Identification of xanthine oxidase inhibitors through hierarchical virtual screening

As a critical enzyme for the uric acid production, xanthine oxidase (XO) has emerged as a primary drug target for antihyperuricemic therapy. A hierarchical virtual screening integrating both ligand-based and structure-based approaches was applied herein to identify potent XO inhibitors. Four compounds, which were previously reported as XO inhibitors, were recognized through the virtual screening protocol, and compound H3, which is distinct from the structures of known XO inhibitors, was identified as a new chemotype inhibitor with IC₅₀ of 2.6 μM. The binding mode of H3 was further investigated by molecular docking and molecular dynamics (MD) simulation. The results suggested the feasibility to discover new chemotypes of XO inhibitors via integrated virtual screening strategies.

A new chemotype of XO inhibitor with the IC₅₀ of 2.6 μM was identified by a hierarchical virtual screening strategy.     

3D-QSAR,molecular docking,and molecular dynamics simulation study of thieno[3,2-b]pyrrole-5-carboxamide derivatives as LSD1 inhibitors

Histone Lysine Specific Demethylase 1 (LSD1) is overexpressed in many cancers and becomes a new target for anticancer drugs. In recent years, small molecule inhibitors with various structures targeting LSD1 have been reported. Here we report the binding interaction modes of a series of thieno[3,2-b]pyrrole-5-carboxamide LSD1 inhibitors using molecular docking, and three-dimensional quantitative structure–activity relationships (3D-QSAR). Comparative molecular field analysis (CoMFA q² = 0.783, r² = 0.944, r_pred² = 0.851) and comparative molecular similarity indices analysis (CoMSIA q² = 0.728, r² = 0.982, r_pred² = 0.814) were used to establish 3D-QSAR models, which had good verification and prediction capabilities. Based on the contour maps and the information of molecular docking, 8 novel small molecules were designed in silico, among which compounds D4, D5 and D8 with high predictive activity were subjected to further molecular dynamics simulations (MD), and their possible binding modes were explored. It was found that Asn535 plays a crucial role in stabilizing the inhibitors. Furthermore, ADME and bioavailability prediction for D4, D5 and D8 were carried out. The results would provide valuable guidance for designing new reversible LSD1 inhibitors in the future.

Novel LSD1 inhibitors with potential activity are designed using a series of computer-aided drug design methods.     

Uracil derivatives as HIV-1 capsid protein inhibitors: design,in silico,in vitro and cytotoxicity studies

A series of novel uracil derivatives such as bispyrimidine dione and tetrapyrimidine dione derivatives were designed based on the existing four-point pharmacophore model as effective HIV capsid protein inhibitors. The compounds were initially docked with an HIV capsid protein monomer to rationalize the ideas of design and to find the potential binding modes. The successful design and computational studies led to the synthesis of bispyrimidine dione and tetrapyrimidine dione derivatives from uracil and aromatic aldehydes in the presence of HCl using novel methodology. The in vitro evaluation in HIV p24 assay revealed five potential uracil derivatives with IC₅₀ values ranging from 191.5 μg ml⁻¹ to 62.5 μg ml⁻¹. The meta-chloro substituted uracil compound 9a showed promising activity with an IC₅₀ value of 62.5 μg ml⁻¹ which is well correlated with the computational studies. As expected, all the active compounds were noncytotoxic in BA/F3 and Mo7e cell lines highlighting the thoughtful design. The structure activity relationship indicates the position priority and lower log P values as the possible cause of inhibitory potential of the uracil compounds.

The paper describes the design, synthesis, computational and biological validation of a series of novel uracil derivatives as effective HIV capsid protein inhibitors.     

