODS

Eighty rats (40 male and 40 female) were randomly assigned to four groups of ten rats per sex/group. For 90 days, Groups I-III received 200, 400, and 600 mg/kg bw of aqueous extract of O. lamiifolium, respectively. Distilled water was given to Group IV (control). Clinical observations, food intake, and rat weight were all recorded during the experiment. In addition, several biochemical parameters, organ weight, and histology of the liver and kidney were all evaluated. For the in-silico toxicity study, GC-MS identified bioactive compounds in O. lamiifolium essential oil were obtained from published articles. The compounds two-dimensional structures were constructed using Chemdraw. The two-dimensional structures were converted into a simplified molecular input line entry system (SMILES) using the Swiss ADMET web tool. Furthermore, the toxicity parameters were predicted using the ProTox II server.

RESULTS

The administration of an aqueous extract of O. lamiifolium leaves significantly (p < 0.05) reduced the test animals' food intake and body weight gain. In the high dose (600 mg/kg bw) treated group, the serum alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase levels were significantly increased (p < 0.05). In female rats given 600 mg/kg bw of O. lamiifolium, the levels of serum urea were also increased. In addition, rats given 600 mg/kg bw had significantly lower blood glucose levels than the control group (p < 0.05). Doses up to 400 mg/kg bw didn't bring a significant change to the histology of the liver. However, in the high dose (600 mg/kg bw) treated group, some female rats' livers showed mild sinusoidal and central vein dilatation, as well as parenchymal necrosis. our findings showed that all compounds derived from the essential oil of O. lamiifolium showed no mutagenicity or cytotoxicity. However, 30% of the compounds tested were hepatotoxic, 20% carcinogenic, and 20% immunotoxin.

CONCLUSION

Our findings showed that oral administration of O. lamiifoliums aqueous extract up to a dose of 400 mg/kg bw is not toxic. However, high-dose (600 mg/kg bw) significantly affected the food consumption and weight gain of the experimental rats and the serum concentration of some liver and kidney enzymes were also significantly increased. Additionally, a considerable proportion of the tested compounds were predicted to be hepatotoxic, carcinogenic and immunotoxin. Furthermore, before employing O. lamiifolium preparations as drugs, a chronic toxicity research on the essential oil as well as its components that exhibited toxicity in the in-silico toxicity study is needed. Finally, use high doses of O. lamiifolium leaves with caution.

In Silico Drug Design and Analysis of Dual Amyloid-Beta and Tau Protein-Aggregation Inhibitors for Alzheimer's Disease Treatment

Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disorder that gradually leads to the state of dementia. The main features of AD include the deposition of amyloid-beta peptides (Aβ), forming senile plaques, and the development of neurofibrillary tangles due to the accumulation of hyperphosphorylated Tau protein (p-tau) within the brain cells. In this report, seven dual-inhibitor molecules (L_1-7) that can prevent the aggregation of both Aβ and p-tau are suggested. The drug-like features and identification of the target proteins are analyzed by the in silico method. L_1-7 show positive results in both Blood-Brain Barrier (BBB) crossing and gastrointestinal absorption, rendering to the results of the permeation method. The molecular docking test performed for L_1-7 shows binding energies in the range of -4.9 to -6.0 kcal/mol towards Aβ, and -4.6 to -5.6 kcal/mol for p-tau. The drug's effectiveness under physiological conditions is assessed by the use of solvation models on the investigated systems. Further, the photophysical properties of L_1-3 are predicted using TD-DFT studies.

Identification of potential drug candidates as TGR5 agonist to combat type II diabetes using in silico docking and molecular dynamics simulation studies

A cell surface bile acid receptor TGR5 being considered as a novel target for Type II diabetes found to be expressed in various tissues. A major role for TGR5 is to maintain blood sugar levels and increase in energy expenditure. These benefits make it a potential candidate for the treatment of type 2 diabetes, obesity and other metabolic disorder. To date, many novel TGR5 agonists have been synthesized and evaluated in the literature, but very few in silico computational studies have been reported. The discovery of a high-resolution crystal structure of TGR5 in 2020 provides an excellent opportunity for computational screening of potential agonists. In this study, we, therefore, aim to search novel, less toxic TGR5 agonists by iteratively analyzing molecular docking against TGR5 (PDB ID: 7CFN) by means of structure-based virtual screening. The docking score of the designed coumarin derivatives that have been docked successfully varies between -9.4 and -9.0 kcal/mol. The molecular docking and ADMET profile examinations of compounds D1, D5 and D15 revealed that these have a strong affinity for the active site residues of TGR5. In addition, molecular dynamics simulation (MDS) studies have shown the stability of compounds that bind to TGR5. It can be summarized that designed coumarin derivatives seem to have promising activity as TGR5 agonists.Communicated by Ramaswamy H. Sarma.

Discovery of octahydropyrrolo [3,2-b] pyridin derivative as a highly selective Type I inhibitor of FGFR3 over VEGFR2 by high-throughput virtual screening

Although the aberrant activity of fibroblast growth factor receptor 3 (FGFR3) is implicated in various cancers, the reported kinase inhibitors of FGFR3 tend to cause side effects resulting from the inhibitory activity on vascular endothelial growth factor receptor 2 (VEGFR2). Therefore, it is necessary to find a novel high-selective inhibitor of FGFR3 over VEGFR2 from the small-molecule compound database. In this study, integrated virtual screening protocols were established to screen for selective inhibitors of FGFR3 over VEGFR2 in Drugbank and Asinex databases by combining three-dimensional pharmacophore model, molecular docking, molecular dynamics (MD) simulation, and molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations. Finally, it is found that Asinex-5082, as an octahydropyrrolo[3,2-b] pyridin derivative, has larger binding free energy with FGFR3 (-39.3 kcal/mol) than reference drug Erdafitinib (-29.9 kcal/mol), while cannot bind with VEGFR2, resulting in considerable inhibitory selectivity. This is because Asinex-5082, unlike Erdafitinib, has not m-dimethoxybenzene with large steric hindrance, thus can enter the larger ATP-binding pocket of FGFR3 with DFG-in conformation to form hydrophobic interaction with residues Met529, Ile539, and Tyr557 as well as hydrogen bond with Ala558. On the other hand, due to the fact that the benzodioxane and N-heterocyclic rings are connected by carbonyl (C=O), Asinex-5082 cannot rotate freely so as to enter the smaller ATP binding pocket of VEGFR2 on the DFG-out conformation. The lead molecule Asinex-5082 may facilitate the rational design and development of novel selective inhibitors of FGFR3 over VEGFR2 as anticancer drugs.

