Discovery of Protease-Activated Receptor 4 (PAR4)-Tethered Ligand Antagonists Using Ultralarge Virtual Screening

Here, we demonstrate a structure-based small molecule virtual screening and lead optimization pipeline using a homology model of a difficult-to-drug G-protein-coupled receptor (GPCR) target. Protease-activated receptor 4 (PAR4) is activated by thrombin cleavage, revealing a tethered ligand that activates the receptor, making PAR4 a challenging target. A virtual screen of a make-on-demand chemical library yielded a one-hit compound. From the single-hit compound, we developed a novel series of PAR4 antagonists. Subsequent lead optimization via simultaneous virtual library searches and structure-based rational design efforts led to potent antagonists of thrombin-induced activation. Interestingly, this series of antagonists was active against PAR4 activation by the native protease thrombin cleavage but not the synthetic PAR4 agonist peptide AYPGKF.

In the Quest for Potent and Selective Malic Enzyme 3 Inhibitors for the Treatment of Pancreatic Ductal Adenocarcinoma

The genome of pancreatic ductal adenocarcinoma (PDAC) is associated with frequent deletion of the tumor suppressor gene SMAD family member 4 (SMAD4) with collateral deletion of its chromosomal neighbor malic enzyme 2 (ME2). In SMAD4 -/- /ME2 -/- PDAC cells, ME3 takes over the function of the ME2 enzyme, and hence therapeutic targeting of ME3 is expected to arrest tumor growth. Hitherto no selective small molecule inhibitor of ME3 has been reported in the context of PDAC. Based on the molecular docking studies and structure-activity relationships with the reported ME1 inhibitor, several analogues of 6-piperazin-1-ylpyridin-3-ol amides have been synthesized and screened for their ME inhibition activity. Among them, compound 16b is identified as the most potent and selective ME3 inhibitor with an IC50 of 0.15 μM on ME3, and with 15- and 9-fold selectivity over ME1 and ME2, respectively. In the cell viability assay, compound 16b exhibited an IC50 of 3.5 μM on ME2-null PDAC cells, viz., BxPC-3.

Design and Evaluation of Bispidine-Based SARS-CoV-2 Main Protease Inhibitors

For the first time, derivatives of 3,7-diazabicyclo[3.3.1]nonane (bispidine) were proposed as potential inhibitors of the SARS-CoV-2 main viral protease (3-chymotrypsin-like, 3CLpro). Based on the created pharmacophore model of the active site of the protease, a group of compounds were modeled and tested for activity against 3CLpro. The 3CLpro activity was measured using the fluorogenic substrate Dabcyl-VNSTLQSGLRK(FAM)MA; the efficiency of the proposed approach was confirmed by comparison with literature data for ebselen and disulfiram. The results of the experiments performed with bispidine compounds showed that 14 compounds exhibited activity in the concentration range 1-10 μM, and 3 samples exhibited submicromolar activity. The structure-activity relationship studies showed that the molecules containing a carbonyl group in the ninth position of the bicycle exhibited the maximum activity. Based on the experimental and theoretical results obtained, further directions for the development of this topic were proposed.

Network Pharmacology and Molecular Docking Approaches to Investigating the Mechanism of Action of Zanthoxylum bungeanum in the Treatment of Oxidative Stress-induced Diseases

BACKGROUND

Zanthoxylum bungeanum Maxim., a traditional Chinese herbal medicine, has been reported to possess therapeutic effects on diseases induced by oxidative stress (DOS), such as atherosclerosis and diabetes complication. However, the active components and their related mechanisms are still not systematically reported.

OBJECTIVE

The current study was aimed to explore the main active ingredients and their molecular mechanisms of Z. bungeanum for treating DOS using network pharmacology combined with molecular docking simulation.

METHODS

The active components of Z. bungeanum pericarps, in addition to the interacting targets, were identified from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. These components were filtered using the parameters of oral bioavailability and drug-likeness, and the targets related to DOS were obtained from the Genecards and OMIM database. Furthermore, the overlapping genes were obtained, and a protein-protein interaction was visualized using the STRING database. Next, the Cytoscape software was employed to build a disease/drug/component/target network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using R software. Finally, the potential active compounds and their related targets were validated using molecular docking technology.

RESULTS

A total of 61 active compounds, 280 intersection genes, and 105 signaling pathways were obtained. Functional enrichment analysis suggested that DOS occurs possibly through the regulation of many biological pathways, such as AGE-RAGE and HIF-1 signaling pathways. Thirty of the identical target genes showed obvious compact relationships with others in the STRING analysis. Three active compounds, quercetin, diosmetin, and beta-sitosterol, interacting with the four key targets, exhibited strong affinities.

