Advances in high-throughput drug screening based on pharmacotranscriptomics.

Prospect on the Composite Drugs Innovation System

Metabonomics is a new "-omics" sicience in post-gene time. Metabonomics can be directly applied to understand the physiological and biochemical situation by its "metabolome profile" as a whole. Therefore it can provide a loft of information that differed from those came out of other "-omics". Metabonomics has been used to evaluate test animal models and to evaluate disease models,action mechanism of drugs,target response,drug safety and screening of new drugs. Therefore,metabonomics is hopeful to be necessary part on research of natural drugs and traditional Chinese medicines.

Traditional Chinese medicine (TCM) has over 2000 years of history and played important role in the peoples' health and social development in Chinese history. In the past 50 years, Chinese scientists have made great effort to modernize TCM to make it a evidence-based medicine from the experence-based origin. The current review has summerized the recent advances in the modern research on the various respects of TCM including the resouces investigation, GAP cultivation, phytochemistry, quality assessment, safety issues, metabolic investigation, pharmacology, systems biology etc. It pointed out that GAP for Chinese herbs is the first and key step in the quality control cycle of traditional Chinese medicine. In addition, the research on TCM active principles and quality control methods were also summarized. Over 12,000 chemical constituents have been isolated from over 600 species of traditional Chinese medicines, among which over 2000 new compounds were discovered, which layed a solid foundation for clarifying the material basis of action and providing reference substances fro the quality control of TCM. Systems biology approach is now being actively practiced for the action mechanism studies of TCMs and their active principles, which provided a valuable approach for complex TCM systems. Currently, genomics, preotenomics and metabolomics have obtained good application in TCM studies. Finally, the progress of TCM new drug research and development has been outlined. Several famous new drugs from TCM or based on TCM have been sucessfully marketed. Examples are artemisinin, artemether, hupzine A, etc. Other types of new drugs include Fufang Danshen Dripping Pill, Diao Xinxuekang, and so on. Acknowledgements: Financial support for this research from Program for Changjiang Scholars and Innovative Team in University (985-2-063-112) and National Supporting Program for TCM from Ministry of Science and Technology of China (2006BAI08B03-03) is gratefully acknowledged.

<p indent="0mm">As a unique model for the development of new traditional Chinese medicine (TCM) drugs, syndrome TCM new drugs adhere to the principle of consistency in “theory, method, prescription, and medicine,” making them the category of TCM compound preparations that best reflect TCM thinking and clinical value. However, since syndrome new drug research is still in its exploratory stage, the lack of authoritative syndrome diagnostic standards and the singularity of efficacy evaluation methods limit its credibility in clinical research. This makes it difficult to provide strong evidence for new drug approval. This article reviews the development history of syndrome new drug research, analyzes the bottlenecks and challenges faced in its market transformation, and proposes preliminary ideas and suggestions for constructing clinical evaluation approaches for syndrome new drugs. (1) Classification of TCM registration and the development of syndrome new drugs. The material basis was previously the criterion for classifying TCM registration categories. However, since 2020, the new classification has shifted the focus of new drug development towards clinical value. Since the category of syndrome TCM new drugs was first proposed in 2007, relevant policy documents have continuously enriched this category. They suggest that the clinical research of syndrome TCM new drugs can adopt various models, including purely TCM syndrome research model, TCM disease-syndrome combined research model, or TCM syndrome integrated with Western disease research model. (2) Bottlenecks in the transformation of syndrome new drugs. The disease-syndrome combined research model emphasizes modern medical “paradigm” indicators, often neglecting or even sacrificing the TCM academic characteristics intrinsic. While the purely syndrome research model firmly grasps the core concept of syndrome in TCM theory, its semi-quantitative research methods still fail to completely address the fundamental issue of propensity bias. The key to the clinical evaluation of syndrome new drugs lies in how to transform subjective qualitative assessments into objective quantitative measures. (3) Construction and practice of clinical evaluation approaches for syndrome new drugs. First, it is necessary to establish evaluation standards and quantitative indicators that can reflect the diagnostic and therapeutic characteristics of syndrome new drugs. Second, it is essential to obtain real and reliable data through objective quantitative detection tools or methods. We suggest identifying clinical biomarkers of syndromes through retrospective analysis, screening for syndrome biomarkers using systems biology, and developing objective measurement tools targeting the main symptoms of syndromes. (4) Prospects and considerations for the development of syndrome new drugs. It is crucial to establish a clinical evaluation system that aligns with the characteristics and development principles of TCM. We propose focusing on four key aspects: the scientific nature of decision-making standards, the innovation of evaluation tools, the gradual improvement of research methods, and the personalization of experimental design. Additionally, special considerations should be given to the registration classification of TCM, such as distinguishing between traditional TCM and modern TCM.