Highlights in TMPRSS2 inhibition mechanism with guanidine derivatives approved drugs for COVID-19 treatment

Transmembrane protease serine 2 (TMPRSS2) has been identified as a critical key for the entry of coronaviruses into human cells by cleaving and activating the spike protein of SARS-CoV-2. To block the TMPRSS2 function, 18 approved drugs, containing the guanidine group were tested against TMPRSS2's ectodomain (7MEQ). Among these drugs, Famotidine, Argatroban, Guanadrel and Guanethidine strongly binds with TMPRSS2 S1 pocket with estimated Fullfitness energies of -1847.12, -1630.87, -1605.81 and -1600.52 kcal/mol, respectively. A significant number of non-covalent interactions such as hydrogen bonding, hydrophobic and electrostatic interactions were detected in protein-ligand complexes. In addition, the ADMET analysis revealed a perfect concurrence with the aptitude of these drugs to be developed as an anti-SARS-CoV-2 therapeutics. Further, MD simulation and binding free energy calculations were performed to evaluate the dynamic behavior and stability of protein-ligand complexes. The results obtained herein highlight the enhanced stability and good binding affinities of the Argatroban and Famotidine towards the target protein, hence might act as new scaffolds for TMPRSS2 inhibition.Communicated by Ramaswamy H. Sarma.

In silico approach to identify novel allosteric intracellular antagonist for blocking the interleukin-8/CXCR2 receptor signaling pathway

The role of interleukin-8 (IL-8) and its receptor CXCR2 in inflammatory responses and tumor development and progression has been well documented. Our study aims to discover novel compounds as CXCR2 antagonists to block the IL-8 signaling pathway using an in silico drug design. Herein, a structure-based pharmacophore model was developed based on the crystal structure of inactive CXCR2 in a complex with an allosteric inhibitor. This model was validated and refined, followed by virtual screening with the ZINC15 database. Subsequent molecular docking allows for predicting the best pose of a ligand inside a receptor binding site. We found that the 35 top-ranked hits exhibited docking scores from -30.81 to -25.28 kJ/mol and better interaction potential comparing the reference inhibitor. Analysis of ADME and toxicity properties revealed the efficacy and safety of the selected seven compounds. To validate the stability of the protein-ligand complex structure MD simulations approach has also been performed and confirmed via the critical parameters. The MD results explained that the CXCR2 receptor bound with two best-proposed molecules, including ZINC77105530 and ZINC93176465, was quite stable states as observed from low RMSD, RMSF, Rg, SASA values, and high occupancy of the interaction types. Finally, our data identified that these compounds play as potential inhibitors of IL-8 signaling pathways with the MM/GBSA binding free energies of -41.77 ± 6.45 kcal/mol and -38.84 ± 6.16 kcal/mol, respectively.Communicated by Ramaswamy H. Sarma.

Identification of vital chemical information via visualization of graph neural networks

Qualitative or quantitative prediction models of structure-activity relationships based on graph neural networks (GNNs) are prevalent in drug discovery applications and commonly have excellently predictive power. However, the network information flows of GNNs are highly complex and accompanied by poor interpretability. Unfortunately, there are relatively less studies on GNN attributions, and their developments in drug research are still at the early stages. In this work, we adopted several advanced attribution techniques for different GNN frameworks and applied them to explain multiple drug molecule property prediction tasks, enabling the identification and visualization of vital chemical information in the networks. Additionally, we evaluated them quantitatively with attribution metrics such as accuracy, sparsity, fidelity and infidelity, stability and sensitivity; discussed their applicability and limitations; and provided an open-source benchmark platform for researchers. The results showed that all attribution techniques were effective, while those directly related to the predicted labels, such as integrated gradient, preferred to have better attribution performance. These attribution techniques we have implemented could be directly used for the vast majority of chemical GNN interpretation tasks.

Molecular docking/dynamics simulations, MEP analysis, bioisosteric replacement and ADME/T prediction for identification of dual targets inhibitors of Parkinson's disease with novel scaffold

Monoamine oxidase B and Adenosine A2A receptors are used as key targets for Parkinson's disease. Recently, hMAO-B and hA2AR Dual-targets inhibitory potential of a novel series of Phenylxanthine derivatives has been established in experimental findings. Hence, the current study examines the interactions between 38 compounds of this series with hMAO-B and hA2AR targets using different molecular modeling techniques to investigate the binding mode and stability of the formed complexes. A molecular docking study revealed that the compounds L24 ((E)-3-(3-Chlorophenyl)-N-(4-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl) phenyl) acrylamide and L32 ((E)-3-(3-Chlorophenyl)-N-(3-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)phenyl)acrylamide) had a high affinity (S-score: -10.160 and -7.344 kcal/mol) with the pocket of hMAO-B and hA2AR targets respectively, and the stability of the studied complexes was confirmed during MD simulations. Also, the MEP maps of compounds 24 and 32 were used to identify the nucleophilic and electrophilic attack regions. Moreover, the bioisosteric replacement approach was successfully applied to design two new analogs of each compound with similar biological activities and low energy scores. Furthermore, ADME-T and Drug-likeness results revealed the promising pharmacokinetic properties and oral bioavailability of these compounds. Thus, compounds L24, L32, and their analogs can undergo further analysis and optimization in order to design new lead compounds with higher efficacy toward Parkinson's disease.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00139-3.

