The effect of Nrf2 deletion on the proteomic signature in a human colorectal cancer cell line.

BACKGROUND: Colorectal cancer is one of the most common cancer and the third leading cause of death worldwide. Increased generation of reactive oxygen species (ROS) is observed in many types of cancer cells. Several studies have reported that an increase in ROS production could affect the expression of proteins involved in ROS-scavenging, detoxification and drug resistance. Nuclear factor erythroid 2 related factor 2 (Nrf2) is a known transcription factor for cellular response to oxidative stress. Several researches exhibited that Nrf2 could exert multiple functions and expected to be a promising therapeutic target in many cancers. Here, Nrf2 was knocked down in colorectal cancer cell line HT29 and changes that occurred in signaling pathways and survival mechanisms were evaluated. METHODS: The influence of chemotherapy drugs (doxorubicin and cisplatin), metastasis and cell viability were investigated. To explore the association between specific pathways and viability in HT29-Nrf2-, proteomic analysis, realtime PCR and western blotting were performed. RESULTS: In the absence of Nrf2 (Nrf2-), ROS scavenging and detoxification potential were dramatically faded and the HT29-Nrf2- cells became more susceptible to drugs. However, a severe decrease in viability was not observed. Bioinformatic analysis of proteomic data revealed that in Nrf2- cells, proteins involved in detoxification processes, respiratory electron transport chain and mitochondrial-related compartment were down regulated. Furthermore, proteins related to MAPKs, JNK and FOXO pathways were up regulated that possibly helped to overcome the detrimental effect of excessive ROS production. CONCLUSIONS: Our results revealed MAPKs, JNK and FOXO pathways connections in reducing the deleterious effect of Nrf2 deficiency, which can be considered in cancer therapy.

Amino-modified-silica-coated gadolinium-copper nanoclusters, conjugated to AS1411 aptamer and radiolabeled with technetium-99 m as a novel multimodal imaging agent.

Hybridimagingtechnology has the potential to provide reliable imagingand accurate detection of cancer cells by combining the advantages and overcoming the shortages of various clinical imaging tools. Nanomaterials with unique targeting properties and their small size have improved biomedical imaging. Indeed, their small size determines local contrast agent concentrations in tumors by enhanced permeability and retention (EPR) effect. In this work, amino-modified silica-coated Gadolinium-Copper Nanoclusters were fabricated and conjugated to AS1411 aptamer (Apt-ASGCuNCs) and radiolabeled with technetium-99 m (99mTc) for in vivo fluorescence imaging, magnetic resonance imaging (MRI) and single-photon emission computed tomography (SPECT). The synthesized nanoconjugate was fully characterized by transmission electron microscopy (TEM), element mapping, fluorescence spectroscopy, and Fourier-transform infrared spectroscopy. Moreover, XTT assay, and apoptosis and necrosis methods were applied to study toxicity. Radiochemical yield was calculated 93% that revealed a great potential for complex formation between Apt-ASGCuNCs and 99mTcO4-. Also, good stability of 99mTc-Apt-ASGCuNCs was found in the human serum up to 4 h. Both Apt-ASGCuNCs and 99mTc-Apt-ASGCuNCs indicated a considerable tumor-targeting in in vivo fluorescence imaging, MRI and SPECT with 4T1 tumor-bearing BALB/c mice. The biodistribution results showed no undesirable accumulation of 99mTc-Apt-ASGCuNCs in the liver, and spleen as it circulated freely in the blood pool. Meanwhile, 99mTc-Apt-ASGCuNCs were removed from the body through the renal clearance system, making it more convenient for future multimodality imaging applications.

Design, synthesis, in vitro, and in silico enzymatic evaluations of thieno[2,3-b]quinoline-hydrazones as novel inhibitors for α-glucosidase.