To analyze the development of coronavirus disease 2019(COVID-19), this study systematically retrieved relevant Chinese and English literatures from both CNKI and Web of Science database platforms by bibliometric research method and CiteSpace 5.5.R2 software to obtain information and visualize relevant literatures. A total of 695 Chinese and 446 English literatures were included in this paper. Statistics showed that China had published most of the literatures and established close cooperation with the United States and the United Kingdom. Through the analysis, Tongji Medical College of Huazhong University of Science and Technology and its affiliated hospitals published the largest number of the publications. Moreover, the highly productive journals including Journal of Traditional Chinese Medicine and The Lancet covered eight major fields, such as medicine, medical virology, radiation medicine, infectious disease, and traditional Chinese medicine. Besides, a total of 35 special COVID-19 funds were recently established to subsidize these studies. The key words and themes analysis indicated that protein structure of COVID-19, receptor targets and mechanisms of action, integration of traditional Chinese and Western medicine, screening and development of antiviral drugs from traditional Chinese medicine and Western medicine, vaccine research as well as epidemiological characteristics and prediction are current study hotspots. This study provides a reference for researchers to rapidly master main study directions of COVID-19 and screen out relevant literatures.

For centuries, Traditional Chinese Medicine (TCM) has been a prominent treatment method in China, incorporating acupuncture, herbal remedies, massage, and dietary therapy to promote holistic health and healing. TCM has played a major role in drug discovery, with over 60% of small-molecule drugs approved by the FDA from 1981 to 2019 being derived from natural products. However, TCM modernization faces challenges such as data standardization and the complexity of TCM formulations. The establishment of comprehensive TCM databases has significantly improved the efficiency and accuracy of TCM research, enabling easier access to information on TCM ingredients and encouraging interdisciplinary collaborations. These databases have revolutionized TCM research, facilitating advancements in TCM modernization and patient care. In addition, advancements in AI algorithms and database data quality have accelerated progress in AI for TCM. The application of AI in TCM encompasses a wide range of areas, including herbal screening and new drug discovery, diagnostic and treatment principles, pharmacological mechanisms, network pharmacology, and the incorporation of innovative AI technologies. AI also has the potential to enable personalized medicine by identifying patterns and correlations in patient data, leading to more accurate diagnoses and tailored treatments. The potential benefits of AI for TCM are vast and diverse, promising continued progress and innovation in the field.

176 Background: Response to neoadjuvant chemotherapy and radiation therapy in the treatment of locally advanced rectal cancer is heterogenous and prognostic of clinical outcomes, necessitating the need for predictive biomarkers to guide personalized treatment recommendations. Sensitivity to a given chemotherapy in patient-derived organoids predicts patient response to that chemotherapy, establishing it as a promising model for efforts to ascertain predictive biomarkers and personalize treatment decisions. This study assessed the feasibility of obtaining patient-derived rectal organoids from standard of care pre-treatment proctoscopy biopsies. Methods: In this clinical trial (NCT04371198), biopsies were obtained from patients with stage II rectal adenocarcinoma prior to receipt of neoadjuvant therapy. Tissue samples were mechanically and enzymatically dissociated to obtain a single cell suspension. Cells were then mixed with matrigel at a ratio of 2,000 cells:5 µL Matrigel in a 50ul dome and plated on a 24 well tissue culture plate with colorectal cancer organoid media at 37oC/5% CO2. Established patient-derived organoids were then used to perform drug screens with clinically-applicable chemotherapeutics including oxaliplatin, irinotecan and 5-FU, followed by high throughput drug screen using our recently published MicroOrganoSpheres platform using the NCI Approved Oncology Drugs Set VI* library. Results: Of the 20 patients enrolled, 17 (85%) patient-derived organoids were created from pre-treatment specimens. 15 (88%) of these samples were successfully established as defined by the ability to passage organoids for at least two passages. All established samples were used to perform standard of care drug screens and high throughout drug screens, which demonstrated differences in drug sensitivities among the samples. Moreover, within two weeks of receiving the sample, four established quickly enough to complete drug screening with oxaliplatin, SN38, and 5-Fluorouracil. Conclusions: These results demonstrate the feasibility of establishing patient-derived rectal organoids from biopsy specimens obtained by proctoscopy, and reinforce the utility of patient-derived organoids as a tractable ex vivo platform to personalize rectal cancer treatment. Planned future directions include in vitro determination of radiation therapy sensitivity as well as systematic assessment of the correlation between individual patients and their organoid model. Clinical trial information: NCT04371198 .

BackgroundAmyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease with death on average within 2–3 years of symptom onset. Mutations in superoxide dismutase 1 (SOD1) have been identified to cause ALS. Riluzole, the only neuroprotective drug for ALS provides life extension of only 3 months on average. Thishighlights the need for compound screening in disease models to identify new neuroprotective therapies for this disease. Zebrafish is an emerging model system that is well suited for the study of diseasepathophysiology and also for high throughput (HT) drug screening. The mutant sod1 zebrafish model of ALS mimics the hallmark features of ALS. Using a fluorescence based readout of neuronal stress, we developed a high throughput (HT) screen to identify neuroprotective compounds.ResultsHere we show that the zebrafish screen is a robust system that can be used to rapidly screen thousands ofcompounds and also demonstrate that riluzole is capable of reducing neuronal stress in this model system. The screen shows optimal quality control, maintaining a high sensitivity and specificity withoutcompromising throughput. Most importantly, we demonstrate that many compounds previously failed in human clinical trials, showed no stress reducing activity in the zebrafish assay.ConclusionWe conclude that HT drug screening using a mutant sod1 zebrafish is a reliable model system which supplemented with secondary assays would be useful in identifying drugs with potential for neuroprotective efficacy in ALS.Electronic supplementary materialThe online version of this article (doi:10.1186/s13024-016-0122-3) contains supplementary material, which is available to authorized users.

BackgroundMiT-Renal Cell Carcinoma (RCC) is characterized by genomic translocations involving microphthalmia-associated transcription factor (MiT) family members TFE3, TFEB, or MITF. MiT-RCC represents a specific subtype of sporadic RCC that is predominantly seen in young patients and can present with heterogeneous histological features making diagnosis challenging. Moreover, the disease biology of this aggressive cancer is poorly understood and there is no accepted standard of care therapy for patients with advanced disease. Tumor-derived cell lines have been established from human TFE3-RCC providing useful models for preclinical studies.MethodsTFE3-RCC tumor derived cell lines and their tissues of origin were characterized by IHC and gene expression analyses. An unbiased high-throughput drug screen was performed to identify novel therapeutic agents for treatment of MiT-RCC. Potential therapeutic candidates were validated in in vitro and in vivo preclinical studies. Mechanistic assays were conducted to confirm the on-target effects of drugs.ResultsThe results of a high-throughput small molecule drug screen utilizing three TFE3-RCC tumor-derived cell lines identified five classes of agents with potential pharmacological efficacy, including inhibitors of phosphoinositide-3-kinase (PI3K) and mechanistic target of rapamycin (mTOR), and several additional agents, including the transcription inhibitor Mithramycin A. Upregulation of the cell surface marker GPNMB, a specific MiT transcriptional target, was confirmed in TFE3-RCC and evaluated as a therapeutic target using the GPNMB-targeted antibody-drug conjugate CDX-011. In vitro and in vivo preclinical studies demonstrated efficacy of the PI3K/mTOR inhibitor NVP-BGT226, Mithramycin A, and CDX-011 as potential therapeutic options for treating advanced MiT-RCC as single agents or in combination.ConclusionsThe results of the high-throughput drug screen and validation studies in TFE3-RCC tumor-derived cell lines have provided in vitro and in vivo preclinical data supporting the efficacy of the PI3K/mTOR inhibitor NVP-BGT226, the transcription inhibitor Mithramycin A, and GPNMB-targeted antibody-drug conjugate CDX-011 as potential therapeutic options for treating advanced MiT-RCC. The findings presented here should provide the basis for designing future clinical trials for patients with MiT-driven RCC.