Molecular docking,pharmacophore based virtual screening and molecular dynamics studies towards the identification of potential leads for the management of H. pylori

The enzyme pantothenate synthetase panC is one of the potential new antimicrobial drug targets, but it is poorly characterized in H. pylori. H. pylori infection can cause gastric cancer and the management of H. pylori infection is crucial in various gastric ulcers and gastric cancer. The current study describes the use of innovative drug discovery and design approaches like comparative metabolic pathway analysis (Metacyc), exploration of database of essential genes (DEG), homology modelling, pharmacophore based virtual screening, ADMET studies and molecular dynamics simulations in identifying potential lead compounds for the H. pylori specific panC. The top ranked virtual hits STOCK1N-60270, STOCK1N-63040, STOCK1N-44424 and STOCK1N-63231 can act as templates for synthesis of new H. pylori inhibitors and they hold a promise in the management of gastric cancers caused by H. pylori.

Computational approaches such as pharmacophore modeling, virtual screening and MD simulations were explored to find the potential hits as H. pylori specific panC inhibitors for the management of gastric ulcers and gastric cancers.     

Importance of protein flexibility in ranking ERK2 Type I1/2 inhibitor affinities: a computational study

Extracellular-regulated kinase (ERK2) has been regarded as an essential target for various cancers, especially melanoma. Recently, pyrrolidine piperidine derivatives were reported as Type I^1/2 inhibitors of ERK2, which occupy both the ATP binding pocket and the allosteric pocket. Due to the dynamic behavior of ERK2 upon the binding of Type I^1/2 inhibitors, it is difficult to predict the binding structures and relative binding potencies of these inhibitors with ERK2 accurately. In this work, the binding mechanism of pyrrolidine piperidines was discussed by using different simulation techniques, including molecular docking, ensemble docking based on multiple receptor conformation, molecular dynamics simulations and free energy calculations. Our computational results show that the traditional docking method cannot predict the relative binding ability of the studied inhibitors with high accuracy, but incorporating ERK2 protein flexibility into docking is an effective method to improve the prediction accuracy. It is worth noting that the binding free energies predicted by MM/GBSA or MM/PBSA based on the MD simulations for the docked poses have the highest correlation with the experimental data, which highlights the importance of protein flexibility for accurately predicting the binding ability of Type I^1/2 inhibitors of ERK2. In addition, the comprehensive analysis of several representative inhibitors indicates that hydrogen bonds and hydrophobic interactions are of significance for improving the binding affinities of the inhibitors. We hope this work will provide valuable information for further design of novel and efficient Type I^1/2 ERK2 inhibitors.

Extracellular-regulated kinase (ERK2) has been regarded as an essential target for various cancers, especially melanoma.     

Selective binding of matrix metalloproteases MMP-9 and MMP-12 to inhibitor-assisted thermolysin-imprinted beads

Protein-imprinted polymers have been synthesized to recognize and specifically bind selected proteins. However, protein imprinting requires substantial amounts of pure protein to efficiently obtain imprinted polymers for large scale applications, e.g. protein purification by affinity chromatography. In the absence of large quantities of a pure protein of interest, an alternative strategy was developed. In this case study, neutral metalloprotease thermolysin was selected as a commercially available surrogate for imprinting polymer beads. Phosphoramidon-assisted thermolysin-imprinted beads were synthesized. During rebinding experiments, it was shown that these beads specifically bind to thermolysin. In addition, it was shown that these beads also bind in CHO cell culture supernatant to the matrix metalloprotease-9 and -12 (MMP-9, -12). Therefore, these beads can be applied as a selective sorbent for the rare metalloproteases MMP-9 and MMP-12 to remove these proteases from CHO cell culture supernatants. The high selectivity of thermolysin-imprinted beads can be extended to other proteases of the family of metalloproteases, and is not limited to thermolysin. This innovative approach is suitable to address the challenges in the field of protease purification and isolation from biotechnologically relevant media.

Dummy-imprinted polymers were prepared for selectively binding metalloproteases MMP-9 and MMP-12 in CHO cell culture supernatant.     