CONCLUSION

The findings of this study not only indicate the main mechanisms involving in oxidative stress-induced diseases but also provide the basis for further research on the active components of Z. bungeanum for treating DOS.

Extraction and Identification of Two Flavonoids in Phlomoides hyoscyamoides as an Endemic Plant of Iran: The Role of Quercetin in the Activation of the Glutathione Peroxidase, the Improvement of the Hydroxyproline and Protein Oxidation in Bile Duct-Ligated Rats

BACKGROUND

Cholestatic liver disease, a serious chronic condition that develops progressive hepatic degeneration through free radicals.

OBJECTIVE

The present study was designed to extract and identify two flavonoids in Phlomoides hyoscyamoides plant, native to Iran and evaluate the role of quercetin identified on the liver injury among bile ductligated rats.

METHODS

This study was conducted on 25 male Wistar rats within three groups of sham control, mere bile duct-ligated, and bile duct-ligated with quercetin. The bile duct-ligated animals received quercetin at a dose of 50 mg/kg/day for 10 days, followed by biochemical tests, oxidative stress markers, activity of antioxidant enzymes and hematoxylin and eosin staining. Molecular docking was used to explore the interactive behavior of quercetin with glutathione peroxidase.

RESULTS

According to analyses of the obtained extract, two main active ingredients of P. hyoscyamoides were rutin and quercetin. Bile duct-ligated group showed a significant liver necrosis, a clear increase in plasma and tissue oxidative stress parameters, and a decrease in glutathione peroxidase activity as compared to sham control group. Quercetin injection in bile duct-ligated rats resulted in significant decrease in hydroxyproline, protein carbonyl and histopathologic indexes and significant increase in glutathione peroxidase activity (P-value≤0.05). Based on the molecular docking, the quercetin was able to regulate the glutathione peroxidase activity.

CONCLUSION

The quercetin acts as an enzyme inducer by renewing the glutathione peroxidase activity and inhibiting the oxidation of proteins and hence decreases the oxidative stress. These results could be a sign of confirming the positive role of quercetin in attenuating the liver damage and degeneration.

Highly Potent and Selective Ectonucleoside Triphosphate Diphosphohydrolase (ENTPDase1, 2, 3 and 8) Inhibitors Having 2-substituted-7- trifluoromethyl-thiadiazolopyrimidones Scaffold

BACKGROUND

The ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) terminate nucleotide signaling via the hydrolysis of extracellular nucleoside-5'-triphosphate and nucleoside- 5'-diphosphate, to nucleoside-5'-monophosphate and composed of eight Ca2+/Mg2+ dependent ectonucleotidases (NTPDase1-8). Extracellular nucleotides are involved in a variety of physiological mechanisms. However, they are rapidly inactivated by ectonucleotidases that are involved in the sequential removal of phosphate group from nucleotides with the release of inorganic phosphate and their respective nucleoside. Ectonucleoside triphosphate diphosphohydrolases (NTPDases) represent the key enzymes responsible for nucleotides hydrolysis and their overexpression has been related to certain pathological conditions. Therefore, the inhibitors of NTPDases are of particular importance in order to investigate their potential to treat various diseases e.g., cancer, ischemia and other disorders of the cardiovascular and immune system.

METHODS

Keeping in view the importance of NTPDase inhibitors, a series of thiadiazolopyrimidones were evaluated for their potential inhibitory activity towards NTPDases by the malachite green assay.

RESULTS

The results suggested that some of the compounds were found as non-selective inhibitors of isozyme of NTPDases, however, most of the compounds act as potent and selective inhibitors. In case of substituted amino derivatives (4c-m), the compounds 4m (IC50 = 1.13 ± 0.09 μM) and 4g (IC50 = 1.72 ± 0.08 μM) were found to be the most potent inhibitors of h-NTPDase1 and 2, respectively. Whereas, compound 4d showed the best inhibitory potential for both h-NTPDase3 (IC50 = 1.25 ± 0.06 μM) and h-NTPDase8 (0.21 ± 0.02 μM). Among 5a-t derivatives, compounds 5e (IC50 = 2.52 ± 0.15 μM), 5p (IC50 = 3.17 ± 0.05 μM), 5n (IC50 = 1.22 ± 0.06 μM) and 5b (IC50 = 0.35 ± 0.001 μM) were found to be the most potent inhibitors of h-NTPDase1, 2, 3 and 8, respectively. Interestingly, the inhibitory concentration values of above-mentioned inhibitors were several folds greater than suramin, a reference control. In order to determine the binding interactions, molecular docking studies of the most potent inhibitors were conducted into the homology models of NTPDases and the putative binding analysis further confirmed that selective and potent compounds bind deep inside the active pocket of the respective enzymes.

