Activity-Based Chemical Proteomics Accelerates Inhibitor Development for Deubiquitylating Enzymes

<div>Abstract<p>Drugs targeting DNA damage repair (DDR) pathways are exciting new agents in cancer therapy. Many of these drugs exhibit synthetic lethality with defects in DNA repair in cancer cells. For example, ovarian cancers with impaired homologous recombination DNA repair show increased sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors. Understanding the activity of different DNA repair pathways in individual tumors, and the correlations between DNA repair function and drug response, will be critical to patient selection for DNA repair targeted agents. Genomic and functional assays of DNA repair pathway activity are being investigated as potential biomarkers of response to targeted therapies. Furthermore, alterations in DNA repair function generate resistance to DNA repair targeted agents, and DNA repair states may predict intrinsic or acquired drug resistance. In this review, we provide an overview of DNA repair targeted agents currently in clinical trials and the emerging biomarkers of response and resistance to these agents: genetic and genomic analysis of DDR pathways, genomic signatures of mutational processes, expression of DNA repair proteins, and functional assays for DNA repair capacity. We review biomarkers that may predict response to selected DNA repair targeted agents, including PARP inhibitors, inhibitors of the DNA damage sensors ATM and ATR, and inhibitors of nonhomologous end joining. Finally, we introduce emerging categories of drugs targeting DDR and new strategies for integrating DNA repair targeted therapies into clinical practice, including combination regimens. Generating and validating robust biomarkers will optimize the efficacy of DNA repair targeted therapies and maximize their impact on cancer treatment. <i>Clin Cancer Res; 22(23); 5651–60. ©2016 AACR</i>.</p></div>

Natural products (NPs) are useful sources of bioactive compounds and play important roles in the development and discovery of new drugs for diverse human diseases. Most natural products originate from terrestrial species, but diverse marine organisms are another source of new agents for cancer therapy. Natural products derived from marine organisms show diverse pharmacological activities via bioactive secondary metabolites. They regulate biological activities, such as cell proliferation, cell viability, induction of ROS production, ER stress, and apoptosis via modulation of cellular mechanisms in many cancers. Many natural products isolated from marine species require further study to elucidate the efficacy of their biological activity and anticancer effects. In this review, we summarize the biological properties and anticancer effects of diverse natural products extracted from marine organisms and their roles in tumor therapy.

Riding the metal wave: A review of the latest developments in metal-based anticancer agents

Natural compounds that target microtubules and disrupt the normal function of the mitotic spindle have proven to be one of the best classes of cancer chemotherapeutic drugs available in clinics to date. There is increasing evidence showing that even minor alteration of microtubule dynamics can engage the spindle checkpoint, arresting cell-cycle progression at mitosis and subsequently leading to cell death. Our improved understanding of tumor biology and our continued appreciation for what the microtubule targeting agents (MTAs) can do have helped pave the way for a new era in the treatment of cancer. The effectiveness of these agents for cancer therapy has been impaired, however, by various side effects and drug resistance. Several new MTAs have shown potent activity against the proliferation of various cancer cells, including resistance to the existing MTAs. Sustained investigation of the mechanisms of action of MTAs, development and discovery of new drugs, and exploring new treatment strategies that reduce side effects and circumvent drug resistance could provide more effective therapeutic options for patients with cancer. This review focuses on the successful cancer chemotherapy from natural compounds in clinical settings and the challenges that may abort their usefulness.

Bio-nanoconjugates of lithocholic acid/IR 780 for ROS-mediated apoptosis and optoacoustic imaging applications in breast cancer

New gold (III) cyanide complex TGS 121 induces ER stress, proteasome inhibition and death of Ras-hyperactivated cells

ABSTRACTThe nephroprotective activity of hydro-alcoholic (HAEAM) and ethyl acetate (EAEAM) extracts of Aegle marmelos leaves were evaluated against nephrotoxicity induced by cisplatin (CP), a widely used chemotherapeutic agent in cancer therapy. Wistar rats were treated with CP (6 mg.kg–1; i.p.). Treatment groups received the same dose of CP, along with HAEAM and EAEAM (200 and 400 mg.kg–1) orally for 5 d. Blood urea nitrogen (BUN), serum creatinine, and antioxidant enzymes were estimated in renal tissues. EAEAM exhibited minimum IC50 values 6.13 ± 1.05, 67.34 ± 1.7, 59.7 ± 3.9, and 49.17 ± 2.19 μg.mL–1. EAEAM (400 mg.kg–1) decreased the creatinine levels from 2.29 ± 0.387 to 0.96 ± 0.095 mg.dL–1 and BUN from 92.06 ± 7.949 to 38.18 ± 5.686 mg.dL–1 and restored the activities of renal antioxidant enzymes, decreased the lipid peroxidasde (LPO) levels from 158.70 ± 3.542 to 106.91 ± 5.876 nM.g–1, and increased superoxide dismutase (SOD) levels from 12.59 ± 0.463 to 29.95 ± 5.222 U.g–1, glutathione (GSH) from 0.24 ± 0.029 to 0.57 ± 0.048 μM.g–1, and catalase (CAT) from 1.14 ± 0.067 to 3.27 ± 0.296 U.mg–1).