In the development of novel anti-α-glucosidase agents, we synthesized novel thieno[2,3-b]quinoline-hydrazones 9a-n by facile and efficient conventional chemical reactions. These compounds were characterized by IR, 1H NMR, 13C NMR, and elemental analysis. Inhibitory activities of the title compounds were evaluated against yeast α-glucosidase. In particular, compounds 9c, 9d, and 9h exhibited high anti-α-glucosidase activity. Representatively, compound 9c with IC50 = 1.3 µM, was 576-times more potent than positive control acarbose. Molecular docking study of the most active compounds showed that these compounds formed important binding interactions at α-glucosidase active site. Molecular dynamics study of compound 9c was also performed and the obtained results were compared with acarbose. Compounds 9c, 9d, and 9h were also evaluated for in silico druglikeness properties and ADMET prediction. These studies showed that the title most potent compounds could be exploited as drug candidates.

Synthesis and in vitro urease inhibitory activity of 5-nitrofuran-2-yl-thiadiazole linked to different cyclohexyl-2-(phenylamino)acetamides, in silico and kinetic studies.

A series of 5-nitrofuran-2-yl-thiadiazole linked to different cyclohexyl-2-(phenylamino)acetamides were rationally designed and synthesized. All synthetic compounds were evaluated for their urease inhibitory activity and exhibited good inhibitory potential against urease with IC50 values in the range of 0.94 - 6.78 µM as compared to the standard thiourea (IC50 = 22.50 µM). Compound 8g (IC50 = 0.94 µM) with a thiophene substituent at the R2 position was found to be the most active member of the series. Kinetic studies exhibited that the compound 8g was a non-competitive inhibitor. In silicostudy showed the critical interactions of potent inhibitors with the active site of the enzyme. These newly identified inhibitors of the urease enzyme can serve as leads for further research and development.

Computational Engineering of Protein L to Achieve an Optimal Affinity Chromatography Resin for Purification of Antibody Fragments.

Protein L affinity chromatography is a useful method for the purification of antibody fragments containing kappa light chains. In affinity chromatography, increasing the binding affinity leads to increased product purity, recovery, and dynamic binding capacity (DBC). In this study, molecular docking and molecular dynamics simulation techniques were used to design the engineered Protein L with higher affinity to the kappa light chain. Each engineered ligand was produced as a recombinant protein and coupled to a solid matrix. The purity, recovery, and DBC of the engineered resins were evaluated and then compared to those of a commercially available resin. The results showed important parameters for engineering more efficient Protein L ligands for affinity chromatography.

DeepCDA: deep cross-domain compound-protein affinity prediction through LSTM and convolutional neural networks.

MOTIVATION: An essential part of drug discovery is the accurate prediction of the binding affinity of new compound-protein pairs. Most of the standard computational methods assume that compounds or proteins of the test data are observed during the training phase. However, in real-world situations, the test and training data are sampled from different domains with different distributions. To cope with this challenge, we propose a deep learning-based approach that consists of three steps. In the first step, the training encoder network learns a novel representation of compounds and proteins. To this end, we combine convolutional layers and long-short-term memory layers so that the occurrence patterns of local substructures through a protein and a compound sequence are learned. Also, to encode the interaction strength of the protein and compound substructures, we propose a two-sided attention mechanism. In the second phase, to deal with the different distributions of the training and test domains, a feature encoder network is learned for the test domain by utilizing an adversarial domain adaptation approach. In the third phase, the learned test encoder network is applied to new compound-protein pairs to predict their binding affinity. RESULTS: To evaluate the proposed approach, we applied it to KIBA, Davis and BindingDB datasets. The results show that the proposed method learns a more reliable model for the test domain in more challenging situations. AVAILABILITY AND IMPLEMENTATION: https://github.com/LBBSoft/DeepCDA.

Drug databases and their contributions to drug repurposing.

Drug repurposing is an interesting field in the drug discovery scope because of reducing time and cost. It is also considered as an appropriate method for finding medications for orphan and rare diseases. Hence, many researchers have proposed novel methods based on databases which contain different information. Thus, a suitable organization of data which facilitates the repurposing applications and provides a tool or a web service can be beneficial. In this review, we categorize drug databases and discuss their advantages and disadvantages. Surprisingly, to the best of our knowledge, the importance and potential of databases in drug repurposing are yet to be emphasized. Indeed, the available databases can be divided into several groups based on data content, and different classes can be applied to find a new application of the existing drugs. Furthermore, we propose some suggestions for making databases more effective and popular in this field.