CONCLUSION

The docking analysis proposed that the inhibitory activity correlates with the hydrogen bonds inside the binding pocket. Thus, these derivatives are of interest and may further be investigated for their importance in medicinal chemistry.

Automated Radiosynthesis and Molecular Docking Studies of Coumarin-Triazole Hybrid with fluorine-18: A feasibility study

BACKGROUND

Fluorine-18 is one of the promising radiotracers that can report target specific information related to its physiology to understand the disease status through PET modality. In current study, the radiochemical synthesis, purification and molecular docking studies of fluorine-18 (18F) radiolabeled coumarin-triazole hybrid have been performed.

OBJECTIVE

To develop target specific fluorine-18 radiotracer for the diagnosis in oncology.

METHODS

GE Tracer-lab FX2N module with few modifications in the line connections was used for the radiosynthesis and purification of target molecule [18F]SG-2, 4-((2,6-dimethylmorpholino) methyl)-7-((1-(4-(fluoro-18F) benzyl)-1H-1,2,3-triazol-4-yl) oxy)-2H-chromen-2-one, through the nucleophilic radiofluorination mechanism. The radiochemical purity was measured by HPLC, and TLC analytical methods. The kryptofix levels were also evaluated by using TLC method. The residual solvents like DMF, ethanol was measured using GC. The Schrödinger drug discovery suite 2018 was used to study the protein and ligand interactions.

RESULTS

The quality control parameters revealed the purity, chemical identity, and limits of residual solvents. The radiochemical purity was 95.5 ± 2.3 %, and dimethyl formamide solvent limit was 89 ± 3 ppm. The molecular docking results had suggested that the cold target molecule has made strong electronic interactions and showed the possible pharmacokinetic (ADME) properties with galectin-1 protein. Overall, these results showed that [18F]SG-2 radiolabeling with 18F radionuclide was feasible, and support of molecular docking studies suggest possible interactions with Galectin-1.

CONCLUSION

we reported feasibility study for labeling coumarin-triazole hybrid with fluorine-18 through aromatic nucleophilic fluorination reaction (SNAr).

Building Admiral, an Automated Molecular Dynamics and Analysis Platform

We present Admiral (Automated Docking and Molecular dynamics InfoRmatics and AnaLysis), a platform which automates the process of running molecular docking and molecular dynamics on compound designs for medicinal chemistry project teams. In addition to running the simulations, Admiral analyzes the simulation and automatically generates a PowerPoint slide, with the goal of having all the information required to decide whether to synthesize the compound in one place. This information includes results and analyses from the MD simulation, predicted ADME and physical-chemical properties, information on similar compounds in the SAR, and an animated GIF of the simulation. This report is then emailed to the compound designer, generally within the same day. Within Eli Lilly and Co., we have developed and deployed Admiral on an internal discovery project where it has been heavily used by the project team. Several additional discovery projects have adopted the platfom in recent months.

Comparison of Bromhexine and its Active Metabolite - Ambroxol as Potential Analgesics Reducing Oxaliplatin-induced Neuropathic Pain - Pharmacodynamic and Molecular Docking Studies

BACKGROUND

Painful peripheral neuropathy is a dose-limiting adverse effect of the antitumor drug oxaliplatin. The main symptoms of neuropathy: tactile allodynia and cold hyperalgesia, appear in more than 80% of patients on oxaliplatin therapy and are due to the overexpression of neuronal sodium channels (Navs) and neuroinflammation.

OBJECTIVE

This study assessed antiallodynic and antihyperalgesic properties of two repurposed drugs with antiinflammatory and Nav-blocking properties (bromhexine and its pharmacologically active metabolite - ambroxol) in a mouse model of neuropathic pain induced by oxaliplatin. Using molecular docking techniques, we predicted targets implicated in the observed in vivo activity of bromhexine.

