Mechanism-based target identification and drug discovery in cancer research

Isolation of active compounds from Streptomyces sennicomposti GMY01 and cytotoxic activity on breast cancer cells line

The occurrence of resistance to anticancer and the emergence of serious side effects due to chemotherapy is one of the main problems in cancer treatment, including breast cancer. The need for effective anticancer with a specific target is urgently required. Streptomyces are widely known as the potential producers of new anticancer molecules. Previously reported that the methanol extract of Streptomyces sennicomposti GMY01 isolated from Krakal Coast, Gunungkidul had very strong cytotoxic activity against MCF-7 and T47D breast cancer cells with IC50 values of 0.6 and 1.3 μg/mL, respectively. The following study aimed to isolate and identify active compounds of the S. sennicomposti GMY01 and evaluate its cytotoxic activity. The study was started by re-culturing and re-fermented optimization of S. sennicomposti GMY01 in a larger volume, then the bacteria were extracted using methanol following the bioassay-guided isolation of the extract obtained. The active compounds obtained were then structurally determined using UV/Vis spectroscopy, Fourier Transform-Infrared (FT-IR), Liquid Chromatography-Mass Spectroscopy (LC-MS), 1H NMR, and 13C NMR and analyzed for their cytotoxic activity using MTT assay on MCF-7 and normal Vero cells line. The results showed that the culture of the S. sennicomposti GMY01 using Starch Nitrate Broth (SNB) media yields the best results compared to other culture media. An active anticancer compound namely mannotriose was successfully isolated from the methanol extract with an IC50 value of 5.6 μg/mL and 687 μg/mL against the MCF-7 and Vero cells lines, respectively, indicating that this compound showed strong cytotoxic activity with high selectivity.

A review for cancer treatment with mushroom metabolites through targeting mitochondrial signaling pathway: In vitro and in vivo evaluations, clinical studies and future prospects for mycomedicine

Resistance to apoptosis stands as a roadblock to the successful pharmacological execution of anticancer drug effect. A comprehensive insight into apoptotic signaling pathways and an understanding of the mechanisms of apoptosis resistance are crucial to unveil new drug targets. At this juncture, researchers are heading towards natural sources in particular, mushroom as their potential drugs leads to being the reliable source of potent bioactive compounds. Given the continuous increase in cancer cases, the potent anticancer efficacy of mushrooms has inevitably become a fascinating object to researchers due to their higher safety margin and multitarget. This review aimed to collect and summarize all the available scientific data on mushrooms from their extracts to bioactive molecules in order to suggest their anticancer attributes via a mitochondrion -mediated intrinsic signaling mechanism. Compiled data revealed that bioactive components of mushrooms including polysaccharides, sterols and terpenoids as well as extracts prepared using 15 different solvents from 53 species could be effective in the supportive treatment of 20 various cancers. The underlying therapeutic mechanisms of the studied mushrooms are explored in this review through diverse and complementary investigations: in vitro assays, pre-clinical studies and clinical randomized controlled trials. The processes mainly involved were ROS production, mitochondrial membrane dysfunction, and action of caspase 3, caspase 9, XIAP, cIAP, p53, Bax, and Bcl-2. In summary, the study provides facts pertaining to the potential beneficial effect of mushroom extracts and their active compounds against various types of cancer and is shedding light on the underlying targeted signaling pathways.

Logic-based modeling and drug repurposing for the prediction of novel therapeutic targets and combination regimens against E2F1-driven melanoma progression

Melanoma presents increasing prevalence and poor outcomes. Progression to aggressive stages is characterized by overexpression of the transcription factor E2F1 and activation of downstream prometastatic gene regulatory networks (GRNs). Appropriate therapeutic manipulation of the E2F1-governed GRNs holds the potential to prevent metastasis however, these networks entail complex feedback and feedforward regulatory motifs among various regulatory layers, which make it difficult to identify druggable components. To this end, computational approaches such as mathematical modeling and virtual screening are important tools to unveil the dynamics of these signaling networks and identify critical components that could be further explored as therapeutic targets. Herein, we integrated a well-established E2F1-mediated epithelial-mesenchymal transition (EMT) map with transcriptomics data from E2F1-expressing melanoma cells to reconstruct a core regulatory network underlying aggressive melanoma. Using logic-based in silico perturbation experiments of a core regulatory network, we identified that simultaneous perturbation of Protein kinase B (AKT1) and oncoprotein murine double minute 2 (MDM2) drastically reduces EMT in melanoma. Using the structures of the two protein signatures, virtual screening strategies were performed with the FDA-approved drug library. Furthermore, by combining drug repurposing and computer-aided drug design techniques, followed by molecular dynamics simulation analysis, we identified two potent drugs (Tadalafil and Finasteride) that can efficiently inhibit AKT1 and MDM2 proteins. We propose that these two drugs could be considered for the development of therapeutic strategies for the management of aggressive melanoma.

Emerging trends and applications of metabolomics in food science and nutrition

The study of all chemical processes involving metabolites is known as metabolomics. It has been developed into an essential tool in several disciplines, such as the study of plant physiology, drug development, human diseases, and nutrition. The field of food science, diagnostic biomarker research, etiological analysis in the field of medical therapy, and raw material quality, processing, and safety have all benefited from the use of metabolomics recently. Food metabolomics includes the use of metabolomics in food production, processing, and human diets. As a result of changing consumer habits and the rising of food industries all over the world, there is a remarkable increase in interest in food quality and safety. It requires the employment of various technologies for the food supply chain, processing of food, and even plant breeding. This can be achieved by understanding the metabolome of food, including its biochemistry and composition. Additionally, Food metabolomics can be used to determine the similarities and differences across crop kinds, as an indicator for tracking the process of ripening to increase crops' shelf life and attractiveness, and identifying metabolites linked to pathways responsible for postharvest disorders. Moreover, nutritional metabolomics is used to investigate the connection between diet and human health through detection of certain biomarkers. This review assessed and compiled literature on food metabolomics research with an emphasis on metabolite extraction, detection, and data processing as well as its applications to the study of food nutrition, food-based illness, and phytochemical analysis. Several studies have been published on the applications of metabolomics in food but further research concerning the use of standard reproducible procedures must be done. The results published showed promising uses in the food industry in many areas such as food production, processing, and human diets. Finally, metabolome-wide association studies (MWASs) could also be a useful predictor to detect the connection between certain diseases and low molecular weight biomarkers.

CuAAC "Click"-Derived Luminescent 2-(2-(4-(4-(Pyridin-2-yl)-1H-1,2,3-triazol-1-yl)butoxy)phenyl)benzo[d]thiazole-Based Ru(II)/Ir(III)/Re(I) Complexes as Anticancer Agents

To enhance the cytoselective behavior of the complexes, we intended to develop a CuAAC "click"-derived synthetic protocol for the preparation of 2-(2-(4-(4-(pyridin-2-yl)-1H-1,2,3-triazol-1-yl)butoxy)phenyl)benzo[d]thiazole-based Ru(II)/Ir(III)/Re(I) complexes, and their cytotoxicity against three different cancer cell lines (MCF-7, HeLa, and U87MG) in consort with one normal cell line (HEK-293) was evaluated. In our detailed investigations, the significant cytotoxic nature of the Ru(II) complex 7a compared to Ir(III) and Re(I) complexes (7b and 7c, respectively) was observed. Complex 7a was capable of MCF-7 cell apoptosis via the inhibition of both S- and G2/M-phase cell cycle arrest in association with a substantial quantity of ROS production and DNA intercalation.