Molecular modeling provides a structural basis for PERK inhibitor selectivity towards RIPK1

Protein kinases are crucial drug targets in cancer therapy. Kinase inhibitors are promiscuous in nature due to the highly conserved nature of the kinase ATP binding pockets. PERK has emerged as a potential therapeutic target in cancer. However, PERK inhibitors GSK2606414 and GSK2656157 also target RIPK1 whereas AMG44 is more specific to PERK. To understand the structural basis for the selectivity of PERK ligands to RIPK1 we have undertaken a detailed in silico analysis using molecular docking followed by molecular dynamics simulations to explore the selectivity profiles of the compounds. Although the binding sites of PERK and RIPK1 are similar, their binding response to small molecules is different. The docking models revealed a common binding mode for GSK2606414 and GSK2656157 in the RIPK1 binding site, similar to its cognate ligand. In contrast, AMG44 had a strikingly different predicted binding profile in the RIPK1 binding site with both rigid docking and induced fit docking settings. Our study shows a molecular mechanism responsible for dual targeting by the GSK ligands. More broadly, this work illustrates the potential of molecular docking to correctly predict the binding towards different kinase structures, and will aid in the design of selective PERK kinase inhibitors.

Molecular modelling explains the lack of selectivity for inhibitors GSK2606414 and GSK2656157, as compared to inhibitor AMG44.     

Angelica gigas ameliorates the destruction of gingival tissues via inhibition of MMP-9 activity

Angelica gigas (AG) has been used for periodontal diseases in traditional Korean medicine. However, the effects of AG on periodontitis have not been clarified yet. In this study, we investigated the ameliorative effects of AG against ligature-induced periodontitis. Sprague-Dawley rats were divided into four groups; non-ligatured (normal), ligatured and treated with vehicle (ligatured), ligatured and treated with 1 mg mL⁻¹ AG (AG1), and ligatured and treated with 100 mg mL⁻¹ AG (AG100). 70% ethanol extracts of AG were topically applied onto both sides of the first molar daily for 14 days. In addition, human dermal fibroblast cells were treated with 1, 10 and 100 μg mL⁻¹ AG to characterize the expression of matrix metallopeptidase 9 (MMP-9). Topical AG treatment reduced alveolar bone resorption, as assessed by methylene blue staining. The structures of soft gingival tissues (periodontal pocket) were recovered in the AG-treated groups. The expression of MMP-9 was decreased, and that of type 1 collagen was significantly increased in AG-treated gingival tissues. In addition, AG treatment inhibited the activity of MMP-9 in LPS-treated human dermal fibroblast cells. This study reveals that topical AG treatment has the potential to ameliorate the destruction of gingival tissues by inhibiting MMP-9 activity. AG may be a candidate for the treatment of periodontitis.

Angelica gigas (AG) has been used for periodontal diseases in traditional Korean medicine.     

Discovery and characterization of naturally occurring potent inhibitors of catechol-O-methyltransferase from herbal medicines

Human catechol-O-methyltransferase (hCOMT) is considered a therapeutic target due to its crucial roles in the metabolic inactivation of endogenous neurotransmitters and xenobiotic drugs. There are nevertheless few safe and effective COMT inhibitors and there lacks a diversity in structure. To discover novel safe and effective hCOMT inhibitors from herbal products, in this study, 53 herbal products were collected and their inhibitory effects against hCOMT were investigated. Among them, Scutellariae radix (SR) displayed the most potent inhibitory effect on hCOMT with an IC₅₀ value of 0.75 μg mL⁻¹. To further determine specific chemicals as COMT inhibitors, an affinity ultrafiltration coupled with liquid chromatography-mass spectrometry method was developed and successfully applied to identify COMT inhibitors from SR extract. The results demonstrated that scutellarein 2, baicalein 9 and oroxylin A 12 were potent COMT inhibitors, showing a high binding index (>3) and very low IC₅₀ values (32.9 ± 3.43 nM, 37.3 ± 4.32 nM and 18.3 ± 2.96 nM). The results of inhibition kinetics assays and docking simulations showed that compounds 2, 9 and 12 were potent competitive inhibitors against COMT-mediated 3-BTD methylation, and they could stably bind to the active site of COMT. These findings suggested that affinity ultrafiltration allows a rapid identification of natural COMT inhibitors from a complex plant extract matrix. Furthermore, scutellarein 2, baicalein 9 and oroxylin A 12 are potent inhibitors of hCOMT in SR, which could be used as promising lead compounds to develop more efficacious non-nitrocatechol COMT inhibitors for biomedical applications.