Artemisinin alleviates cisplatin-induced damage in GC-1 spermatogonia through ER stress mechanisms

Although the use of viruses as oncolytic agents is an historic concept, the use of genetically modified viruses to selectively target tumour cells is relatively novel and recent. The ability of viruses to efficiently infect and lyse cells, combined with the potential augmentation of this effect by progeny viruses throughout the tumour provide justification for exploitation of these agents in cancer therapy. Before application to humans, though, issues related to tumour cell selectivity, lack of toxicity to normal tissues and the effect of the antiviral immune response, will have to be clarified. The more commonly used oncolytic viruses are based on mutant strains of herpes simplex virus, adenovirus and reovirus. The tumour selectivity of each of these strains is discussed, particularly the complementation of the viral defect by cellular pathways involved in tumourigenesis. The combination of oncolytic viruses with radiation, chemotherapy and gene therapy is also reviewed. Further study of the interaction of viral proteins with cellular pathways involved in cell cycle control will provide the rationale for viral mutants with increased selectivity for tumour cells.

Many forms of cancer lack efficacious treatments, despite continuing advances in our understanding of molecular biology, and the development of precisely targeted agents that exploit relevant drivers and pathways of malignancy. To date the effectiveness of most tumor cell-focused molecularly targeted agents, in terms of event free and overall survival appears to be modest [1]. What is more, these new drugs come with a high price tag as companies seek to recoup development costs and to generate a return on investment (in part a consequence of a high attrition rate in oncological drug development, high regulatory burdens and expensive clinical trial costs) [2]. In the developing economies of the world, where cancer incidence is rising, the problems of unmet patient need is exacerbated by these high costs, putting many cancer treatments out of reach of patients and imposing strains on local health systems [3]. An alternative approach to seeking new drug treatments for cancer is not to start with molecular targets in mind, but to assess those drugs – approved for any indication – in our existing armamentarium which show some evidence of anticancer activity. This is the field of drug repurposing in oncology and there is now an increasing interest in the use of non-cancer drugs as anticancer therapeutics. There are two main advantages of repurposing. Firstly, by starting with well-known and well-characterized drugs we can draw on existing and detailed knowledge of pharmacodynamics, pharmacokinetics, bioavailability, toxicities, established protocols and dosing. This body of knowledge is far in excess of what can be gained in early phase clinical trials of new agents, particularly for first in class drugs. This is not to say that repurposed drugs do not need Phase I trials, since they may be used for cancer in schedules and combinations that differ from their accepted use, but it does represent a considerable short-circuiting of the preclinical phase of the drug d evelopment life cycle [4]. Secondly, many of the candidate drugs for repurposing are available at low cost; indeed many are available as generics. This is in stark contrast to the very high costs associated with the newest agents emerging from current pharmaceutical pipelines.

Chloroquine and its analogs: A new promise of an old drug for effective and safe cancer therapies

Drug discovery has traditionally been a time consuming and expensive endeavor. Additionally, drugs weren’t as effectively designed as those that are being predicted and developed through AI and ML today. Machine learning is a form of artificial intelligence that develops and evolves based on experience (similarly to the human mind), and is more recently being utilized in drug discovery and design. The integration of AI and ML into the drug discovery and development process has allowed for higher target precision, lower toxicity, and better dosage formulations. AI more generally has been introduced to and has been leveraged at, each step of drug development, including target identification and validation, hit identification, as well as hit to lead optimization, and has been key in shortening the previously lengthy drug screening process. AI and ML has also been applied downstream in drug formulation where it has maximized resource utilization and is allowing for web-based 3D printing of drugs. Application of AI in the drug development process has also been extended to the modeling of novel drug-like compounds to predict their ADMET properties. This review will address the stages of drug discovery and development in which the application of AI and ML modeling has altered the traditional development of drugs. Keywords: Drug discovery, machine learning, artificial intelligence, computational drug development.