Recent advances in targeting the "undruggable" proteins: from drug discovery to clinical trials

Undruggable proteins are a class of proteins that are often characterized by large, complex structures or functions that are difficult to interfere with using conventional drug design strategies. Targeting such undruggable targets has been considered also a great opportunity for treatment of human diseases and has attracted substantial efforts in the field of medicine. Therefore, in this review, we focus on the recent development of drug discovery targeting "undruggable" proteins and their application in clinic. To make this review well organized, we discuss the design strategies targeting the undruggable proteins, including covalent regulation, allosteric inhibition, protein-protein/DNA interaction inhibition, targeted proteins regulation, nucleic acid-based approach, immunotherapy and others.

OncoRTT: Predicting novel oncology-related therapeutic targets using BERT embeddings and omics features

Late-stage drug development failures are usually a consequence of ineffective targets. Thus, proper target identification is needed, which may be possible using computational approaches. The reason being, effective targets have disease-relevant biological functions, and omics data unveil the proteins involved in these functions. Also, properties that favor the existence of binding between drug and target are deducible from the protein’s amino acid sequence. In this work, we developed OncoRTT, a deep learning (DL)-based method for predicting novel therapeutic targets. OncoRTT is designed to reduce suboptimal target selection by identifying novel targets based on features of known effective targets using DL approaches. First, we created the “OncologyTT” datasets, which include genes/proteins associated with ten prevalent cancer types. Then, we generated three sets of features for all genes: omics features, the proteins’ amino-acid sequence BERT embeddings, and the integrated features to train and test the DL classifiers separately. The models achieved high prediction performances in terms of area under the curve (AUC), i.e., AUC greater than 0.88 for all cancer types, with a maximum of 0.95 for leukemia. Also, OncoRTT outperformed the state-of-the-art method using their data in five out of seven cancer types commonly assessed by both methods. Furthermore, OncoRTT predicts novel therapeutic targets using new test data related to the seven cancer types. We further corroborated these results with other validation evidence using the Open Targets Platform and a case study focused on the top-10 predicted therapeutic targets for lung cancer.

DrugAI: a multi-view deep learning model for predicting drug-target activating/inhibiting mechanisms

Understanding the mechanisms of candidate drugs play an important role in drug discovery. The activating/inhibiting mechanisms between drugs and targets are major types of mechanisms of drugs. Owing to the complexity of drug-target (DT) mechanisms and data scarcity, modelling this problem based on deep learning methods to accurately predict DT activating/inhibiting mechanisms remains a considerable challenge. Here, by considering network pharmacology, we propose a multi-view deep learning model, DrugAI, which combines four modules, i.e. a graph neural network for drugs, a convolutional neural network for targets, a network embedding module for drugs and targets and a deep neural network for predicting activating/inhibiting mechanisms between drugs and targets. Computational experiments show that DrugAI performs better than state-of-the-art methods and has good robustness and generalization. To demonstrate the reliability of the predictive results of DrugAI, bioassay experiments are conducted to validate two drugs (notopterol and alpha-asarone) predicted to activate TRPV1. Moreover, external validation bears out 61 pairs of mechanism relationships between natural products and their targets predicted by DrugAI based on independent literatures and PubChem bioassays. DrugAI, for the first time, provides a powerful multi-view deep learning framework for robust prediction of DT activating/inhibiting mechanisms.

Drug Repurposing at the Interface of Melanoma Immunotherapy and Autoimmune Disease

Cancer cells have a remarkable ability to evade recognition and destruction by the immune system. At the same time, cancer has been associated with chronic inflammation, while certain autoimmune diseases predispose to the development of neoplasia. Although cancer immunotherapy has revolutionized antitumor treatment, immune-related toxicities and adverse events detract from the clinical utility of even the most advanced drugs, especially in patients with both, metastatic cancer and pre-existing autoimmune diseases. Here, the combination of multi-omics, data-driven computational approaches with the application of network concepts enables in-depth analyses of the dynamic links between cancer, autoimmune diseases, and drugs. In this review, we focus on molecular and epigenetic metastasis-related processes within cancer cells and the immune microenvironment. With melanoma as a model, we uncover vulnerabilities for drug development to control cancer progression and immune responses. Thereby, drug repurposing allows taking advantage of existing safety profiles and established pharmacokinetic properties of approved agents. These procedures promise faster access and optimal management for cancer treatment. Together, these approaches provide new disease-based and data-driven opportunities for the prediction and application of targeted and clinically used drugs at the interface of immune-mediated diseases and cancer towards next-generation immunotherapies.

Chemopreventive and Therapeutic Efficacy of Enhalus acoroides against Diethylnitrosamine Induced Hepatocellular Carcinoma in Wistar Albino Rats

Hepatocellular carcinoma is the second most cause of death among the various cancers worldwide. Recent research searching an alternative therapy for cancer treatment without or less side effects. Many studies indicated the beneficial effects of Enhalus acoroides. There has been no scientific validation on antioxidant and chemopreventive potential of ethanolic extract E. acoroides against hepatoma. To assess the hepatoprotective activity of E. acoroides (EEEA) against DEN-induced hepatoma using Wistar albino rats. Animals were distributed into five groups, each containing six rats. To Group I - control rats - normal saline given. Groups II, III, IV and V rats were injection of DEN at a dose of 100 mg/kg body weight i.p. to induce liver cancer. At the commencement of 6th week, Group III rats supplemented with EEEA at a dose of 200 mg/kg body weight/day upto 16 weeks. Group IV rats supplemented with EEEA for 1 week before the administration of DEN and continued till the sixteenth week. Group V supplementation of silymarin at a dose of 100 mg/kg body weight at the beginning of 6th week after the injection of DEN and continued upto 16 weeks and considered as positive control rats. The efficiency of E. acoroides for its antioxidant hepatoprotective and activity evaluated in rats against DEN-induced liver damage. The hepatoprotective ability of EEEA at a dose of 200 mg/kg was examined against DEN at a dose of 100 mg/kg/b.w. induced hepatotoxicity and analysed by evaluating serum liver and kidney marker levels, lipid profile (TG, HDL, LDL and total cholesterol) and serum tumour markers (DNA, RNA, AFP and CEA). Supplementation of EEEA to DEN treated rats was determined by evaluating various antioxidant biomarkers (SOD, CAT, GPx, GSH, Vit E and Vit C). Histopathological studies and morphometric gross analysis were also support the consequences of this study. A significant improvement of antioxidant defence and declined MDA levels within the serum of EEEA treated animals compared to the DEN-induced hepatoma. The supplementation of EEEA declined the serum liver, kidney and serum tumour marker levels and lipid profile as comparatively to Group I rats. The histopathological changes were changed on supplementation of EEEA demonstrating its protecting effects on hepatocytes as comparatively to Group I rats. Our significances recognized that crude extract (ethanol) of E. acoroides revealed a potential impact against DEN-induced hepatoma and assists as a superior choice for chemopreventive treatments.