Structure-Based Identification of Natural-Product-Derived Compounds with Potential to Inhibit HIV-1 Entry

Broadly neutralizing antibodies (bNAbs) are potent in neutralizing a wide range of HIV strains. VRC01 is a CD4-binding-site (CD4-bs) class of bNAbs that binds to the conserved CD4-binding region of HIV-1 envelope (env) protein. Natural products that mimic VRC01 bNAbs by interacting with the conserved CD4-binding regions may serve as a new generation of HIV-1 entry inhibitors by being broadly reactive and potently neutralizing. This study aimed to identify compounds that mimic VRC01 by interacting with the CD4-bs of HIV-1 gp120 and thereby inhibiting viral entry into target cells. Libraries of purchasable natural products were virtually screened against clade A/E recombinant 93TH057 (PDB: 3NGB) and clade B (PDB ID: 3J70) HIV-1 env protein. Protein-ligand interaction profiling from molecular docking and dynamics simulations showed that the compounds had intermolecular hydrogen and hydrophobic interactions with conserved amino acid residues on the CD4-binding site of recombinant clade A/E and clade B HIV-1 gp120. Four potential lead compounds, NP-005114, NP-008297, NP-007422, and NP-007382, were used for cell-based antiviral infectivity inhibition assay using clade B (HXB2) env pseudotype virus (PV). The four compounds inhibited the entry of HIV HXB2 pseudotype viruses into target cells at 50% inhibitory concentrations (IC₅₀) of 15.2 µM (9.7 µg/mL), 10.1 µM (7.5 µg/mL), 16.2 µM (12.7 µg/mL), and 21.6 µM (12.9 µg/mL), respectively. The interaction of these compounds with critical residues of the CD4-binding site of more than one clade of HIV gp120 and inhibition of HIV-1 entry into the target cell demonstrate the possibility of a new class of HIV entry inhibitors.

Ligand-based pharmacophore modeling and QSAR approach to identify potential dengue protease inhibitors

The viral disease dengue is transmitted by the Aedes mosquito and is commonly seen to occur in the tropical and subtropical regions of the world. It is a growing public health concern. To date, other than supportive treatments, there are no specific antiviral treatments to combat the infection. Therefore, finding potential compounds that have antiviral activity against the dengue virus is essential. The NS2B-NS3 dengue protease plays a vital role in the replication and viral assembly. If the functioning of this protease were to be obstructed then viral replication would be halted. As a result, this NS2B-NS3 proves to be a promising target in the process of anti-viral drug design. Through this study, we aim to provide suggestions for compounds that may serve as potent inhibitors of the dengue NS2B-NS3 protein. Here, a ligand-based pharmacophore model was generated and the ZINC database was screened through ZINCPharmer to identify molecules with similar features. 2D QSAR model was developed and validated using reported 4-Benzyloxy Phenyl Glycine derivatives and was utilized to predict the IC50 values of unknown compounds. Further, the study is extended to molecular docking to investigate interactions at the active pocket of the target protein. ZINC36596404 and ZINC22973642 showed a predicted pIC50 of 6.477 and 7.872, respectively. They also showed excellent binding with NS3 protease as is evident from their binding energy of -8.3and -8.1 kcal/mol, respectively. ADMET predictionsofcompounds have shown high drug-likeness. Finally, the molecular dynamic simulations integrated with MM-PBSA binding energy calculations confirmedboth identified ZINC compounds as potential hit moleculeswith good stability.

In silico Study of Antiviral Activity of Polyphenol Compounds from Ocimum basilicum by Molecular Docking, ADMET, and Drug-Likeness Analysis

Aim

The SARS-CoV-2 virus is a disease that has mild to severe effects on patients, which can even lead to death. One of the enzymes that act as DNA replication is the main protease, which becomes the main target in the inhibition of the SARS-CoV-2 virus. In finding effective drugs against this virus, Ocimum basilicum is a potential herbal plant because it has been tested to have high phytochemical content and bioactivity. Apigenin-7-glucuronide, dihydrokaempferol-3-glucoside, and aesculetin are polyphenolic compounds found in Ocimum basilicum.

Purpose

The purpose of this study was to analyze the mechanism of inhibition of the three polyphenolic compounds in Ocimum basilicum against the main protease and to predict pharmacokinetic activity and the drug-likeness of a compound using the Lipinski Rule of Five.

Patients and Methods

The method used is to predict the molecular docking inhibition mechanism using Autodock 4.0 tools and use pkcsm and protox online web server to analyze ADMET and Drug-likeness.

Results

The binding affinity for apigenin-7-glucuronide was -8.77 Kcal/mol, dihydrokaempferol-3-glucoside was -8.96 Kcal/mol, and aesculetin was -5.79 Kcal/mol. Then, the inhibition constant values were 375.81 nM, 270.09 nM, and 57.11 µM, respectively. Apigenin-7-glucuronide and dihydrokaempferol-3-glucoside bind to the main protease enzymes on the active sites of CYS145 and HIS41, while aesculetin only binds to the active sites of CYS145. On ADMET analysis, these three compounds met the predicted pharmacokinetic parameters, although there are some specific parameters that must be considered especially for aesculetin compounds. Meanwhile, on drug-likeness analysis, apigenin-7-glucuronide and dihydrokaempferol-3-glucoside compounds have one violation and aesculetin have no violation.