Technetium-99 m-PEGylated dendrimer-G2-(Dabcyle-Lys6,Phe7)-pHBSP: A novel Nano-Radiotracer for molecular and early detecting of cardiac ischemic region.

In cardiac ischemic disorder, pyroglutamate helix B surface peptide (pHBSP) which derived from erythropoietin causes to increase cell stability. To improve the serum stability of pHBSP, two lipophilic amino acids Arg6, Ala7 were replaced with Fmoc-(Dabcyle)-Lys-OH and Fmoc-Phe-OH during the peptide synthesis. This peptide was subsequently conjugated to PEGylated dendrimer-G2 and labeled with 99mTcO4- to detect cardiac ischemic region. Radiochemical purity (RCP) of 99mTc-PEGylated dendrimer-G2-(Dabcyle-Lys6,Phe7)-pHBSP was evaluated by ITLC method. In addition, the radiopeptide was investigated for stability in human serum and binding affinity to hypoxic cells in myocardium H9c2 cell lines. Biodistribution and SPECT/CT scintigraphy were assessed in cardiac ischemic rats. Radiochemical yield indicated that the anionic dendrimer has a very high potential to complex formation with 99mTcO-4 (RCP > 94%) which was stable in human serum with RCP 89% up to 6 h. The binding of 99mTc- nanoconjugate to hypoxic cells was significantly more than normoxic cells (3-fold higher compared to normoxic cells at 1 h). In biodistribution studies, erythropoietin receptor-Beta common receptor (EPO-BcR)-positive uptake in the cardiac ischemic region was 3.62 ± 0.44% ID/g 30 min post injection. SPECT imaging showed a prominent uptake of 99mTc-nanoconjugate in EPO-BcR expressing ischemic heart.

Novel N,N-dimethylbarbituric-pyridinium derivatives as potent urease inhibitors: Synthesis, in vitro, and in silico studies.

A new series of N,N-dimethylbarbituric-pyridinium derivatives 7a-n was synthesized and evaluated as Helicobacter pylori urease inhibitors. All the synthesized compounds (IC50 = 10.37 ± 1.0-77.52 ± 2.7 µM) were more potent than standard inhibitor hydroxyurea against urease (IC50 = 100.00 ± 0.2 µM). Furthermore, comparison of IC50 values of the synthesized compounds with the second standard inhibitor thiourea (IC50 = 22.0 ± 0.03 µM) revealed that compounds 7a-b and 7f-h were more potent than thiourea. Molecular modeling study of the most potent compounds 7a, 7b, 7f, and 7g was also conducted. Additionally, the drug-likeness properties of the synthesized compounds, based on Lipinski rule and other filters, were evaluated.

Efficient synthesis, biological evaluation, and docking study of isatin based derivatives as caspase inhibitors.

ABTRACT In this paper, a new series of isatin-sulphonamide based derivatives were designed, synthesised and evaluated as caspase inhibitors. The compounds containing 1-(pyrrolidinyl)sulphonyl and 2-(phenoxymethyl)pyrrolidin-1-yl)sulphonyl substitution at C5 position of isatin core exhibited better results compared to unsubstituted derivatives. According to the results of caspase inhibitory activity, compound 20d showed moderate inhibitory activity against caspase-3 and -7 in vitro compared to Ac-DEVD-CHO (IC50 = 0.016 ± 0.002 µM). Among the studied compounds, some active inhibitors with IC50s in the range of 2.33-116.91 µM were identified. The activity of compound 20d was rationalised by the molecular modelling studies exhibiting the additional van der Waals interaction of N-phenylacetamide substitution along with efficacious T-shaped π-π and pi-cation interactions. The introduction of compound 20d with good caspase inhibitory activity will help researchers to find more potent agents.

Synthesis, Biological Evaluation and Molecular Docking of Deferasirox and Substituted 1,2,4-Triazole Derivatives as Novel Potent Urease Inhibitors: Proposing Repositioning Candidate.