Strategies for active tumor targeting-an update

A complete cure for cancer is still the holy grail for scientists. The existing treatment of cancer is primarily focused on surgery, radiation and conventional chemotherapy. However, chemotherapeutic agents also affect healthy tissues or organs due to a lack of specificity. While passive targeting is studied for anticancer drugs focused on the enhanced permeability and retention effect, it failed to achieve drug accumulation at the tumor site and desired therapeutic efficacy. This review presents an outline of the current significant targets for active tumor drug delivery systems and provides insight into the direction of active tumor-targeting strategies. For this purpose, a systematic understanding of the physiological factors, tumor microenvironment and its components, overexpressed receptor and associated proteins are covered here. We focused on angiogenesis mediated targeting, receptor-mediated targeting and peptide targeting. This active targeting along with integration with nano delivery systems helps in achieving specific action, thus reducing the associated adverse effects to healthy tissues. Although the tumor-targeting methods and possibilities explored so far seem revolutionary in cancer treatment, in-depth clinical studies data is required for its commercial translation.

Cysteine derivatives as acetyl lysine mimics to inhibit zinc-dependent histone deacetylases for treating cancer

Zinc-dependent histone deacetylases (HDACs) are important epigenetic regulators that have become important drug targets for treating cancer. Although five HDAC inhibitors have been approved for treating several cancers, there is still a huge demand on discovering new HDAC inhibitors to explore the therapeutic potentials for treating solid tumor cancers. Substrate mimics are a powerful rational design approach for the development of potent inhibitors. Here we describe the rational design, synthesis, biological evaluation, molecular docking and in vivo efficacy study of a class of HDAC inhibitors using N^ε-acetyl lysine mimics that are derived from cysteine. As a result, compounds 7a, 9b and 13d demonstrated pan-HDAC inhibition and broad cytotoxicity against several cancer cell lines, comparable to the approved HDAC inhibitor SAHA. Furthermore, 13d significantly inhibited tumor growth in a A549 xenograft mice model without any obvious weight loss, supporting that the cysteine-derived acetyl lysine mimics are promising HDAC inhibitors with therapeutic potentials for treating cancer.

Recent Trends in Tubulin-Binding Combretastatin A-4 Analogs for Anticancer Drug Development

Although significant progress over several decades has been evidenced in cancer therapy, there still remains a need for the development of novel and effective therapeutic strategies to treat several relapsed and intractable cancers. In this regard, tubulin protein has become one of the efficient and major targets for anticancer drug discovery. Considering the antimitotic ability, several tubulin inhibitors have been developed to act against various cancers. Among various tubulin inhibitors available, combretastatin-A4 (CA-4), a naturally occurring lead molecule, offers exceptional cytotoxicity (including the drug-resistant cell lines) and antivascular effects. Although CA-4 offers exceptional therapeutic efficacy, several new advancements have been proposed, such as the structural modification via A and B rings, as well as cis-olefinic bridging, which provide highly efficient analogs with improved tubulin-binding efficiency to meet the anticancer drug development requirements. This review systematically emphasizes the recent trends and latest developments in the anticancer drug design & discovery, using CA-4 analogs as the tubulin inhibiting agents, highlighting their structure-activity relationships (SAR) and resultant pharmacological efficacies.

Proteomic Research on the Antitumor Properties of Medicinal Mushrooms

Medicinal mushrooms are increasingly being recognized as an important therapeutic modality in complementary oncology. Until now, more than 800 mushroom species have been known to possess significant pharmacological properties, of which antitumor and immunomodulatory properties have been the most researched. Besides a number of medicinal mushroom preparations being used as dietary supplements and nutraceuticals, several isolates from mushrooms have been used as official antitumor drugs in clinical settings for several decades. Various proteomic approaches allow for the identification of a large number of differentially regulated proteins serendipitously, thereby providing an important platform for a discovery of new potential therapeutic targets and approaches as well as biomarkers of malignant disease. This review is focused on the current state of proteomic research into antitumor mechanisms of some of the most researched medicinal mushroom species, including Phellinus linteus, Ganoderma lucidum, Auricularia auricula, Agrocybe aegerita, Grifola frondosa, and Lentinus edodes, as whole body extracts or various isolates, as well as of complex extract mixtures.

Natural Product-Based Studies for the Management of Castration-Resistant Prostate Cancer: Computational to Clinical Studies

Background: With prostate cancer being the fifth-greatest cause of cancer mortality in 2020, there is a dire need to expand the available treatment options. Castration-resistant prostate cancer (CRPC) progresses despite androgen depletion therapy. The mechanisms of resistance are yet to be fully discovered. However, it is hypothesized that androgens depletion enables androgen-independent cells to proliferate and recolonize the tumor. Objectives: Natural bioactive compounds from edible plants and herbal remedies might potentially address this need. This review compiles the available cheminformatics-based studies and the translational studies regarding the use of natural products to manage CRPC. Methods: PubMed and Google Scholar searches for preclinical studies were performed, while ClinicalTrials.gov and PubMed were searched for clinical updates. Studies that were not in English and not available as full text were excluded. The period of literature covered was from 1985 to the present. Results and Conclusion: Our analysis suggested that natural compounds exert beneficial effects due to their broad-spectrum molecular disease-associated targets. In vitro and in vivo studies revealed several bioactive compounds, including rutaecarpine, berberine, curcumin, other flavonoids, pentacyclic triterpenoids, and steroid-based phytochemicals. Molecular modeling tools, including machine and deep learning, have made the analysis more comprehensive. Preclinical and clinical studies on resveratrol, soy isoflavone, lycopene, quercetin, and gossypol have further validated the translational potential of the natural products in the management of prostate cancer.

Bile-Acid-Appended Triazolyl Aryl Ketones: Design, Synthesis, In Vitro Anticancer Activity and Pharmacokinetics in Rats

A library of bile-acid-appended triazolyl aryl ketones was synthesized and characterized by detailed spectroscopic techniques such as ¹H and ¹³C NMR, HRMS and HPLC. All the synthesized conjugates were evaluated for their cytotoxicity at 10 µM against MCF-7 (human breast adenocarcinoma) and 4T1 (mouse mammary carcinoma) cells. In vitro cytotoxicity studies on the synthesized conjugates against MCF-7 and 4T1 cells indicated one of the conjugate 6cf to be most active against both cancer cell lines, with IC₅₀ values of 5.71 µM and 8.71 µM, respectively, as compared to the reference drug docetaxel, possessing IC₅₀ values of 9.46 µM and 13.85 µM, respectively. Interestingly, another compound 6af (IC₅₀ = 2.61 µM) was found to possess pronounced anticancer activity as compared to the reference drug docetaxel (IC₅₀ = 9.46 µM) against MCF-7. In addition, the potent compounds (6cf and 6af) were found to be non-toxic to normal human embryonic kidney cell line (HEK 293), as evident from their cell viability of greater than 86%. Compound 6cf induces higher apoptosis in comparison to 6af (46.09% vs. 33.89%) in MCF-7 cells, while similar apoptotic potential was observed for 6cf and 6af in 4T1 cells. The pharmacokinetics of 6cf in Wistar rats showed an MRT of 8.47 h with a half-life of 5.63 h. Clearly, these results suggest 6cf to be a potential candidate for the development of anticancer agents.