Conclusion

Based on the data obtained, Apigenin-7-glucuronide and dihydrokaempferol-3-glucoside are compounds that have more potential to have an antiviral effect on the main protease enzyme than aesculetin. Based on pharmacokinetic parameters and drug-likeness, three compounds can be used as lead compounds for further research.

Structure-based drug design of novel M. tuberculosis InhA inhibitors based on fragment molecular orbital calculations

2-trans enoyl-acyl carrier protein reductase (InhA) is a promising target for developing novel chemotherapy agents for tuberculosis, and their inhibitory effects on InhA activity were widely investigated by the physicochemical experiments. However, the reason for the wide range of their inhibitory effects induced by similar agents was not explained by only the difference in their chemical structures. In our previous molecular simulations, a series of heteroaryl benzamide derivatives were selected as candidate inhibitors against InhA, and their binding properties with InhA were investigated to propose novel derivatives with higher binding affinity to InhA. In the present study, we extended the simulations for a series of 4-hydroxy-2-pyridone derivatives to search widely for more potent inhibitors against InhA. Using ab initio fragment molecular orbital (FMO) calculations, we elucidated the specific interactions between InhA residues and the derivatives at an electronic level and highlighted key interactions between InhA and the derivatives. The FMO results clearly indicated that the most potent inhibitor has strong hydrogen bonds with the backbones of Tyr158, Thr196, and NADH of InhA. This finding may provide informative structural concepts for designing novel 4-hydroxy-2-pyridone derivatives with higher binding affinity to InhA. Our previous and present molecular simulations could provide important guidelines for the rational design of more potent InhA inhibitors.

Molecular docking analysis of imidazole quinolines with gingipain R from Porphyromonas gingivalis

Porphyromonas gingivalis is known to produce major virulence factor, Gingipain R that could penetrate the gingivae and cause tissue destruction. In this research we aim to target the gingipain R protein with imidazole quinoline derivatives (1-6) via insilico means. Molecular docking results show, compounds (1-6) have better affinity and amino acid interactions compared to the standard clinically proven drugs used as control group, and they obey Lipinski's rule of five and can be used as potential drug candidates to inhibit gingipain R.

Ursolic Acid and Solasodine as Potent Anti-Mycobacterial Agents for Combating Paratuberculosis: An Anti-Inflammatory and In Silico Analysis

Mycobacterium avium subspecies paratuberculosis (MAP) infection in domestic livestock causes persistent diarrhea, weight loss, and death and is also a potential cause of Crohn's disease (CD) in humans; notably, treatments against MAP are insufficient, costly, and can cause adverse reactions. Hence, plant-derived bioactive constituents have been taken into consideration in this regard. Herein, we present the results of two bioactive constituents (Solasodine and Ursolic acid) that were evaluated for their safety and efficacy against MAP protein (Dephospho-Coenzyme A kinase (DPCK) by utilizing in vitro assays and different tools of in silico biology. The ADME/t-test, the drug-likeness property test, pharmacophore modelling, and PASS prediction have proven that both the constituents have better binding capacities than the available antibiotic drugs used to target protein inhibition pathways. Through our observations, it can be inferred that these two phytochemicals can be adequately used to treat paratuberculosis, thereby combating inflammatory bowel disorders (IBD) of an autoimmune nature.

Machine Learning Toxicity Prediction: Latest Advances by Toxicity End Point

Machine learning (ML) models to predict the toxicity of small molecules have garnered great attention and have become widely used in recent years. Computational toxicity prediction is particularly advantageous in the early stages of drug discovery in order to filter out molecules with high probability of failing in clinical trials. This has been helped by the increase in the number of large toxicology databases available. However, being an area of recent application, a greater understanding of the scope and applicability of ML methods is still necessary. There are various kinds of toxic end points that have been predicted in silico. Acute oral toxicity, hepatotoxicity, cardiotoxicity, mutagenicity, and the 12 Tox21 data end points are among the most commonly investigated. Machine learning methods exhibit different performances on different data sets due to dissimilar complexity, class distributions, or chemical space covered, which makes it hard to compare the performance of algorithms over different toxic end points. The general pipeline to predict toxicity using ML has already been analyzed in various reviews. In this contribution, we focus on the recent progress in the area and the outstanding challenges, making a detailed description of the state-of-the-art models implemented for each toxic end point. The type of molecular representation, the algorithm, and the evaluation metric used in each research work are explained and analyzed. A detailed description of end points that are usually predicted, their clinical relevance, the available databases, and the challenges they bring to the field are also highlighted.

Preclinical Studies and Drug Combination of Low-Cost Molecules for Chagas Disease

Chagas disease is caused by the protozoan Trypanosoma cruzi (T. cruzi). It remains the major parasitic disease in Latin America and is spreading worldwide, affecting over 10 million people. Hundreds of new compounds with trypanosomicidal action have been identified from different sources such as synthetic or natural molecules, but they have been deficient in several stages of drug development (toxicology, scaling-up, and pharmacokinetics). Previously, we described a series of compounds with simple structures, low cost, and environmentally friendly production with potent trypanosomicidal activity in vitro and in vivo. These molecules are from three different families: thiazolidenehydrazines, diarylideneketones, and steroids. From this collection, we explored their capacity to inhibit the triosephosphate isomerase and cruzipain of T. cruzi. Then, the mechanism of action was explored using NMR metabolomics and computational molecular dynamics. Moreover, the mechanism of death was studied by flow cytometry. Consequently, five compounds, 314, 793, 1018, 1019, and 1260, were pre-clinically studied and their pharmacologic profiles indicated low unspecific toxicity. Interestingly, synergetic effects of diarylideneketones 793 plus 1018 and 793 plus 1019 were evidenced in vitro and in vivo. In vivo, the combination of compounds 793 plus 1018 induced a reduction of more than 90% of the peak of parasitemia in the acute murine model of Chagas disease.