A series of new deferasirox derivatives were synthesized through the reaction of monosubstituted hydrazides with 2-(2-hydroxyphenyl)-4H-benzo[e][1,3]oxazin-4-one. For the first time, deferasirox and some of its derivatives were evaluated for their in vitro inhibitory activity against Jack bean urease. The potencies of the members of this class of compounds are higher than that of acetohydroxamic acid. Two compounds, bearing tetrazole and hydrazine derivatives (bioisoester of carboxylate group), represented the most potent urease inhibitory activity with IC50 values of 1.268 and 3.254 µm, respectively. In silico docking studies were performed to delineate possible binding modes of the compounds with the enzyme, urease. Docking analysis suggests that the synthesized compounds were anchored well in the catalytic site and extending to the entrance of binding pocket and thus restrict the mobility of the flap by interacting with its crucial amino acid residues, CME592 and His593. The overall results of urease inhibition have shown that these target compounds can be further optimized and developed as a lead skeleton for the discovery of novel urease inhibitors.

New 1,2,3-triazole-(thio)barbituric acid hybrids as urease inhibitors: Design, synthesis, in vitro urease inhibition, docking study, and molecular dynamic simulation.

A new series of 1,2,3-triazole-(thio)barbituric acid hybrids 8a-n was designed and synthesized on the basis of potent pharmacophores with urease inhibitory activity. Therefore, these compounds were evaluated against Helicobacter pylori urease. The obtained result demonstrated that all the synthesized compounds, 8a-n, were more potent than the standard urease inhibitor, hydroxyurea. Moreover, among them, compounds 8a, 8c-e, 8g,h, and 8k,l exhibited higher urease inhibitory activities than the other standard inhibitor used: thiourea. Docking studies were performed with the synthesized compounds. Furthermore, molecular dynamic simulation of the most potent compounds, 8e and 8l, showed that these compounds interacted with the conserved residues Cys592 and His593, which belong to the active site flap and are essential for enzymatic activity. These interactions have two consequences: (a) blocking the movement of a flap at the entrance of the active site channel and (b) stabilizing the closed active site flap conformation, which significantly reduces the catalytic activity of urease. Calculation of the physicochemical and topological properties of the synthesized compounds 8a-n predicted that all these compounds can be orally active. The ADME prediction of compounds 8a-n was also performed.

Deep Transferable Compound Representation across Domains and Tasks for Low Data Drug Discovery.

The main problem of small molecule-based drug discovery is to find a candidate molecule with increased pharmacological activity, proper ADME, and low toxicity. Recently, machine learning has driven a significant contribution to drug discovery. However, many machine learning methods, such as deep learning-based approaches, require a large amount of training data to form accurate predictions for unseen data. In lead optimization step, the amount of available biological data on small molecule compounds is low, which makes it a challenging problem to apply machine learning methods. The main goal of this study is to design a new approach to handle these situations. To this end, source assay (auxiliary assay) knowledge is utilized to learn a better model to predict the property of new compounds in the target assay. Up to now, the current approaches did not consider that source and target assays are adapted to different target groups with different compounds distribution. In this paper, we propose a new architecture by utilizing graph convolutional network and adversarial domain adaptation network to tackle this issue. To evaluate the proposed approach, we applied it to Tox21, ToxCast, SIDER, HIV, and BACE collections. The results showed the effectiveness of the proposed approach in transferring the related knowledge from source to target data set.

Isoindolin-1-one derivatives as urease inhibitors: Design, synthesis, biological evaluation, molecular docking and in-silico ADME evaluation.

An efficient, one-pot and four-component synthesis of a new series of 2,3-disubstituted isoindolin-1-ones is described and their Jack bean urease inhibitory activities are evaluated. Heating a mixture of 1,1-bis(methylthio)-2-nitroethene, a 1,2-diamine, a 2-formylbenzoic acid and a primary amine in EtOH for 3.5 h afforded the corresponding 2,3-disubstituted isoindolin-1-ones in good to excellent yields. All sixteen synthesized isoindolin-1-one derivatives 5a-p showed urease inhibitory activity. Among them, 5c showed the most urease inhibitory activity (IC50 = 10.07 ±â€¯0.28 µM) being over 2-fold more potent than thiourea (IC50 = 22.01 ±â€¯0.10 µM) and 10-fold than hydroxyurea (IC50 = 100.00 ±â€¯0.02 µM) as the standard inhibitors, respectively. Also, results from molecular docking studies were in good agreement with those obtained from in vitro tests.