Designing potent inhibitors against the multidrug resistance P-glycoprotein

The multidrug transporter P-glycoprotein is an ATP binding cassette (ABC) exporter responsible for resistance to tumor cells during chemotherapy. This study was designed with computational approaches aimed at identifying the best potent inhibitors of P-glycoprotein. Although many compounds have been suggested to inhibit P-glycoprotein, however, their information on bioavailability, selectivity, ADMET properties, and molecular interactions has not been revealed. Molecular docking, ADMET analysis, molecular dynamics, Principal component analysis (PCA), and binding free energy calculations were performed. Two compounds D1 and D2 showed the best docking score against P-glycoprotein and both compounds have 4-thiazolidinone derivatives containing indolin-3 one moiety are novel anti-tumor compounds. ADMET calculation analysis predicted D1 and D2 to have acceptable pharmacokinetic properties. The MD simulation discloses that D1-P-glycoprotein and D2-P-glycoprotein complexes are in stable conformation as apo-form. Hydrophobic amino acid such as phenylalanine plays significant on the interactions of inhibitors. Principal component analysis shows that both complexes are relatively similar variables as apo-form except planarity and Columbo energy profile. In addition, Quantitative Structural Activity Relationship (QSAR) of the ligand candidates were subjected to the principal component analysis (PCA) for pattern recognition. Partial-least-square (PLS) regression analysis was further utilized to model drug candidates' QSAR for subsequent prediction of the binding energy of validated drug candidates. PCA revealed groupings of the drug candidates based on the similarity or differences in drug candidates QSAR. Moreover, the developed PLS regression accurately predicted the values of the binding energy of drug candidates, with low residual error of prediction.Communicated by Ramaswamy H. Sarma.

Combination of HDE and BIIB021 efficiently inhibits cell proliferation and induces apoptosis via downregulating hTERT in myelodysplastic syndromes

Treatment for higher-risk patients with myelodysplastic syndrome (MDS) should aim to modify the disease course by avoiding progression to acute myeloid leukemia and improving survival. When a patient is not eligible for intensive chemotherapy and lacks a donor hematopoietic cell source, or for a patient in a poor economic situation, consideration can be given to the use of Chinese herbal medicine. Numerous plant extracts, such as camptothecin, vinblastine and paclitaxel, have been reported to display antitumor effects, serving as potential therapeutic strategies for cancer. In the present study, the ultra-performance liquid chromatography-tandem mass spectrometry system (Waters Corporation) was used to detect the main chemical components of HDE, CCK-8 assay to detect the effects of HDE and BIIB021 on the proliferation of SKM-1 cells; and designed hTERT-small interfering (si)RNAs to detect the effects of HDE and BIIB021 on SKM-1 cell apoptosis after HTERT gene knockdown. The present study investigated a newly extracted coumarin HDE, the active component in Oldenlandia diffusa Willd, which efficiently inhibited SKM-1 (MDS cell line) proliferation and induced apoptosis, as determined by performing Cell Counting Kit-8 and flow cytometry assays, respectively. The effect of HDE was associated with decreased telomerase activity. Moreover, heat shock protein 90 inhibitor BIIB021 significantly enhanced the antitumor effects of HDE on SKM-1 cells. In addition, SKM-1 cell apoptosis was increased in human telomerase reverse transcriptase (hTERT)-knockdown cells compared with the negative control group. Cell apoptosis in hTERT-knockdown SKM-1 cells was further enhanced following HDE, BIIB021 or combination treatment, as evidenced by increased levels of cleaved caspase 3, cleaved caspase 8 and cleaved poly ADP ribose polymerase. Collectively, the results indicated synergistic antitumor effects of HDE and BIIB021, providing a novel therapeutic combination for higher-risk MDS.

Novel piperazine-chalcone hybrids and related pyrazoline analogues targeting VEGFR-2 kinase; design, synthesis, molecular docking studies, and anticancer evaluation

New piperazine–chalcone hybrids and related pyrazoline derivatives have been designed and synthesised as potential vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors. The National Cancer Institute (NCI) has selected six compounds to evaluate their antiproliferative activity in vitro against 60 human cancer cells lines. Preliminary screening of the examined compounds indicated promising anticancer activity against number of cell lines. The enzyme inhibitory activity against VEGFR-2 was evaluated and IC₅₀ of the tested compounds ranged from 0.57 µM to 1.48 µM. The most potent derivatives Vd and Ve were subjected to further investigations. A cell cycle analysis showed that both compounds mainly arrest HCT-116 cell cycle in the G2/M phase. Annexin V-FITC apoptosis assay showed that Vd and Ve induced an approximately 18.7-fold and 21.2-fold total increase in apoptosis compared to the control. Additionally, molecular docking study was performed against VEGFR (PDB ID: 4ASD) using MOE 2015.10 software and Sorafenib as a reference ligand.

Synthesis of (Z)-3-(arylamino)-1-(3-phenylimidazo[1,5-a]pyridin-1-yl)prop-2-en-1-ones as potential cytotoxic agents

The new derivatives based on (Z)-3-(arylamino)-1-(3-phenylimidazo[1,5-a]pyridin-1-yl)prop-2-en-1-one scaffold was synthesized and evaluated for their in vitro cytotoxic potential against a panel of cancer cell lines, viz., A549 (human lung cancer), HCT-116 (human colorectal cancer), B16F10 (murine melanoma cancer), BT-474 (human breast cancer), and MDA-MB-231 (human triple-negative breast cancer). Among them, many of the synthesized compounds exhibited promising cytotoxic potential against the panel of tested cancer cell lines with IC₅₀ <30 µM. Based on the preliminary screening results, the structure-activity relationship (SAR) of the compounds was established. Among the synthesized compounds, 15i displayed a potential anti-proliferative activity against HCT-116 cancer cell line with an IC₅₀ value of 1.21 ± 0.14 µM. Flow cytometric analysis revealed that compound 15i arrested the G0/G1 phase of the cell cycle. Moreover, increased reactive oxygen species (ROS) generation, clonogenic assay, acridine orange staining, DAPI nuclear staining, measurement of mitochondrial membrane potential (ΔΨm), and annexin V-FITC assays revealed that compound 15i promoted cell death through apoptosis.

Nanotherapy delivery of c-myc inhibitor targets Protumor Macrophages and preserves Antitumor Macrophages in Breast Cancer

Tumor-associated macrophages (TAMs) enhance tumor growth in mice and are correlated with a worse prognosis for breast cancer patients. While early therapies sought to deplete all macrophages, current therapeutics aim to reprogram pro-tumor macrophages (M2) and preserve those necessary for anti-tumor immune responses (M1). Recent studies have shown that c-MYC (MYC) is induced in M2 macrophages in vitro and in vivo where it regulates the expression of tumor-promoting genes. In a myeloid lineage MYC KO mouse model, MYC had important roles in macrophage maturation and function leading to reduced tumor growth. We therefore hypothesized that targeted delivery of a MYC inhibitor to established M2 TAMs could reduce polarization toward an M2 phenotype in breast cancer models.