Pharmacokinetics, drug-likeness, antibacterial and antioxidant activity of secondary metabolites from the roots extracts of Crinum abyssinicum and Calotropis procera and in silico molecular docking study

Crinum abyssinicum and Calotropis procera were traditionally used for the treatment of different diseases such as hypertension, diabetes, hepatitis B, skin infection, anticancer, asthma, fever, and diarrhea. The structures of the compounds were characterized by 1H NMR, 13C NMR, and DEPT-135 spectra. Compounds 1-3 were reported herein for the first time from the species of C. abyssinicum. The DCM/MeOH (1:1) and MeOH roots extracts of C. abyssinicum showed significant inhibitory activity against S. aureus and P. aeruginosa with a mean inhibition zone of 16.67 ± 1.20 and 16.33 ± 0.33 mm, respectively. Compounds 4 and 5 showed promising activity against E. coli with a mean inhibition zone of 17.7  0.8 and 17.7  1.2 mm, respectively. The results of DPPH activity showed the DCM: MeOH (1:1) and MeOH roots extracts of C. abyssinicum inhibited the DPPH radical by 52.86  0.24 % and 45.6  0.11 %, respectively, whereas compound 5 displayed 85.7 % of inhibition. The drug-likeness analysis showed that compounds 2-4 satisfy Lipinski’s rule of five with zero violations. Compounds 2, and 6 showed binding affinities of −6.0, and −6.7 kcal/mol against E. coli DNA gyrase B, respectively, while 3 and 5 showed −5.0 and −5.0 kcal/mol, respectively against human peroxiredoxin 5. Therefore, the in vitro antibacterial, radical scavenging activity along with the molecular docking analysis suggest the potential use of the extracts of C. abyssinicum and compounds 2, 5, 6, and 3, 5 can be considered as promising antibacterial agents and free radical scavengers, respectively.

In Silico and In Vitro Analysis of Sulforaphane Anti-Candida Activity

Oropharyngeal candidiasis/candidosis is a common and recurrent opportunistic fungal infection. Fluconazole (FLZ), one of the most used and effective antifungal agents, has been associated with a rise of resistant Candida species in immunocompromised patients undergoing prophylactic therapy. Sulforaphane (SFN), a compound from cruciferous vegetables, is an antimicrobial with yet controversial activities and mechanisms on fungi. Herein, the in silico and antifungal activities of SFN against C. albicans were investigated. In silico analyzes for the prediction of the biological activities and oral bioavailability of SFN, its possible toxicity and pharmacokinetic parameters, as well as the estimates of its gastrointestinal absorption, permeability to the blood-brain barrier and skin, and similarities to drugs, were performed by using different software. SFN in vitro anti-Candida activities alone and in combination with fluconazole (FLZ) were determined by the broth microdilution method and the checkerboard, biofilm and hyphae formation tests. Amongst the identified probable biological activities of SFN, nine indicated an antimicrobial potential. SFN was predicted to be highly absorbable by the gastrointestinal tract, to present good oral availability, and not to be irritant and/or hepatotoxic. SFN presented antifungal activity against C. albicans and prevented both biofilm and hyphae formation by this microorganism. SFN was additive/synergistic to FLZ. Overall, the data highlights the anti-Candida activity of SFN and its potential to be used as an adjuvant therapy to FLZ in clinical settings.

Limoniastrum monopetalum-Mediated Nanoparticles and Biomedicines: In Silico Study and Molecular Prediction of Biomolecules

An in silico approach applying computer-simulated models helps enhance biomedicines by sightseeing the pharmacology of potential therapeutics. Currently, an in silico study combined with in vitro assays investigated the antimicrobial ability of Limoniastrum monopetalum and silver nanoparticles (AgNPs) fabricated by its aid. AgNPs mediated by L. monopetalum were characterized using FTIR, TEM, SEM, and DLS. L. monopetalum metabolites were detected by QTOF-LCMS and assessed using an in silico study for pharmacological properties. The antibacterial ability of an L. monopetalum extract and AgNPs was investigated. PASS Online predictions and the swissADME web server were used for antibacterial activity and potential molecular target metabolites, respectively. Spherical AgNPs with a 68.79 nm average size diameter were obtained. Twelve biomolecules (ferulic acid, trihydroxy-octadecenoic acid, catechin, pinoresinol, gallic acid, myricetin, 6-hydroxyluteolin, 6,7-dihydroxy-5-methoxy 7-O-β-d-glucopyranoside, methyl gallate, isorhamnetin, chlorogenic acid, 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-O-(6-deoxy-β-l-mannopyranosyl)-β-d-glucopyranoside) were identified. The L. monopetalum extract and AgNPs displayed antibacterial effects. The computational study suggested that L. Monopetalum metabolites could hold promising antibacterial activity with minimal toxicity and an acceptable pharmaceutical profile. The in silico approach indicated that metabolites 8 and 12 have the highest antibacterial activity, and swissADME web server results suggested the CA II enzyme as a potential molecular target for both metabolites. Novel therapeutic agents could be discovered using in silico molecular target prediction combined with in vitro studies. Among L. Monopetalum metabolites, metabolite 12 could serve as a starting point for potential antibacterial treatment for several human bacterial infections.