METHODS

Oxaliplatin (a single intraperitoneal dose of 10 mg/kg) induced tactile allodynia and cold hyperalgesia in CD-1 mice and the effectiveness of single-dose or repeated-dose bromhexine and ambroxol to attenuate pain hypersensitivity was assessed in von Frey and cold plate tests. Additionally, Veber analysis and molecular docking experiments of bromhexine on mouse (m) and human (h) Nav1.6-1.9 were carried out.

RESULTS

At the corresponding doses, ambroxol was more effective than bromhexine as an antiallodynic agent. However, at the dose of 150 mg/kg, ambroxol induced motor impairments in mice. Repeated-dose bromhexine and ambroxol partially attenuated the development of late-phase tactile allodynia in oxaliplatin-treated mice. Only 7-day administration of bromhexine attenuated the development of late-phase cold hyperalgesia. Bromhexine was predicted to be a strong inhibitor of mNav1.6, mNav1.7, mNav1.9, and hNav1.7-hNav1.9.

CONCLUSION

The conversion of bromhexine to other than ambroxol active metabolites should be considered when interpreting some of its in vivo effects. Nav-blocking properties of bromhexine (and previously also predicted for ambroxol) might underlie its ability to attenuate pain caused by oxaliplatin.

The Molecular and Enzyme Kinetic Basis for Altered Activity of Three Cytochrome P450 2C19 Variants Found in the Chinese Population

BACKGROUND

There is a large inter-individual variation in cytochrome P450 2C19 (CYP2C19) activity. The variability can be caused by the genetic polymorphism of CYP2C19 gene. This study aimed to investigate the molecular and kinetics basis for activity changes in three alleles including CYP2C19*23, CYP2C19*24 and CYP2C19*25found in the Chinese population.

METHODS

The three variants expressed by bacteria were investigated using substrate (omeprazole and 3- cyano-7-ethoxycoumarin[CEC]) and inhibitor (ketoconazole, fluoxetine, sertraline and loratadine) probes in enzyme assays along with molecular docking.

RESULTS

All alleles exhibited very low enzyme activity and affinity towards omeprazole and CEC (6.1% or less in intrinsic clearance). The inhibition studies with the four inhibitors, however, suggested that mutations in different variants have a tendency to cause enhanced binding (reduced IC50 values). The enhanced binding could partially be explained by the lower polar solvent accessible surface area of the inhibitors relative to the substrates. Molecular docking indicated that G91R, R335Q and F448L, the unique mutations in the alleles, have caused slight alteration in the substrate access channel morphology and a more compact active site cavity hence affecting ligand access and binding. It is likely that these structural alterations in CYP2C19 proteins have caused ligand-specific alteration in catalytic and inhibitory specificities as observed in the in vitro assays.

CONCLUSION

This study indicates that CYP2C19 variant selectivity for ligands was not solely governed by mutation-induced modifications in the active site architecture, but the intrinsic properties of the probe compounds also played a vital role.

Lead Molecule Prediction and Characterization for Designing MERS-CoV 3C-like Protease Inhibitors: An In silico Approach

BACKGROUND

3C-like protease also called the main protease is an essential enzyme for the completion of the life cycle of Middle East Respiratory Syndrome Coronavirus. In our study we predicted compounds which are capable of inhibiting 3C-like protease, and thus inhibit the lifecycle of Middle East Respiratory Syndrome Coronavirus using in silico methods.

METHODS

Lead like compounds and drug molecules which are capable of inhibiting 3C-like protease was identified by structure-based virtual screening and ligand-based virtual screening method. Further, the compounds were validated through absorption, distribution, metabolism and excretion filtering.

RESULTS

Based on binding energy, ADME properties, and toxicology analysis, we finally selected 3 compounds from structure-based virtual screening (ZINC ID: 75121653, 41131653, and 67266079) having binding energy -7.12, -7.1 and -7.08 Kcal/mol, respectively and 5 compounds from ligandbased virtual screening (ZINC ID: 05576502, 47654332, 04829153, 86434515 and 25626324) having binding energy -49.8, -54.9, -65.6, -61.1 and -66.7 Kcal/mol respectively. All these compounds have good ADME profile and reduced toxicity. Among eight compounds, one is soluble in water and remaining 7 compounds are highly soluble in water. All compounds have bioavailability 0.55 on the scale of 0 to 1. Among the 5 compounds from structure-based virtual screening, 2 compounds showed leadlikeness. All the compounds showed no inhibition of cytochrome P450 enzymes, no blood-brain barrier permeability and no toxic structure in medicinal chemistry profile. All the compounds are not a substrate of P-glycoprotein.