Methods: In this study, we developed a MYC inhibitor prodrug (MI3-PD) for encapsulation within perfluorocarbon nanoparticles, which can deliver drugs directly to the cytosol of the target cell through a phagocytosis independent mechanism. We have previously shown that M2-like TAMs express significant levels of the vitronectin receptor, integrin β3, and in vivo targeting and therapeutic potential was evaluated using αvβ3 integrin targeted rhodamine-labeled nanoparticles (NP) or integrin αvβ3-MI3-PD nanoparticles.

Results: We observed that rhodamine, delivered by αvβ3-rhodamine NP, was incorporated into M2 tumor promoting macrophages through both phagocytosis-independent and dependent mechanisms, while NP uptake in tumor suppressing M1 macrophages was almost exclusively through phagocytosis. In a mouse model of breast cancer (4T1-GFP-FL), M2-like TAMs were significantly reduced with αvβ3-MI3-PD NP treatment. To validate this effect was independent of drug delivery to tumor cells and was specific to the MYC inhibitor, mice with integrin β3 knock out tumors (PyMT-Bo1 β3KO) were treated with αvβ3-NP or αvβ3-MI3-PD NP. M2 macrophages were significantly reduced with αvβ3-MI3-PD nanoparticle therapy but not αvβ3-NP treatment.

Conclusion: These data suggest αvβ3-NP-mediated drug delivery of a c-MYC inhibitor can reduce protumor M2-like macrophages while preserving antitumor M1-like macrophages in breast cancer.

Discovery of 4-(3,5-dimethoxy-4-(((4-methoxyphenethyl)amino)methyl)phenoxy)-N-phenylaniline as a novel c-myc inhibitor against colorectal cancer in vitro and in vivo

Proto-oncogene c-Myc plays an essential role in the development of colorectal cancer (CRC), since downregulation of c-Myc inhibits intestinal polyposis, which is the most cardinal pathological change in the development of CRC. Herein, a series of novel phenoxy-N-phenylaniline derivatives were designed and synthesized. The cytotoxicity activities of all the derivatives were measured by MTT assay in different colon cancer cells, 4-(3,5-dimethoxy-4-(((4-methoxyphenethyl)amino)methyl)phenoxy)-N-phenylaniline (42) was discovered, the lead compound 42 with excellent cytotoxicity activity of IC₅₀ = 0.32 μM, IC₅₀ = 0.51 μM, in HT29 and HCT 15 cells, respectively. Compound 42 had a good inhibitory activity of c-Myc/MAX dimerization and DNA binding. Besides, compound 42 could effectively induce apoptosis and induced G2/M arrest in low concentration and G0/G1 arrest in high concentration to prevent the proliferation and differentiation in colon cancer cells. Western blot analysis confirmed the 42 strongly down-regulated expression of c-Myc. Furthermore, during 30 days treatment 42 exhibited excellent efficacy in HT29 tumor xenograft model without causing significant weight loss and toxicity. Consequently, 42 could be a promising drug candidate for CRC therapy.

Identification and Validation of VEGFR2 Kinase as a Target of Voacangine by a Systematic Combination of DARTS and MSI

Although natural products are an important source of drugs and drug leads, identification and validation of their target proteins have proven difficult. Here, we report the development of a systematic strategy for target identification and validation employing drug affinity responsive target stability (DARTS) and mass spectrometry imaging (MSI) without modifying or labeling natural compounds. Through a validation step using curcumin, which targets aminopeptidase N (APN), we successfully standardized the systematic strategy. Using label-free voacangine, an antiangiogenic alkaloid molecule as the model natural compound, DARTS analysis revealed vascular endothelial growth factor receptor 2 (VEGFR2) as a target protein. Voacangine inhibits VEGFR2 kinase activity and its downstream signaling by binding to the kinase domain of VEGFR2, as was revealed by docking simulation. Through cell culture assays, voacangine was found to inhibit the growth of glioblastoma cells expressing high levels of VEGFR2. Specific localization of voacangine to tumor compartments in a glioblastoma xenograft mouse was revealed by MSI analysis. The overlap of histological images with the MSI signals for voacangine was intense in the tumor regions and showed colocalization of voacangine and VEGFR2 in the tumor tissues by immunofluorescence analysis of VEGFR2. The strategy employing DARTS and MSI to identify and validate the targets of a natural compound as demonstrated for voacangine in this study is expected to streamline the general approach of drug discovery and validation using other biomolecules including natural products.

Targeting STAT-3 signaling pathway in cancer for development of novel drugs: Advancements and challenges

Signal transducers and activators of transcription 3 (STAT-3) is a transcription factor that regulates the gene expression of several target genes. These factors are activated by the binding of cytokines and growth factors with STAT-3 specific receptors on cell membrane. Few years ago, STAT-3 was considered an acute phase response element having several cellular functions such as inflammation, cell survival, invasion, metastasis and proliferation, genetic alteration, and angiogenesis. STAT-3 is activated by several types of inflammatory cytokines, carcinogens, viruses, growth factors, and oncogenes. Thus, the STAT3 pathway is a potential target for cancer therapeutics. Abnormal STAT-3 activity in tumor development and cellular transformation can be targeted by several genomic and pharmacological methodologies. An extensive review of the literature has been conducted to emphasize the role of STAT-3 as a unique cancer drug target. This review article discusses in detail the wide range of STAT-3 inhibitors that show antitumor effects both in vitro and in vivo. Thus, targeting constitutive STAT-3 signaling is a remarkable therapeutic methodology for tumor progression. Finally, current limitations, trials and future perspectives of STAT-3 inhibitors are also critically discussed.

Synthesis of Benzo[d]imidazo[2,1-b]thiazole-Propenone Conjugates as Cytotoxic and Apoptotic Inducing Agents

BACKGROUND

Cancer can be considered as a disease in which normal cells start behaving badly, multiplying uncontrollably, ignoring signals to stop and accumulating to form a mass that is generally termed as a tumor. Apoptosis or programmed cell death is a physiological process that enables organisms to control their cell numbers in many developmental and physiological settings and to eliminate unwanted cells and it plays essential role in chemotherapy-induced tumor-cell killing. The correct balance between apoptosis and inhibition of apoptosis is important in animal development as well as in tissue homeostasis. The aim of this paper is to introduce the readers about the design strategy and synthesis of effective cytotoxic and apoptotic inducing agents based on benzo[d]imidazo[2,1-b]thiazole scaffold.

METHODS

Benzo[d]imidazo[2,1-b]thiazole-propenone conjugates were synthesized by the condensation of 7- methoxy-2-(aryl)benzo[d]imidazo[2,1-b]thiazol-3-yl)prop-2-yn-1-ones with aryl/hetero aryl amines in ethanol at room temperature. These in turn were obtained from 7-methoxy-2-(aryl)benzo[d]imidazo[2,1-b]thiazole-3- carbaldehydes on treatment with ethynylmagnesium bromide followed by oxidation.