Discovery and characterization of natural human catechol-O-methyltransferase (hCOMT) inhibitors for Parkinson''s disease treatment.     

Discovery of novel inhibitors of RNA silencing suppressor P19 based on virtual screening

To control plant viruses, viral RNA silencing suppressors are important drug targets due to their key roles in interfering antiviral RNA silencing. Here we have presented a strategy, combining virtual and experimental screening, to discover the inhibitors of viral suppressor. By docking 157 026 compounds from a natural product library into P19 model, eighteen candidate compounds were selected. Candidates VS2, VS12, VS14 and VS15 displayed strong binding ability to P19 in the surface plasmon resonance imaging assay with K_D values of 136.2, 111.6, 81.2 and 124.5 nM, respectively. Then the inhibition activities of these inhibitors on the association between P19 and siRNA were also affirmed by electrophoretic mobility shift assay. Moreover, the antiviral effects on plants showed that compounds VS14 and VS15 both exhibited antiviral activities against Tomato bushy stunt virus (TBSV) in vivo with inhibition rates of 32.35% and 16.61% in 11 dpi, respectively. This strategy would be a powerful tool for the discovery of novel antiviral agents and provide new insights into the control of plant viruses.

The combined virtual and experimental screening method is a efficient strategy to discover inhibitors of RNA silencing suppressor.     

Pharmacoinformatics approaches to identify potential hits against tetraacyldisaccharide 4′-kinase (LpxK) of Pseudomonas aeruginosa

Pseudomonas aeruginosa infection can cause pneumonia and urinary tract infection and the management of Pseudomonas aeruginosa infection is critical in multidrug resistance, hospital-acquired bacteremia and ventilator-associated pneumonia. The key enzymes of lipid A biosynthesis in Pseudomonas aeruginosa are promising drug targets. However, the enzyme tetraacyldisaccharide 4′-kinase (LpxK) has not been explored as a drug target so far. Several pharmacoinformatics tools such as comparative metabolic pathway analysis (Metacyc), data mining from a database of essential genes (DEG), homology modeling, molecular docking, pharmacophore based virtual screening, ADMET prediction and molecular dynamics simulation were used in identifying novel lead compounds against this target. The top virtual hits STOCK6S-33288, 43621, 39892, 37164 and 35740 may serve as the templates for the design and synthesis of potent LpxK inhibitors in the management of serious Pseudomonas aeruginosa infection.

Homology modeling, docking, pharmacophore based VS and molecular dynamics identified potential hits against P. aeruginosa specific LpxK.     

Correction: Highly porous core–shell chitosan beads with superb immobilization efficiency for Lactobacillus reuteri 121 inulosucrase and production of inulin-type fructooligosaccharides

Correction for ‘Highly porous core–shell chitosan beads with superb immobilization efficiency for Lactobacillus reuteri 121 inulosucrase and production of inulin-type fructooligosaccharides’ by Thanapon Charoenwongpaiboon et al., RSC Adv., 2018, 8, 17008–17016.

The authors regret that Fig. 9 in the original article was displayed incorrectly. The correct version is shown below.Open in a separate windowFig. 9Batch reusability of INU-CSBs for IFOS synthesis. Reaction condition: 10 U mL⁻¹ of biocatalysts were incubated with 200 g L⁻¹ sucrose in acetate buffer pH 5.5, 40 °C and 2 h per batch.The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.     

Isolation ssDNA aptamers specific for both live and viable but nonculturable state Vibrio vulnificus using whole bacteria-SEILEX technology

Vibrio vulnificus is a ubiquitous marine bacterium that may cause rapid and deadly infection, threatening lives of people living around natural bodies of water, especially in coastal regions. However, traditional culture-based methods are time-consuming and unable to detect Viable But Non-Culturable (VBNC) V. vulnificus cells. In this work, we isolated a batch of detection aptamers specifically binding to V. vulnificus in all culture status. With traditional whole bacteria-SELEX (Systematic Evolution of Ligands by EXponential enrichment), flow cytometer analysis and imaging, we identify 18 candidates and validated two of them (V8 and V13) as applicable aptamers. Their truncated sequences also showed comparable performance. The dissociation constant (KD) value of V8 is shown to be as low as 11.22 ± 1.32 nM. Optimal aptamers V8 and V13 are also validated to be effective to detect different Vibrio vulnificus strains under different binding environments using flow cytometry. As for detection parameters, the LOD of the V8 from cytometry is 29.96 CFU mL⁻¹, and the linear range is 10²–5 × 10⁵ CFU mL⁻¹. This is the first case demonstrating that aptamers can detect the existence of VBNC bacteria as well as live bacteria.