Evaluating different web applications to assess the toxicity of plasticizers

Plasticizers increase the flexibility of plastics. As environmental leachates they lead to increased water and soil pollution, as well as to serious harm to human health. This study was set out to explore various web applications to predict the toxicological properties of plasticizers. Web-based tools (e.g., BOILED-Egg, LAZAR, PROTOX-II, CarcinoPred-EL) and VEGA were accessed via an 5th-10th generation computer in order to obtain toxicological predictions. Based on the LAZAR mutagenicity assessment was only bisphenol F predicted as mutagenic. The BBP and DBP in RF; DEHP in RF and XGBoost; DNOP in RF and XGBoost models were predicted as carcinogenic in the CarcinoPred-EL web application. From the bee predictive model (KNN/IRFMN) BPF, di-n-propyl phthalate, diallyl phthalate, dibutyl phthalate, and diisohexyl phthalate were predicted as strong bee toxicants. Acute toxicity for fish using the model Sarpy/IRFMN predicted 19 plasticizers as strong toxicants with LC50 values of less than 1 mg/L. This study also considered plasticizer effects on gastrointestinal absorption and other toxicological endpoints.

Structure-based virtual screening and molecular dynamics of potential inhibitors targeting sodium-bile acid co-transporter of carcinogenic liver fluke Clonorchis sinensis

Background

Clonorchis sinensis requires bile acid transporters as this fluke inhabits bile juice-filled biliary ducts, which provide an extreme environment. Clonorchis sinensis sodium-bile acid co-transporter (CsSBAT) is indispensable for the fluke’s survival in the final host, as it circulates taurocholate and prevents bile toxicity in the fluke; hence, it is recognized as a useful drug target.

Methodology and principal findings

In the present study, using structure-based virtual screening approach, we presented inhibitor candidates targeting a bile acid-binding pocket of CsSBAT. CsSBAT models were built using tertiary structure modeling based on a bile acid transporter template (PDB ID: 3zuy and 4n7x) and were applied into AutoDock Vina for competitive docking simulation. First, potential compounds were identified from PubChem (holding more than 100,000 compounds) by applying three criteria: i) interacting more favorably with CsSBAT than with a human homolog, ii) intimate interaction to the inward- and outward-facing conformational states, iii) binding with CsSBAT preferably to natural bile acids. Second, two compounds were identified following the Lipinski’s rule of five. Third, other two compounds of molecular weight higher than 500 Da (Mr > 500 Da) were presumed to efficiently block the transporter via a feasible rational screening strategy. Of these candidates, compound 9806452 exhibited the least hepatotoxicity that may enhance drug-likeness properties.

Conclusions

It is proposed that compound 9806452 act as a potential inhibitor toward CsSBAT and further studies are warranted for drug development process against clonorchiasis.

ZnO Nanoparticle-Assisted Synthesis of Thiazolo[3,2-α]Pyrimidine Analogs: Antibacterial and Antioxidant Activity, In Silico Molecular Docking, and ADMET Prediction Study

In the present study, a new series of nine Thiazolo[3,2-α] pyrimidine analogs were synthesized in good to excellent yields (87.9–96.9%) and improved reaction time using a ZnO nanoparticle-assisted protocol. All the synthesized compounds were characterized using a combination of physicochemical parameters, UV-visible, 1H-NMR, and 13C-NMR spectroscopic methods. Among the synthesized compounds, the in vitro antibacterial activity displayed by compound 16 was higher (14.67 ± 0.58 mm at 500 μg/mL) against P. aeruginosa compared to amoxicillin (12.33 ± 0.58 mm at 500 μg/mL), whereas compounds 14 and 18 showed comparable activity (12.00 ± 0.00 mm and 12.33 ± 0.58 mm at 500 μg/mL and 250 μg/mL, respectively) against the same strain. The activities displayed by compounds 14, 16, 18, and 20 were comparable (12.33 ± 1.15 mm, 12.65 ± 0.58 mm, 12.33 ± 0.58 mm, and 12.00 ± 1.00 mm, respectively, at 500 μg/mL) to amoxicillin (13.33 ± 1.15 mm at the same concentration) against E. coli. Compound 19 showed good activity (12.00 ± 1.72 mm at 500 μg/mL) against S. aureus compared to amoxicillin (16.33 ± 0.58 mm at the same concentration). Compound 19 displayed the highest percent inhibition of DPPH with an IC50 value of 9.48 g/mL using the DPPH free radical scavenging assay compared to ascorbic acid (3.21 g/mL) and promising inhibition of peroxide formation (76.28 ± 0.12%), demonstrating its potential in preventing the formation of lipid peroxides. Thus, according to our findings, both the biological activities and in silico computational results revealed that compounds 14, 16, and 18 are good antibacterial agents against P. aeruginosa and E. coli, whereas compound 19 was found to be a promising antibacterial agent against S. aureus and an antioxidant agent. The present study revealed that the synthesized compounds appear to be lead compounds for rational drug design.

Screening of Phytoconstituents from Traditional Plants against SARSCoV- 2 using Molecular Docking Approach

Background:

The emergence of COVID-19 as a fatal viral disease encourages researchers to develop effective and efficient therapeutic agents. The intervention of in silico studies has led to revolutionary changes in the conventional method of testing the bioactivity of plant constituents.

Objective:

The current study deals with the investigation of some traditional immunomodulators of plant origin to combat this ailment.

Materials and Methods:

A total of 151 phytomolecules of 12 immunomodulatory plants were evaluated for their inhibitory action against the main protease (PDB ID: 7D1M) and NSP15 endoribonuclease (PDB ID: 6WLC) by structure-based virtual screening. In addition, the promising molecules with ligand efficiency of more than -0.3(kcal/mol)/heavy atoms were further predicted for pharmacokinetic properties and druggability using the SwissADME web server, and their toxicity was also evaluated using Protox-II.

Result:

Myricetin-3-O-arabinofuranoside of cranberry plant was found to be the most potential candidate against both enzymes: main protease (–14.2 kcal/mol) and NSP15 endoribonuclease (–12.2 kcal/mol).

Conclusion:

The promising outcomes of the current study may be implemented in future drug development against coronavirus. The findings also help in the development of lead candidates of plant origin with a better ADMET profile in the future.