RESULTS

3-Arylaminopropenone linked 2-arylbenzo[d]imidazo[2,1-b]thiazole conjugates prepared in this investigation exhibited significant cytotoxic activity and arrested HeLa cancer cells in G1 phase. The treatment of the conjugate led to 40% of loss of mitochondrial membrane potential (DΨm) in HeLa cells and 4 fold increase in the levels of reactive oxygen species (ROS). In addition, it induces apoptosis in HeLa cells, this was examined by the wound healing assay, Actin filaments and Hoechst staining assay.

CONCLUSION

The encouraging biological profile exhibited by these 3-arylaminopropenone 2-aryl linked benzo[d]imidazo[2,1-b]thiazole conjugates demonstrate that they have the potential to be developed as a lead by further structural modifications to obtain potential chemotherapeutic agents that are likely to target the HeLa cancer cells.

Nanomedicinal strategies as efficient therapeutic interventions for delivery of cancer vaccines

The applications of gene therapy-based treatment of cancers were started almost two decades back as a boon over the chemotherapeutic treatment strategies. Gene therapy helps in correcting the genetic sequences for treatment of cancers, thus also acts like a vaccine to induce the cellular and humoral immunity. However, the cancer vaccines typically suffer from a series of biopharmaceutical challenges due to poor solubility, low systemic availability and lack of targeting ability. Owing to these challenges, the physicians and pharmaceutical scientists have explored the applications of nanocarriers as quite promising systems for effective treatment against the tumors. A series of nanotherapeutic systems are available to date for diverse drug therapy applications. Systematic understanding on the preparation, evaluation and application of nanomedicines as a carrier system for delivering the cancer vaccines is highly important. The present review article provides an in-depth understanding on the challenges associated with cancer vaccine delivery and current opportunities with diverse nanomedicinal carriers being available for treatment of cancers.

Repurposing of ginseng extract as topoisomerase I inhibitor based on the comparative analysis of gene expression patterns

Repositioning of plant extracts and chemical drugs can accelerate drug development. However, its success rate may depend on what the clue is for the repositioning. Recently, repositioning based on correction of unwarranted gene expression pattern has suggested the possibility of new drug development. Here, we designed a similar method for the repositioning of nutraceutical ginseng (Panax ginseng C.A.Mey.), which is one of the most validated natural therapeutic products for various diseases. We analyzed ginseng-induced gene expression profiles using the connectivity map algorithm, which is a database that connects diseases, chemical drugs, and gene expression. Ginseng was predicted to show the same effects as those of topoisomerase I inhibitors. In a subsequent in vitro assay, ginseng extract unwound coiled or supercoiled DNA, an effect comparable to that of the topoisomerase I inhibitor, camptothecin. Furthermore, ginseng extract induced synthetic lethality with suppression of the Werner syndrome gene. The collected data implicate ginseng as a candidate antitumor agent owing to its topoisomerase I inhibitory activity and further validate the usefulness of differentially expressed gene similarity-based repurposing of other natural products.

Ampelopsin E Reduces the Invasiveness of the Triple Negative Breast Cancer Cell Line, MDA-MB-231

Breast cancer is the most common and the second leading cause of cancer-related deaths in women. It has two distinctive hallmarks: rapid abnormal growth and the ability to invade and metastasize. During metastasis, cancer cells are thought to form actin-rich protrusions, called invadopodia, which degrade the extracellular matrix. Current breast cancer treatments, particularly chemotherapy, comes with adverse effects like immunosuppression, resistance development and secondary tumour formation. Hence, naturally-occurring molecules claimed to be less toxic are being studied as new drug candidates. Ampelopsin E, a natural oligostilbene extracted from Dryobalanops species, has exhibited various pharmacological properties, including anticancer and anti-inflammatory activities. However, there is yet no scientific evidence of the effects of ampelopsin E towards metastasis. Scratch assay, transwell migration and invasion assays, invadopodia and gelatin degradation assays, and ELISA were used to determine the effects of ampelopsin E towards the invasiveness of MDA-MB-231 cells. Strikingly in this study, ampelopsin E was able to halt migration, transmigration and invasion in MDA-MB-231 cells by reducing formation of invadopodia and its degradation capability through significant reduction (p < 0.05) in expression levels of PDGF, MMP2, MMP9 and MMP14. In conclusion, ampelopsin E reduced the invasiveness of MDA-MB-231 cells and was proven to be a potential alternative in treating TNBC.

Apoptotic effect of enterodiol, the final metabolite of edible lignans, in colorectal cancer cells

BACKGROUND

Enterodiol (END) is transformed by human intestinal bacteria from lignans contained in various whole-grain cereals, nuts, legumes, flaxseed, and vegetables. It is known to have several physiological effects, but its effects on mitogen-activated protein kinase (MAPK) signaling and apoptosis in colorectal cancer (CRC) cells have not yet been elucidated. We therefore investigated the effects of END on apoptosis in CRC cells and whether these effects are mediated via MAPK signaling.

RESULTS

Cell proliferation was decreased by END treatment in a time-dependent manner. In particular, END treatment resulted in an apoptosis rate of up to 40% in CT26 cells but showed no cytotoxicity toward RAW264.7 macrophages. Treatment with END also suppressed the migration of CRC cells in a concentration-dependent manner. The phosphorylation of extracellular signal-regulated kinase (ERK), jun N-terminal kinase (JNK), and p38 was down-regulated with END treatment. Furthermore, END decreased the expression levels of anti-apoptotic proteins in CRC cells.

CONCLUSION

Enterodiol inhibited the growth of CRC cells by controlling the MAPK signaling pathway involved in proliferation and apoptosis. These results demonstrate that END has an apoptotic effect in CRC cells. © 2018 Society of Chemical Industry.

Design and Synthesis of Novel Cytotoxic Indole-Thiosemicarbazone Derivatives: Biological Evaluation and Docking Study

In this work, two novel series of indole-thiosemicarbazone derivatives were designed, synthesized, and evaluated for their cytotoxic activity against MCF-7, A-549, and Hep-G2 cell lines in comparison to etoposide and colchicine as the reference drugs. Generally, the synthesized compounds showed better cytotoxicity towards A-549 and Hep-G2 than MCF-7. Among them, (2E)-2-{[2-(4-chlorophenyl)-1H-indol-3-yl]methylidene}-N-(4-methoxyphenyl)hydrazinecarbothioamide (8l) was found to be the most potent compound against A-549 and Hep-G2, at least three times more potent than etoposide. The morphological analysis by the acridine orange/ethidium bromide double staining test and flow cytometry analysis indicated that compound 8l induced apoptosis in A-549 cells. Moreover, molecular docking methodology was exploited to elucidate the details of molecular interactions of the studied compounds with putative targets.

Drug Repositioning Inferred from E2F1-Coregulator Interactions Studies for the Prevention and Treatment of Metastatic Cancers

Metastasis management remains a long-standing challenge. High abundance of E2F1 triggers tumor progression by developing protein-protein interactions (PPI) with coregulators that enhance its potential to activate a network of prometastatic transcriptional targets.