With whole-bacteria SELEX, we got aptamers that can bind to V. vulnificus in VBNC Status for the first time.     

Discovery of human TyrRS inhibitors by structure-based virtual screening,structural optimization,and bioassays

The human tyrosyl transfer-RNA (tRNA) synthetase (TyrRS), which is well known for its essential aminoacylation function in protein synthesis, has been shown to translocate to the nucleus and protect against DNA damage caused by external stimuli. Small molecules that can fit into the active site pocket of TyrRS are thought to affect the nuclear role. The exploitation of TyrRS inhibitors has attracted attention recently. In this investigation, we adopted a structure-based virtual screening strategy and subsequent structure–activity relationship analysis to discover new TyrRS inhibitors, and identified a potent compound 5,7-dihydroxy-6,8-bis((3-hydroxyphenyl)thio)-2-phenyl-4H-chromen-4-one (compound 11, K_i = 8.8 μM). In intact HeLa cells, this compound showed a protective effect against DNA damage. Compound 11 is a good lead compound for the further development of drugs against disorders caused by DNA damage.

A small molecule with potent activity diverts human Tyrosyl-tRNA synthetase (TyrRS) to the nucleus for protection against DNA damage.     

Remarkably selective biocompatible turn-on fluorescent probe for detection of Fe3+ in human blood samples and cells

The robust nature of a biocompatible fluorescent probe is demonstrated, by its detection of Fe³⁺ even after repeated rounds of quenching (reversibility) by acetate in real human blood samples and cells in vitro. Significantly trace levels of Fe³⁺ ions up to 8.2 nM could be detected, remaining unaffected by the existence of various other metal ions. The obtained results are validated by AAS and ICP-OES methods. A portable test strip is also fabricated for quick on field detection of Fe³⁺. As iron is a ubiquitous metal in cells and plays a prominent role in biological processes, the use of this probe to image Fe³⁺ in cells is a substantial development towards biosensing. Cytotoxicity studies also proved the nontoxic nature of this probe.

The robust nature of a biocompatible fluorescent probe is demonstrated, by its detection of Fe³⁺ even after repeated rounds of quenching (reversibility) by acetate in real human blood samples and cells in vitro.     

Discovery of VEGFR2 inhibitors by integrating naïve Bayesian classification,molecular docking and drug screening approaches

The high morbidity and mortality of cancer make it one of the leading causes of global death, thus it is an urgent need to develop effective drugs for cancer therapy. Vascular endothelial growth factor receptor-2 (VEGFR2) acts as a central modulator of angiogenesis, and is therefore an important pharmaceutical target for developing anti-angiogenic agents. In this study, ligand-based naïve Bayesian (NB) models and structure-based molecular docking were combined to develop a virtual screening (VS) pipeline for identifying potential VEGFR2 inhibitors from FDA-approved drugs. The best validated naïve Bayesian model (NB-c) gave Matthews correlation coefficients of 0.966 and 0.951 for the test set and external validation set, respectively. 1841 FDA-approved drugs were sequentially screened by the optimal model NB-c and molecular docking module LibDock. By analyzing the results of VS, 9 top ranked drugs with EstPGood value ≥ 0.6 and LibDock Score ≥ 120 were chosen for biological validation. VEGFR2 kinase assay results demonstrated that flubendazole, rilpivirine and papaverine showed VEGFR2 inhibitory activities with IC₅₀ values ranging from 0.47 to 6.29 μM. Binding mode analysis with CDOCKER revealed the action mechanism of the 3 hit drugs binding to VEGFR2. In summary, we not only proposed an integrated VS pipeline for potential VEGFR2 inhibitors screening, but also identified 3 FDA-approved drugs as novel VEGFR2 inhibitors, which could be used to design and develop new antiangiogenic agents.