Design, Synthesis, Molecular Docking, and Cholinesterase Inhibitory Potential of Phthalimide-Dithiocarbamate Hybrids as New Agents for Treatment of Alzheimer's Disease.

A novel series of phthalimide-dithiocarbamate hybrids was synthesized and evaluated for in vitro inhibitory potentials against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). The anti-cholinesterase results indicated that among the synthesized compounds, the compounds 7g and 7h showed the most potent anti-AChE and anti-BuChE activities, respectively. Molecular docking and dynamic studies of the compounds 7g and 7h, respectively, in the active site of AChE and BuChE revealed that these compounds as well interacted with studied cholinesterases. These compounds also possessed drug-like properties and were able to cross the BBB.

Structure-based pharmacophore design and virtual screening for novel potential inhibitors of epidermal growth factor receptor as an approach to breast cancer chemotherapy.

Cancer cells are described with features of uncontrolled growth, invasion and metastasis. The epidermal growth factor receptor subfamily of tyrosine kinases (EGFR-TK) plays a crucial regulatory role in the control of cellular proliferation and progression of various cancers. Therefore, its inhibition might lead to the discovery of a new generation of anticancer drugs. In the present study, structure-based pharmacophore modeling, molecular docking and molecular dynamics simulations were applied to identify potential hits, which exhibited good inhibition on the proliferation of MCF-7 breast cancer cell line and favorable binding interactions on EGFR-TK. Selected compounds were examined for their anticancer activity against the Michigan Cancer Foundation-7 (MCF-7) breast cancer cell line which overexpresses EGFR using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) tetrazolium reduction assay. Compounds 1 and 2, with an isoindoline-1-one core, induced significant inhibition of breast cancer cells proliferation with IC[Formula: see text] values 327 and 370 nM, respectively.

Synthesis, evaluation, and molecular docking studies of aryl urea-triazole-based derivatives as anti-urease agents.

Considering the importance of urease inhibitors in the treatment of ureolytic bacterial infections, in this work, the synthesis of novel, aryl urea-triazole-based derivatives as effective urease inhibitors is described. Dichloro-substituted derivative 4o, with IC50 = 22.81 ± 0.05 µM, is found to be the most potent urease inhibitor, determined by Berthelot colorimetric assay. Docking studies were also carried out for compound 4o to confirm the effective interactions with the urease active site.

Characterization of the DNA mismatch repair proteins MutS and MutL in a hypermutator Acinetobacter baumannii.

Mutations of mutS and mutL genes have been linked with the emergence of hypermutator (HPM) phenotype in several bacteria. Nevertheless, there is scarce evidence that these mutations occurred in HPM Acinetobacter baumannii, therefore, it remains unknown whether the mutations located in domains mediating the functions of MutS and MutL. To address this information gap, the nucleotide sequences of mutS and mutL were characterized and their mutations were identified. Additionally, we proposed in silico models of mutated proteins and analyzed the secondary and tertiary structures, and the interaction interfaces of MutL and MutS. The HPM A. baumannii and a wild-type strain were subjected to PCR amplification of full length mutS and mutL, cloning, and sequencing. Following several reads of both strands of each gene and sequence assembly, the mutations were identified. Thereafter, the three-dimensional (3-D) structure of A. baumannii ATCC 19606 was developed and utilized as a template for homology modeling of the mutated amino acid sequences using the Phyre2 and I-TASSER, VMD 1.9.3, LigPlus v.1.4.5, PyMOL v.0.99 software. Regardless of silent mutations (n = 43), 11 missense mutations were identified in the MutS domains of HPM strain such as A4T, T272S, D278N in N-terminus, connector, and core domains, respectively. Three mutations -I357T, A408S, N447S- and 16 silent mutations were observed in MutL. Secondary structure prediction of MutS revealed that the amount of alpha helices, beta sheets, and coils in HPM were 35, 29, and 63, respectively, while these values were 36, 28, and 63 for A. baumannii ATCC 19606 as non mutator. In the case of MutL, for both HPM and non-mutator, 20, 21, and 39 of complete protein were alpha helices, beta sheets, and coils, respectively. Superimposition of structures of MutS of HPM on non-mutator revealed that T272, D278, G457, S528, A533, Y715, and E747 are closely matched with S272, D278, A457, P528, V533, C715, and K747, respectively in non-mutator strain. When the structure of MutL model in HPM was superimposed on its counterpart in non-mutator, all but residues S447, S408, and T357 were identical. Many mutations along the mutS and mutL were noted, but most of the mutations were observed in the interaction interfaces of MutS and MutL. Other substitutions were predominantly detected in C-terminus of MutS that may lead to reduced ATP binding and hydrolysis. Three substitution mutations were adjacent to C-terminus of MutL and are raising the suggestion of reduction in MutL dimerization. It seems that a combination of these mutations is implicated in increased mutation frequency and accordingly emergence of HPM strain.