Methods: To identify E2F1-coregulators, we integrated high-throughput Co-immunoprecipitation (IP)/mass spectometry, GST-pull-down assays, and structure modeling. Potential inhibitors of PPI discovered were found by bioinformatics-based pharmacophore modeling, and transcriptome profiling was conducted to screen for coregulated downstream targets. Expression and target gene regulation was validated using qRT-PCR, immunoblotting, chromatin IP, and luciferase assays. Finally, the impact of the E2F1-coregulator complex and its inhibiting drug on metastasis was investigated in vitro in different cancer entities and two mouse metastasis models.

Results: We unveiled that E2F1 forms coactivator complexes with metastasis-associated protein 1 (MTA1) which, in turn, is directly upregulated by E2F1. The E2F1:MTA1 complex potentiates hyaluronan synthase 2 (HAS2) expression, increases hyaluronan production and promotes cell motility. Disruption of this prometastatic E2F1:MTA1 interaction reduces hyaluronan synthesis and infiltration of tumor-associated macrophages in the tumor microenvironment, thereby suppressing metastasis. We further demonstrate that E2F1:MTA1 assembly is abrogated by small-molecule, FDA-approved drugs. Treatment of E2F1/MTA1-positive, highly aggressive, circulating melanoma cells and orthotopic pancreatic tumors with argatroban prevents metastasis and cancer relapses in vivo through perturbation of the E2F1:MTA1/HAS2 axis.

Conclusion: Our results propose argatroban as an innovative, E2F-coregulator-based, antimetastatic drug. Cancer patients with the infaust E2F1/MTA1/HAS2 signature will likely benefit from drug repositioning.

Artemisinin-indole and artemisinin-imidazole hybrids: Synthesis, cytotoxic evaluation and reversal effects on multidrug resistance in MCF-7/ADR cells

A series of artemisinin derivatives with MDR reversal activity were designed and synthesized. All hybrids were screened to anticancer activities against four human cancer cell lines (A549, MCF-7, HepG-2, MDA-MB-231) and normal human hepatic cell (L02) in vitro. Most of the new compounds showed higher anticancer activities than artemisinin, among which compounds 11a and 11c displayed superior potency with IC₅₀ 6.78 μM and 5.25 μM against MCF-7, respectively. The further research indicated that the most potent 11c induced cell cycle arrest at G2 phase in MCF-7. Additionally, compound 11c showed remarkable MDR reversal activity which reversed adriamycin against MCF-7/ADR cells with IC₅₀ 0.76 μM.

Synthesis and X-ray study of dispiro 8-nitroquinolone analogues and their cytotoxic properties against human cervical cancer HeLa cells

A series of unique dispiro analogues containing an oxindole pyrrolidine 8-nitroquinolone hybrid has been obtained through a one-pot three-component 1,3-dipolar cycloaddition of azomethine ylides generated in situ from the condensation of isatins and benzylamine with (E)-3-arylidene-2,3-dihydro-8-nitro-4-quinolones. The structures of the newly synthesized compounds were characterized by using different spectroscopic techniques and by X-ray diffraction studies of their regio- and stereochemistry. All the synthesized compounds were screened for in vitro cytotoxic activity against the human cervical cancer cell line HeLa. The compounds have exhibited potent inhibition against human cervical cancer cells and insignificant toxicity to normal cells. The compounds 6d, 6a, 6h, 6b, and 6e induced apoptosis of HeLa cells, through ROS influx. The expression levels of proteins involved in the mitochondrion-related pathways were detected, and Western blot analysis showed that apoptosis occurred via activation of caspase-3.

Genetic variation at the glycosaminoglycan metabolism pathway contributes to the risk of psoriatic arthritis but not psoriasis

OBJECTIVE

Psoriatic arthritis (PsA) is a chronic inflammatory arthritis affecting up to 30% of patients with psoriasis (Ps). To date, most of the known risk loci for PsA are shared with Ps, and identifying disease-specific variation has proven very challenging. The objective of the present study was to identify genetic variation specific for PsA.

METHODS

We performed a genome-wide association study in a cohort of 835 patients with PsA and 1558 controls from Spain. Genetic association was tested at the single marker level and at the pathway level. Meta-analysis was performed with a case-control cohort of 2847 individuals from North America. To confirm the specificity of the genetic associations with PsA, we tested the associated variation using a purely cutaneous psoriasis cohort (PsC, n=614) and a rheumatoid arthritis cohort (RA, n=1191). Using network and drug-repurposing analyses, we further investigated the potential of the PsA-specific associations to guide the development of new drugs in PsA.

RESULTS

We identified a new PsA risk single-nucleotide polymorphism at B3GNT2 locus (p=1.10e-08). At the pathway level, we found 14 genetic pathways significantly associated with PsA (p_FDR<0.05). From these, the glycosaminoglycan (GAG) metabolism pathway was confirmed to be disease-specific after comparing the PsA cohort with the cohorts of patients with PsC and RA. Finally, we identified candidate drug targets in the GAG metabolism pathway as well as new PsA indications for approved drugs.

CONCLUSION

These findings provide insights into the biological mechanisms that are specific for PsA and could contribute to develop more effective therapies.

Mathematical models of cytotoxic effects in endpoint tumor cell line assays: critical assessment of the application of a single parametric value as a standard criterion to quantify the dose-response effects and new unexplored proposal formats

The development of convenient tools for describing and quantifying the effects of standard and novel therapeutic agents is essential for the research community, to perform more precise evaluations. Although mathematical models and quantification criteria have been exchanged in the last decade between different fields of study, there are relevant methodologies that lack proper mathematical descriptions and standard criteria to quantify their responses. Therefore, part of the relevant information that can be drawn from the experimental results obtained and the quantification of its statistical reliability are lost. Despite its relevance, there is not a standard form for the in vitro endpoint tumor cell lines' assays (TCLA) that enables the evaluation of the cytotoxic dose-response effects of anti-tumor drugs. The analysis of all the specific problems associated with the diverse nature of the available TCLA used is unfeasible. However, since most TCLA share the main objectives and similar operative requirements, we have chosen the sulforhodamine B (SRB) colorimetric assay for cytotoxicity screening of tumor cell lines as an experimental case study. In this work, the common biological and practical non-linear dose-response mathematical models are tested against experimental data and, following several statistical analyses, the model based on the Weibull distribution was confirmed as the convenient approximation to test the cytotoxic effectiveness of anti-tumor compounds. Then, the advantages and disadvantages of all the different parametric criteria derived from the model, which enable the quantification of the dose-response drug-effects, are extensively discussed. Therefore, model and standard criteria for easily performing the comparisons between different compounds are established. The advantages include a simple application, provision of parametric estimations that characterize the response as standard criteria, economization of experimental effort and enabling rigorous comparisons among the effects of different compounds and experimental approaches. In all experimental data fitted, the calculated parameters were always statistically significant, the equations proved to be consistent and the correlation coefficient of determination was, in most of the cases, higher than 0.98.