The high morbidity and mortality of cancer make it one of the leading causes of global death, thus it is an urgent need to develop effective drugs for cancer therapy.     

Structure-based discovery and bio-evaluation of a cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one as a phosphodiesterase 10A inhibitor

Phosphodiesterase10A (PDE10A) is a potential therapeutic target for the treatment of several neurodegenerative disorders. Thus, extensive efforts of medicinal chemists have been directed toward developing potent PDE10A inhibitors with minimal side effects. However, PDE10A inhibitors are not approved as a treatment for neurodegenerative disorders, possibly due to the lack of research in this area. Therefore, the discovery of novel and diverse scaffolds targeting PDE10A is required. In this study, we described the identification of a new PDE10A inhibitor by structure-based virtual screening combining pharmacophore modelling, molecular docking, molecular dynamics simulations, and biological evaluation. Zinc42657360 with a cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one scaffold from the zinc database exhibited a significant inhibitory activity of 1.60 μM against PDE10A. The modelling studies demonstrated that Zinc42657360 is involved in three hydrogen bonds with ASN226, THR187 and ASP228, and two aromatic interactions with TYR78 and PHE283, besides the common interactions with the P-clamp residues PHE283 and ILE246. The novel scaffold of Zinc42657360 can be used for the rational design of PDE10A inhibitors with improved affinity.

Phosphodiesterase10A (PDE10A) is a potential therapeutic target for the treatment of several neurodegenerative disorders.     

Exploring the binding mechanisms of PDE5 with chromeno[2,3-c]pyrrol-9(2H)-one by theoretical approaches

Cyclic nucleotide phosphodiesterase type 5 (PDE5), exclusively specific for the cyclic guanosine monophosphate (cGMP), is an important drug target for the treatment of erectile dysfunction and pulmonary arterial hypertension (PAH). Although many PDE5 inhibitors have been approved, such as sildenafil, vardenafil, tadalafil and so on, extensive studies have reported some side effects, such as vision disturbance and hearing loss as a result of the amino acid sequence and the secondary structural similarity of other PDEs to the catalytic domain of PDE5. In this study, multiple docking strategies, molecular dynamics (MD) simulations, free energy calculations and decomposition were employed to explore the structural determinants of PDE5 with a series of chromeno[2,3-c]pyrrol-9(2H)-one derivatives. First, reliable docking results were obtained using quantum mechanics/molecular mechanics (QM/MM) docking. Then, MD simulations and MM/GBSA free energy calculations were used to explore the dynamic binding process and characterize the binding modes of the inhibitors with different activities. The predicted binding free energies are in good agreement with the experimental data, and the MM/GBSA free energy decomposition analysis sheds light on the importance of hydrogen bonds with Gln817, π–π stacks against Phe820 and hydrophobic residues for the PDE5 binding of the studied inhibitors. The structural and energetic insights obtained here are useful for understanding the molecular mechanism of ligand binding and designing novel potent and selective PDE5 inhibitors with new scaffolds.

Cyclic nucleotide phosphodiesterase type 5 (PDE5) is exclusively specific for the cyclic guanosine monophosphate (cGMP), and PDE5 is an important drug target for the treatment of erectile dysfunction and pulmonary arterial hypertension (PAH).     

KOtBu-promoted oxidative dimerizations of 2-methylquinolines to 2-alkenyl bisquinolines with molecular oxygen

KO^tBu-promoted oxidative dimerizations of 2-methylquinolines with molecular oxygen as the oxidant have been developed for the first time. The mild reaction conditions allow the homo- and cross-dimerizations of 2-methylquinolines to give functionalized 2-alkenyl bisquinolines in highly trans-selective manners.

KO^tBu-promoted oxidative dimerizations of 2-methylquinolines with molecular oxygen as the oxidant have been developed for the first time.