Dynamic microphysiological system chip platform for high-throughput, customizable, and multi-dimensional drug screening

Three-dimensional growth conditions reflect the natural environment of cancer cells and are crucial to be performed at drug screens. We developed a 3D assay for cellular transformation that involves growth in low attachment (GILA) conditions and is strongly correlated with the 50-year old benchmark assay-soft agar. Using GILA, we performed high-throughput screens for drugs and genes that selectively inhibit or increase transformation, but not proliferation. This phenotypic approach is complementary to our genetic approach that utilizes single-cell RNA-sequencing of a patient sample to identify putative oncogenes that confer sensitivity to drugs designed to specifically inhibit the identified oncoprotein. Currently, we are dealing with a big challenge in our field- the limited number of cells that might be extracted from a biopsy. Small patient-derived samples are hard to test in the traditional multiwell plate and it will be helpful to minimize the culture area and the experimental system. We managed to design a suitable microfluidic device for limited number of cells and perform the assay using image analysis. We aim to test drugs on tumor cells, outside of the patient body- and recommend on the ideal treatment that is tailored to the individual. This device will help to minimize biopsy-sampling volumes and minimize interventions in the patient’s tumor.

Microfluidics-based drug-screening systems have enabled efficient and high-throughput drug screening, but their routine uses in ordinary labs are limited due to the complexity involved in device fabrication and system setup. In this work, we report an easy-to-use and low-cost arbitrarily accessible 3D microfluidic device that can be easily adopted by various labs to perform combinatorial assays for high-throughput drug screening. The device is capable of precisely performing automatic and simultaneous reagent loading and aliquoting tasks and performing multistep assays with arbitrary sequences. The device is not intended to compete with other microfluidic technologies regarding ultra-low reaction volume. Instead, its freedom from tubing or pumping systems and easy operation makes it an ideal platform for routine high-throughput drug screening outside traditional microfluidic labs. The functionality and quantitative reliability of the 3D microfluidic device were demonstrated with a histone acetyltransferase-based drug-screening assay using the recombinant Plasmodium falciparum GCN5 enzyme, benchmarked with a traditional microtiter plate-based method. This arbitrarily accessible, multistep capable, low-cost, and easy-to-use device can be widely adopted in various combinatorial assays beyond high-throughput drug screening.

G protein-coupled receptors (GPCRs) widely exist in vivo and participate in many physiological processes, thus emerging as important targets for drug development. Approximately 30% of the Food and Drug Administration (FDA)-approved drugs target GPCRs. To date, the ‘one disease, one target, one molecule’ strategy no longer meets the demands of drug development. Meanwhile, small-molecule drugs account for 60% of FDA-approved drugs. Traditional Chinese medicine (TCM) has garnered widespread attention for its unique theoretical system and treatment methods. TCM involves multiple components, targets and pathways. Centered on GPCRs and TCM, this paper discusses the similarities and differences between TCM and GPCRs from the perspectives of syndrome of TCM, the consistency of TCM’s multi-component and multi-target approaches and the potential of GPCRs and TCM in the development of novel drugs. A novel strategy, ‘simultaneous screening of drugs and targets’, was proposed and applied to the study of GPCRs. We combine GPCRs with TCM to facilitate the modernisation of TCM, provide valuable insights into the rational application of TCM and facilitate the research and development of novel drugs. This study offers theoretical support for the modernisation of TCM and introduces novel ideas for development of safe and effective drugs.

Our laboratory has previously developed a qRT-PCR assay to assess drug efficacy on the growth of Cryptosporidium parvum in vitro by detecting the levels of parasite 18S rRNA. This approach displayed up to four orders of magnitude of linear dynamic range and was much less labor-intensive than the traditional microscopic methods. However, conventional qRT-PCR protocol is not very amendable to high-throughput analysis when total RNA needs to be purified by lengthy, multi-step procedures. Recently, several commercial reagents are available for preparing cell lysates that could be directly used in downstream qRT-PCR analysis (e.g., Ambion Cell-to-cDNA kit and Bio-Rad iScript sample preparation reagent). Using these reagents, we are able to adapt the qRT-PCR assay into high-throughput screening of drugs in vitro (i.e., 96-well and 384-well formats for the cultivation of parasites and qRT-PCR detection, respectively). This qRT-PCR protocol is able to give a >150-fold linear dynamic range using samples isolated from cells infected with various numbers of parasites. The new assay is also validated by the NIH-recommended intra-plate, inter-plate, and inter-day uniformity tests. The robustness and effectiveness of the assay are also confirmed by evaluating the anti-cryptosporidial efficacy of paromomycin and by a small scale screening of compounds.

An effective method to quantify the parasite loads is the key to the evaluation of anti-cryptosporidial drug efficacy in vitro. However, high-throughput screening (HTS) of drugs against Cryptosporidium parvum in vitro was impractical by the labor-intensive traditional assays. Here we describe a simplified quantitative RT-PCR assay suitable for HTS of compounds and for evaluating drug efficacy against the growth of C. parvum in vitro.