Computational screening of chalcones acting against topoisomerase IIα and their cytotoxicity towards cancer cell lines

Targeted cancer therapy has become one of the high potential cancer treatments. Human topoisomerase II (hTopoII), which catalyzes the cleavage and rejoining of double-stranded DNA, is an important molecular target for the development of novel cancer therapeutics. In order to diversify the pharmacological activity of chalcones and to extend the scaffold of topoisomerase inhibitors, a series of chalcones was screened against hTopoIIα by computational techniques, and subsequently tested for their in vitro cytotoxicity. From the experimental IC₅₀ values, chalcone 3d showed a high cytotoxicity with IC₅₀ values of 10.8, 3.2 and 21.1 µM against the HT-1376, HeLa and MCF-7 cancer-derived cell lines, respectively, and also exhibited an inhibitory activity against hTopoIIα-ATPase that was better than the known inhibitor, salvicine. The observed ligand-protein interactions from a molecular dynamics study affirmed that 3d strongly interacts with the ATP-binding pocket residues. Altogether, the newly synthesised chalcone 3d has a high potential to serve as a lead compound for topoisomerase inhibitors.

Snake Venoms in Cancer Therapy: Past, Present and Future

Cancer is one of the leading causes of morbidity and mortality worldwide, and the discovery of new drugs for cancer therapy is one of the most important objectives for the pharmaceutical industry. Snake venoms are complex mixtures containing different peptides, proteins, enzymes, carbohydrates and other bioactive molecules, which are secreted by the snake in the predation or defending against threats. Understanding the snake venoms may turn the toxins into a valuable source of new lead compounds in drug discovery. Captopril, the first angiotensin-converting enzyme inhibitor approved in 1981 by FDA, was designed based on the structure of a peptide isolated from the snake venom. The earliest reports about snake venoms used in cancer treatments appeared in the 1930s. Since then, numerous studies on the activities, isolations, purifications and structure elucidations of the components from snake venoms were published. The comprehensive structural and functional investigations of snake venoms would contribute to the development of novel anti-cancer drugs. Our review will focus on the past, present and the future of the studies on snake venoms in cancer target therapy.

A new method for the high-precision assessment of tumor changes in response to treatment

Motivation

Imaging demonstrates that preclinical and human tumors are heterogeneous, i.e. a single tumor can exhibit multiple regions that behave differently during both development and also in response to treatment. The large variations observed in control group, tumors can obscure detection of significant therapeutic effects due to the ambiguity in attributing causes of change. This can hinder development of effective therapies due to limitations in experimental design rather than due to therapeutic failure. An improved method to model biological variation and heterogeneity in imaging signals is described. Specifically, linear Poisson modeling (LPM) evaluates changes in apparent diffusion co-efficient between baseline and 72 h after radiotherapy, in two xenograft models of colorectal cancer. The statistical significance of measured changes is compared to those attainable using a conventional t-test analysis on basic apparent diffusion co-efficient distribution parameters.

Results

When LPMs were applied to treated tumors, the LPMs detected highly significant changes. The analyses were significant for all tumors, equating to a gain in power of 4-fold (i.e. equivalent to having a sample size 16 times larger), compared with the conventional approach. In contrast, highly significant changes are only detected at a cohort level using t-tests, restricting their potential use within personalized medicine and increasing the number of animals required during testing. Furthermore, LPM enabled the relative volumes of responding and non-responding tissue to be estimated for each xenograft model. Leave-one-out analysis of the treated xenografts provided quality control and identified potential outliers, raising confidence in LPM data at clinically relevant sample sizes.

Availability and implementation

TINA Vision open source software is available from www.tina-vision.net.

Supplementary information

Supplementary data are available at Bioinformatics online.

Bioinformatics and Translation Elongation

Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.

Synthesis, docking and anticancer activity of azo-linked hybrids of 1,3,4-thia-/oxadiazoles with cyclic imides

A series of novel analogues based on a diazole-imide pharmacophore were synthesized by diazotizing substituted 1,3,4-thia-/oxadiazol-2-amines and subsequently coupling the resulting diazonium salts with N-substituted cyclic imides. The resulting compounds C1 to C28 were characterized by various spectral methods, viz. IR, NMR and mass spectroscopy. All the synthesized compounds were tested against two human cancer cell lines: human breast adenocarcinoma cell line MCF-7 and colorectal adenocarcinoma cell line HT-29. Among the synthesized compounds, C14 (2-(4-chloro-3-((5-(4-nitrophenyl)-1,3,4-thiadiazol-2-yl)diazenyl)phenyl)-4,5,6,7-tetrahydro-1H-isoindole-1,3(2H)-dione) emerged as a potential candidate against both MCF-7 and HT-29 with [Formula: see text] values of 0.09 ± 0.02 [Formula: see text]M and 0.11 ± 0.03 [Formula: see text]M, respectively. Similarly, compound C16 displayed highest anticancer activity against MCF-7 cell line with [Formula: see text] = 0.07 ± 0.02 [Formula: see text]M. Target fishing (inverse docking) using ChemMapper server identified EGFR tyrosine and CDK2 kinases as high priority targets for this pharmacophore. Computational docking (AutoDock 4.2) was used to analyse the interactions between the target proteins and active compounds.

Isatin based macrocyclic Schiff base ligands as novel candidates for antimicrobial and antioxidant drug design: In vitro DNA binding and biological studies

In the present work, five macrocyclic compounds, C₁₈H₁₂N₂O₄ (1), C₃₈H₂₄N₈O₆ (1a), C₃₈H₂₄N₈O₄S₂ (1b), C₄₀H₃₂N₈O₄ (2a) and C₄₈H₃₂N₈O₄ (2b) have been synthesized and thoroughly characterized by elemental analysis, FT-IR, 1D & 2D NMR and electron spray ionization mass spectral analysis. The DNA binding ability of these compounds were investigated in vitro by UV-Visible, fluorescence, circular dichroism (CD) spectroscopy and viscosity measurements. The results indicate that these compounds possess strong DNA binding affinity via intercalation, while the order of binding strength followed the trend 2b (1.52 ± 0.06 × 10⁵ M^-1) > 2a (1.12 ± 0.11 × 10⁵ M^-1) > 1b (1.05 ± 0.04 × 10⁵ M^-1) > 1a (0.97 ± 0.14 × 10⁴ M^-1) > 1 (0.75 ± 0.21 × 10⁴ M^-1). The radical scavenging potencies of the compounds were explored by employing DPPH, OH and NO assays, in which 1a exhibited highest inhibitory effect on the radicals (IC₅₀ = 23.59 μM (DPPH), 26.14 μM (OH), 28.41 μM (NO)). The in vitro antibacterial studies showed that these compounds have the potential to arrest the growth of bacteria, among which, 1a was found to be vulnerable against the bacterial stains. In addition, in silico molecular docking stimulations were also performed to position these compounds into the active sites of bacterial membrane proteins. The results of in vitro and in silico investigations reveal that the compounds apprehend the bacterial growth significantly. The data obtained from this piece of work would be helpful to design antibacterial drugs incorporating isatin based macrocyclic frameworks.