Display of B. pumilus chitinase on the surface of B. subtilis spore as a potential biopesticide.

BACKGROUND: Chitinases can inhibit the growth of many fungal diseases which are a great threat for global agricultural production. Biological control of pathogens like fungi, is believed to be one of the best ways to eliminate the adverse effects of plant pathogens. To this end, we expressed and displayed a chitinase from Bacillus pumilus (ChiS) on the surface of Bacillus subtilis spores, as a biocontrol agent. RESULT: ChiS enzyme from B. pumilus was expressed on the spores of B. subtilis using CotG as a carrier protein. Immunofluorescence microscopy confirmed the expression of ChiS on the surface of the spores. Enzyme activity assay showed that the surface displayed ChiS was active and was also able to inhibit the growth of Rhizoctonia solani and Trichoderma harzianum fungi. Western blot analysis also indicated that CotG-ChiS is partially processed after display. Molecular dynamics simulation showed that the stability of the heterologous protein was decreased after fusion. CONCLUSION: ChiS was successfully displayed on the surface of Bacillus spores by fusion to the CotG, one of the main spore coat proteins. In-vitro experiments showed that the displayed enzyme was effective in growth inhibition of R. solani and T. harzianum fungi.

A case-control study of bisphenol A and endometrioma among subgroup of Iranian women.

BACKGROUND: Endometriosis is a multifactorial hormonally related complex disease with unknown etiology. Epidemiologic data were suggested the possible effects of endocrine disrupting chemicals such as bisphenol A (BPA) on endometriosis. BPA is similar to endogenous estrogen and has the ability to interact with estrogen receptors and stimulate estrogen production. Our aim was to evaluate the relationship between urinary BPA concentrations in women with endometrioma. MATERIALS AND METHODS: This case-control study consisted of fifty women who have been referred to gynecology and infertility center with endometrioma and were candidates for operative laparoscopy and ovarian cystectomy as cases. Fifty women who had not any evidence of endometrioma in clinical and ultrasound evaluation and came to the same clinic for routine check-up were selected as controls. One-time urine sample was collected after receiving informed consent before surgery and medical intervention. Total BPA in urine was measured with high-performance liquid chromatography method and detection limit was 0.33 ng/mL. RESULTS: Percentage of urine samples containing BPA was 86% of cases and 82.4% of control. Urinary BPA showed a right-skewed distribution. The mean concentration of BPA was 5.53 ± 3.47 ng/mL and 1.43 ± 1.57 ng/mL in endometriosis and control group, respectively (P < 0.0001, Mann-Whitney U-test). The logistic regression showed that the odds ratio of the BPA was 1.74 (95% confidence interval: 1.40-2.16) after adjustment of age, parity, body mass index <30, and educational status. CONCLUSION: This study showed a positive association between urinary BPA concentrations and endometrioma. However, further large-scale studies are needed to confirm this hypothesis.