Computational study of potential inhibitors for fat mass and obesity-associated protein from seaweed and plant compounds

Background

Over the past three decades, with substantial changes in lifestyle, the tendency to gain weight has increased, which is resulting in significant consequences affecting an individual's well-being. The fat mass and obesity-associated (FTO) gene is involved in food intake and energy expenditure and plays a crucial role in regulating homeostasis and controlling energy expenditure by hindering signals that generate from the brain. Edible seaweeds have been shown to enhance satiety owing to their health benefits.

Methods

Extensive screening of plant-derived anti-obesity compounds and seaweed compounds was conducted and validated for ADME properties and toxicity prediction. Further, the top ranked compounds were docked against the FTO protein to identify potential inhibitors and were subjected to molecular dynamic simulation studies to understand the binding stability of ligand protein complex. Finally, MM/PBSA studies were performed to calculate the binding free energy of the protein-ligand complexes.

Results

Through the virtual screening of 1,210 compounds, 443 compounds showed good docking scores less than -7.00 kcal/mol. Drug likeness screenings of 443 compounds showed that only 369 compounds were in accordance with these properties. Further toxicity prediction resulted in 30 non-toxic compounds. Molecular docking studies revealed four top ranked marine compounds. Finally, RL074 (2-hydroxyluzofuranone B) and RL442 (10-acetoxyangasiol) from marine red alga Laurencia sp showed good stability from molecular dynamic simulation studies. MM/PBSA results revealed that BT012 (24ε-hydroperoxy-6β-hydroxy-24-ethylcholesta-4,-28(29)-dien-3-one), an oxygenated fucosterol from brown alga Turbinaria conoides, possessed higher binding energy. Hence, with all the data obtained it could be concluded that three seaweed compounds, BT012, RL074 and RL442, may act as a potential anti-obesity lead compound in targeting FTO.

Synthesis, Antibacterial, and Antioxidant Activities of Thiazolyl-Pyrazoline Schiff Base Hybrids: A Combined Experimental and Computational Study

Thiazole-pyrazoline Schiff base hybrids have a broad range of pharmacological potential with an ability to control the activity of numerous metabolic enzymes. In this work, a greener and more efficient approach has been developed to synthesize a novel series of thiazole-pyrazoline Schiff base hybrids using ZnO nanoparticle-assisted protocol in good to excellent yields (78.3–96.9%) and examined their antibacterial activity against Gram-positive and Gram-negative bacteria, as well as their antioxidant activity. Compound 24 (IZD = 18.67 ± 0.58) displayed better activity against P. aeruginosa compared with amoxicillin (IZD = 14.33 ± 2.52) at 250 μg/mL, whereas compounds 22 and 24 (IZD = 13.33 ± 0.58 mm and 17.00 ± 1.00 mm, respectively) showed better activity against E. coli compared with amoxicillin (IZD = 14.67 ± 0.58 mm) at 500 μg/mL. The remaining compounds showed moderate to weak activity against the tested bacterial strains. Compound 21 displayed significant inhibition of DPPH (IC50 = 4.63 μg/mL) compared with ascorbic acid (IC50 = 3.21 μg/mL). Compound 21 displayed 80.01 ± 0.07% inhibition of peroxide formation, suggesting its potential in preventing the formation of lipid peroxides. The results of the ADMET study showed that all synthesized compounds obeyed Lipinski's rule of five. In silico pharmacokinetic study demonstrated that compound 24 had superior intestinal absorption compared with amoxicillin. In silico molecular docking analysis revealed a binding affinity of −9.9 Kcal/mol for compound 24 against PqsA compared with amoxicillin (−7.3 Kcal/mol), whereas compounds 22 and 24 displayed higher binding affinity (−8.5 and −7.9 Kcal/mol, respectively) with DNA gyrase B compared with amoxicillin (-7.1 Kcal/mol), in good agreement with in vitro antibacterial activity against P. aeruginosa and E. coli. In silico toxicity study showed that all synthesized compounds had LD50 (mg/kg) values ranging from 800 to 1,000 putting them in ProTox-II class 4. The in vitro antibacterial activity and molecular docking analysis showed that compound 24 is a promising antibacterial therapeutic agent against P. aeruginosa and E. coli and compound 22 is a promising antibacterial agent against E. coli, whereas compound 21 is found to be a potential natural antioxidant agent. Moreover, the green synthesis approach using ZnO nanoparticle as catalyst was found to be a very efficient method to synthesize biologically active thiazole-pyrazoline Schiff base hybrids compared with the conventional method.

Tetraclinis articulata (vahl) masters: An insight into its ethnobotany, phytochemistry, toxicity, biocide and therapeutic merits

Tetraclinis articulata (Vahl) Masters, commonly known as Sandarac tree and Araâr, is the only species representing the genus Tetraclinis Masters. The plant has been extensively used for medicinal, artistic, and ritual purposes since its first recorded use in 1800 B.C. Recently, a full range of ethnobotanical investigations has been undertaken to document the plant’s empirical knowledge. They reported the use of different parts, such as leaves, stems, cones, bark, and roots, as part of folk healing practices to manage diabetes mellitus, hypertension, fever, stomach disorders, and diarrhea, among others. The phytochemical studies have identified at least 130 compounds from leaves, cones, resin, bark, and woods. These chemical constituents are categorized into phenolic acids, flavonoids and their derivatives, volatile compounds, phytosterols, and fatty acids, among others. Furthermore, they have strongly been correlated with the promising antimicrobial, antioxidant, neuroprotective, antiurolithiatic, anti-inflammatory, antidiabetic, and cytotoxic properties of the plant. Toxicological studies argued that the plant is quite safe and devoid of eventual toxicity; however, in-depth investigations are required to validate the safety of the plant. The remarkable antimicrobial and antioxidant potencies of various extracts from the plant against a wide range of foodborne pathogens support their possible use to increase the shelf life of foodstuffs in the food industry. Likewise, various plant-based extracts have been proven to exert substantial biocidal properties, making them potential alternatives to synthetic pesticides in agriculture. The present review provides an up-to-date comprehensive insight about the ethnobotanical uses of T. articulata, along with its phytochemistry and biological activities to furnish directions for further studies. We also discussed the biocidal potency of the plant and highlighted its usage to extend the shelf life of perishable foods.