CONCLUSION

Our predicted compounds may be capable of inhibiting 3C-like protease but need some further validation in wet lab.

Molecular Dynamics and Biological Evaluation of 2-chloro-7-cyclopentyl- 7H-pyrrolo[2,3-d]pyrimidine Derivatives Against Breast Cancer

AIM AND OBJECTIVE

Inspired by the impressive biological properties of pyrrolo[2,3- d]pyrimidine units, the objective of this study was to synthesize some new derivatives of heterocyclic compounds with different substituent's using solvent-free microwave irradiation conditions from readily available starting material. The synthesized compounds were screened for their in vitro anti-microbial, anti-oxidant, anti-cancer activities and theoretical molecular docking studies.

MATERIAL AND METHODS

Structural elucidation of the synthesized compounds was determined on the basis of various spectroscopic methods. Synthesized compounds have been evaluated for their in vitro antimicrobial activity (MIC) against various microbial strains. After the primary screening, synthesised compounds are further studied for anti-oxidant activity using DPPH assay method, anticancer activity against MCF-7 cell line using MTT assay and molecular docking studies. Moreover, molecular dynamics and simulation was done for best compound using GROMACS.

RESULTS

A series of 2-chloro-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidine derivatives 6(a-f), 7(a-c) and 8(a-c) were synthesised using solvent-free microwave irradiation technique. Among all the synthesized compounds, compounds 6e (51.35 μg/mL) and 6f (60.14 µg/mL) showed better activity profile against MCF-7 cell line for breast cancer activity. Compounds 6f and 6d have shown potent antibacterial activity against most of the employed strains, especially against S. pneumoniae, B. cerus and S. aureus. Compound 7a (52.21 µg/mL) showed high potential activity for antioxidant using DPPH assay. Molecular docking study showed good binding of these compounds to the active site of ER- alpha with binding energy ranging from -7.12 kcal/mol to -1.21 kcal/mol. Furthermore, molecular dynamics and simulation was conducted for best pose interacted compound 6e with active site of protein to study its stability and behaviour in nanoscale.

CONCLUSION

The present research work is intended for facile and efficient green synthesis of various biologically useful potent bio-active molecules from inexpensive and readily available starting substrates under mild reaction condition. These classes of synthesized various heterocyclic compounds holds a great importance to discover newer anti-microbial, anti-oxidant and anti-cancer drugs in future prospects. Further structural modification in these structures will be of interest and may result in compounds having a better therapeutic and biological activity. Hence, this efficient green synthetic protocol and biological results of newly synthesized heterocyclic derivatives are found to be interesting lead molecules for bioactivity in the near future. It could be considered for investigation of their mode of action and for further development.

[Biologically active composition for regulation of lipolysis process in the organism under obesity]

The aim of the research was to study the mechanism of intermolecular interaction of allicin and lecithin with pancreatic lipase, and developing the composition, contributing to the inactivation process of lipolysis, and reduce the absorption of fats in the organism. Methods of computer chemistry have been used for modeling spatial structures of allicin and lecithin. Geometric optimization was carried out, quantum chemical characteristics and the distribution of charge density of the molecules of the studied biologically active substances and pancreatic lipase were studied. In the study of the molecular properties of the lipase of pancreatic juice before and after molecular docking, it was found that one molecule of lecithin didn't fully block the active site of the enzyme. For complete inactivation of lipase, two molecules of lecithin or one molecule of allicin were required (Epot. = -412.36 and -159.4 kcal, respectively). An optimal composition of supplement to blocking pancreatic lipase has been set: allicin containing additive - 95% (75% sunflower oil, 25% chopped garlic), lecithin - 5%. The efficacy of lipase inactivation by supplement stored at 2-4 °C in fat-water mixture has been studied. It was found that after storage for three days the developed composition retained its properties. Acid number of fat, subjected to enzymatic treatment varies slightly (0.1 to 0.25 mg KOH/g). Peroxide value and microbiological characteristics of the investigated fraction also did not exceed the permissible norms. When evaluating the biological value of the developed composition in the experiment on white BALB/c mice (with initial body weight of 20-30 g), it was found that its administration on the background of high fat (19%) diet at a dose of 6% of the diet fat from the 15th to the 40th day was accompanied by 1.5 fold reduce in body weight increasing in comparison with animals which received no additives. Their blood levels of total lipids, cholesterol, triglycerides and glucose reduced while the level of total protein and urea increased to the level of the control group (without obesity).