Abstract: Successfully cancer therapies aim to induce apoptosis in cancer cell lines. Recent advances in cancer therapy based on the use of some recombinant proteins such as tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). TRAIL is a new member of the TNF superfamily. In this paper, we report the expression, purification, and preparation of a recombinant form of the extracelluar domain of the TRAIL (sTRAIL) in Escherichia coli rosetta gami under the control of T7 promoter; which may selectively induce apoptosis of tumor cells in vitro. To obtain recombinant sTRAIL protein, the encoding region for sTRAIL was cloned between Xho 1 and Bam HI in pET28a expression vector. The results showed that the recombinant sTRAIL was efficiently produced in Ecoli rosetta gami strain. I ntroductio n : Apoptosis is an evolutionarily conserved and essential for maintenance of tissue homeostasis and removal of unwanted cells. TRAIL belongs to the group of therapeutic agents selectively targeting a wide variety of cancer cells without affecting the normal cells .The therapeutic potential of TRAIL is attributed to its receptor expression in a variety of tissues; which initiates apoptosis in cancer cells through interaction with the death receptors DR4 and DR5. Due to its selective nature, it is considered as a significant therapeutic agent in cancer therapy. The purpose of this study was to produce recombinant human sTRAIL in Rosetta Gami2 E.coli strain and its functions on cancerous cells in vitro. Methods and results: we optimized the coding sequence of this protein. The recombinant plasmid was transformed into Rosetta Gami2 E.coli strain for expression. The transformed bacteria which contain recombinant plasmid were cultured in 37oC with 250 rpm in LB and in 20oC in TB medium for 18 hours. TRAIL was purified by Ni sepharose column, and the presence of the recombinant protein was confirmed by SDS-PAGE. The concentration of purified protein was measured by Bradford assay. Our finding showed that the recombinant protein (34kD) has been successfully produced for next experiments, the purified protein was desalted and applied toward cancerous cells. Conclusions: In summary, TRAIL can be considered as a promising therapeutic agent for effective, targeted and less toxic agents for treatment of cancers. Key words: TRAIL, Codon optimization, Rosetta gami2, Cancer therapy

Hydroxytyrosol [2-(3,4-dihydroxyphenyl)ethanol, HTyr] is a phenolic compound found in olive leaves and fruits and extra-virgin olive oil, which has well-known strong antioxidant and radical-scavenging properties. Recently, it has received particular attention for its antiproliferative and apoptotic activities and its anti-inflammatory properties. During the past few years, more efforts have been focused on synthesizing HTyr-derived compounds with enhanced biological activities for their potential use in different chronic degenerative diseases. In this paper, we report a dissertation on the current knowledge of selected synthetic HTyr derivatives and analogues and their potential use in cancer prevention and therapy, which are related to their antioxidant, antiproliferative/apoptotic, and anti-inflammatory properties. On the basis of the perspective of using HTyr-derived compounds as anticancer agents, we have taken into account only studies that were performed in experimental cell-based models.

Certain bacteria demonstrate the ability to target and colonize the tumor microenvironment, a characteristic that positions them as innovative carriers for delivering various therapeutic agents in cancer therapy. Nevertheless, our understanding of how bacteria adapt their physiological condition to the tumor microenvironment remains elusive. In this work, we employed liquid chromatography-tandem mass spectrometry to examine the proteome of E. coli colonized in murine tumors. Compared to E. coli cultivated in the rich medium, we found that E. coli colonized in tumors notably upregulated the processes related to ferric ions, including the enterobactin biosynthesis and iron homeostasis. This finding indicated that the tumor is an iron-deficient environment to E. coli. We also found that the colonization of E. coli in the tumor led to an increased expression of lipocalin 2 (LCN2), a host protein that can sequester the enterobactin. We therefore engineered E. coli in order to evade the nutritional immunity provided by LCN2. By introducing the IroA cluster, the E. coli synthesizes the glycosylated enterobactin, which creates steric hindrance to avoid the LCN2 sequestration. The IroA-E. coli showed enhanced resistance to LCN2 and significantly improved the anti-tumor activity in mice. Moreover, the mice cured by the IroA-E. coli treatment became resistant to the tumor re-challenge, indicating the establishment of immunological memory. Overall, our study underscores the crucial role of bacteria’s ability to acquire ferric ions within the tumor microenvironment for effective cancer therapy.