toxCSM: comprehensive prediction of small molecule toxicity profiles

Drug discovery is a lengthy, costly and high-risk endeavour that is further convoluted by high attrition rates in later development stages. Toxicity has been one of the main causes of failure during clinical trials, increasing drug development time and costs. To facilitate early identification and optimisation of toxicity profiles, several computational tools emerged aiming at improving success rates by timely pre-screening drug candidates. Despite these efforts, there is an increasing demand for platforms capable of assessing both environmental as well as human-based toxicity properties at large scale. Here, we present toxCSM, a comprehensive computational platform for the study and optimisation of toxicity profiles of small molecules. toxCSM leverages on the well-established concepts of graph-based signatures, molecular descriptors and similarity scores to develop 36 models for predicting a range of toxicity properties, which can assist in developing safer drugs and agrochemicals. toxCSM achieved an Area Under the Receiver Operating Characteristic (ROC) Curve (AUC) of up to 0.99 and Pearson's correlation coefficients of up to 0.94 on 10-fold cross-validation, with comparable performance on blind test sets, outperforming all alternative methods. toxCSM is freely available as a user-friendly web server and API at http://biosig.lab.uq.edu.au/toxcsm.

Virtual screening reveals liquiritigenin as a broad-spectrum inhibitor of SARS-CoV-2 variants of concern: an in silico study

The SARS-CoV-2 has severely impacted the lives of people worldwide. Global concern is on the rise due to a large number of unexpected mutations in the viral genome, resulting in new variants. Nature-based bioactive phytochemicals hold great promise as inhibitors against pathogenic viruses. The current study was aimed at evaluating some bioactive antiviral phytochemicals against SARS-CoV-2 variants of concern. A total of 46 phytochemicals were screened against the pathogenic spike protein of Alpha, Beta, Delta, Gamma, and Omicron variants. In addition to molecular docking, screening for favorable pharmacokinetic and pharmacodynamic properties such as absorption, distribution, metabolism, excretion, and toxicity was undertaken. For each of the aforementioned five SARS-CoV-2 variants of concern, a 100 ns molecular dynamics simulation was run to assess the stability of the complexes between their respective spike protein receptor-binding domain and the best-selected compound. From our current investigation, the natural compound liquiritigenin turned out to be the most promising potential lead compound against almost all the variants. These findings could pave the way for the development of effective medications against SARS-CoV-2 variants. However, in vivo trials in future studies are necessary for further validation of our results.Communicated by Ramaswamy H. Sarma.

Experimental and Computational Study of Novel Pyrazole Azo Dyes as Colored Materials for Light Color Paints

This paper presents the synthesis of eight new pyrazole azo dyes using ethyl 5-amino-3-methyl-1H-pyrazole-4-carboxylate as the diazotization component and various active methylene derivatives as coupling components. These new azo dyes were characterized by spectroscopic (FT-IR, UV-VIS), and spectrometric (¹H NMR, ¹³C NMR, MS) analyses. The dye structures were modeled by the MMFF94s force field and quantum chemical density functional theory (DFT) calculations using the B3LYP functional and the 6-311G(d,p) basis set, in the gas phase. Weak electrostatic hydrogen bonds for the azo and hydrazo dye tautomers were found in the ground state. The CIS, TD (using the B3LYP and M06-2X functionals), and ZINDO methods were used to estimate the dye UV-VIS spectra in ethanol, which were compared with the experimental ones. The anti-configuration arrangement of the π-bonds and the presence of the prevalent hydrazo dye tautomer were supported by the computed ¹H NMR and ¹³C NMR spectra. A good accordance between the experimental and predicted absorption maxima and chemical shifts was observed. Color investigations using the CIEL*a*b* space were conducted for all dyes in powder and for their mixtures in water-based acrylic resins. The results confirm the newly synthesized dyes' color properties and that they might be used for light color paints in the varnishes industry.

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.

Synthesis, spectroscopic characterization of novel phthalimides derivatives bearing a 1,2,3-triazole unit and examination as potential SARS-CoV-2 inhibitors via in silico studies

In the present study, novel phthalimide derivatives 8(a-f) and 9(a-f) bearing a 1,2,3-triazole subunit were synthesized via CuAAC reactions and characterized by ¹H, ¹³C NMR, HR-MS, and FT-IR analyses. To support the fight against SARS-CoV-2, in silico molecular docking studies were carried out to examine their interactions with the proteins of SARS-CoV-2 (Mpro and PLpro) and the protein-protein interactions (PPI) between the ACE2-spike (S1) in comparison with various inhibitors reported to be active by in vitro experiments. The ligand-protein stabilities of compounds 8a-Mpro, 8b-PLpro, and 9a-'ACE2-S1' showing the best binding energy and predicted inhibition constant values (Ki) were examined by molecular dynamics simulation studies. Finally, in silico ADMET properties of the target compounds were investigated using the Swiss ADME and ProTox-II web tools. According to in silico results, all phthalimide analogs may block the PPI between S1 and ACE2. The compounds may also inhibit the progression of the Mpro, and PLpro proteins of SARS-CoV-2. Additionally, it has been estimated that the compounds are suitable for oral administration and exhibit low levels of toxicity.

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.