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Chemical patents represent a valuable source of information about new chemical compounds, which is critical to the drug discovery process. Automated information extraction over chemical patents is, however, a challenging task due to the large volume of existing patents and the complex linguistic properties of chemical patents. The Cheminformatics Elsevier Melbourne University (ChEMU) evaluation lab 2020, part of the Conference and Labs of the Evaluation Forum 2020 (CLEF2020), was introduced to support the development of advanced text mining techniques for chemical patents. The ChEMU 2020 lab proposed two fundamental information extraction tasks focusing on chemical reaction processes described in chemical patents: (1) chemical named entity recognition , requiring identification of essential chemical entities and their roles in chemical reactions, as well as reaction conditions; and (2) event extraction , which aims at identification of event steps relating the entities involved in chemical reactions. The ChEMU 2020 lab received 37 team registrations and 46 runs. Overall, the performance of submissions for these tasks exceeded our expectations, with the top systems outperforming strong baselines. We further show the methods to be robust to variations in sampling of the test data. We provide a detailed overview of the ChEMU 2020 corpus and its annotation, showing that inter-annotator agreement is very strong. We also present the methods adopted by participants, provide a detailed analysis of their performance, and carefully consider the potential impact of data leakage on interpretation of the results. The ChEMU 2020 Lab has shown the viability of automated methods to support information extraction of key information in chemical patents., Competing Interests: SA, CD, CT, RH, and ZA are employed by the company Elsevier. DN is employed by the company VinAI. HY is employed by the company Fujitsu. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 He, Nguyen, Akhondi, Druckenbrodt, Thorne, Hoessel, Afzal, Zhai, Fang, Yoshikawa, Albahem, Cavedon, Cohn, Baldwin and Verspoor.)

The bis-indole indirubin is an active ingredient of Danggui Longhui Wan, a traditional Chinese medicine recipe used in the treatment of chronic diseases such as leukemias. The antitumoral properties of indirubin appear to correlate with their antimitotic effects. Indirubins were recently described as potent (IC(50): 50-100 nm) inhibitors of cyclin-dependent kinases (CDKs). We report here that indirubins are also powerful inhibitors (IC(50): 5-50 nm) of an evolutionarily related kinase, glycogen synthase kinase-3beta (GSK-3 beta). Testing of a series of indoles and bis-indoles against GSK-3 beta, CDK1/cyclin B, and CDK5/p25 shows that only indirubins inhibit these kinases. The structure-activity relationship study also suggests that indirubins bind to GSK-3 beta's ATP binding pocket in a way similar to their binding to CDKs, the details of which were recently revealed by crystallographic analysis. GSK-3 beta, along with CDK5, is responsible for most of the abnormal hyperphosphorylation of the microtubule-binding protein tau observed in Alzheimer's disease. Indirubin-3'-monoxime inhibits tau phosphorylation in vitro and in vivo at Alzheimer's disease-specific sites. Indirubins may thus have important implications in the study and treatment of neurodegenerative disorders. Indirubin-3'-monoxime also inhibits the in vivo phosphorylation of DARPP-32 by CDK5 on Thr-75, thereby mimicking one of the effects of dopamine in the striatum. Finally, we show that many, but not all, reported CDK inhibitors are powerful inhibitors of GSK-3 beta. To which extent these GSK-3 beta effects of CDK inhibitors actually contribute to their antimitotic and antitumoral properties remains to be determined. Indirubins constitute the first family of low nanomolar inhibitors of GSK-3 beta to be described.

Purpose: To assess antitumor response and time to progression (TTP) with docetaxel compared with doxorubicin in first-line treatment of advanced and/or metastatic soft tissue sarcoma., Patients and Methods: Patients with measurable soft tissue sarcoma lesions and adequate bone marrow, liver, and renal function were entered onto the study. They were randomized to either docetaxel 100 mg/m(2) given as a 1-hour intravenous infusion every 3 weeks or doxorubicin 75 mg/m(2) given as a bolus injection every 3 weeks. A maximum of seven cycles of treatment were scheduled. The study was designed as a randomized phase III study evaluating TTP by log-rank model. There was a clause for premature closure of the trial if fewer than five responses were observed among the first 25 assessable patients in the docetaxel treatment arm., Results: Eighty-six patients were entered onto the study; 85 were assessable for toxicity and 83 for response. The rate of severe granulocytopenia was not significantly different between the two arms. Nausea (P =.001), vomiting (P <.001), and stomatitis (P =.005) were more common with doxorubicin therapy, whereas neurotoxicity was more frequent with docetaxel treatment. The response rate to doxorubicin therapy was 30% (95% confidence interval, 17% to 46%), whereas no responses to docetaxel therapy were seen (P <.001). In view of this, the trial was closed prematurely and the phase III study part was not conducted., Conclusion: Docetaxel is inactive in soft tissue sarcomas and cannot be recommended for further use in treatment of this disease.

Indirubin is the active ingredient of Danggui Longhui Wan, a mixture of plants that is used in traditional Chinese medicine to treat chronic diseases. Here we identify indirubin and its analogues as potent inhibitors of cyclin-dependent kinases (CDKs). The crystal structure of CDK2 in complex with indirubin derivatives shows that indirubin interacts with the kinase's ATP-binding site through van der Waals interactions and three hydrogen bonds. Indirubin-3'-monoxime inhibits the proliferation of a large range of cells, mainly through arresting the cells in the G2/M phase of the cell cycle. These results have implications for therapeutic optimization of indigoids.