Solovev Ilya A, Golubev Denis A, Yagovkina Arina I, Kotelina Nadezhda O
Laboratory of Translational Bioinformatics and Systems Biology, Medical Institute, Pitirim Sorokin Syktyvkar State University, Oktyabrsky Prosp. 55, 167000 Syktyvkar, Russia.
Clocks Sleep. 2025 Jun 23;7(3):30. doi: 10.3390/clockssleep7030030.
Chronobiotics represent a pharmacologically diverse group of substances, encompassing both experimental compounds and those utilized in clinical practice, which possess the capacity to modulate the parameters of circadian rhythms. These substances influence fluctuations in various physiological and biochemical processes, including the expression of core "clock" genes in model organisms and cell cultures, as well as the expression of clock-controlled genes. Despite their chemical heterogeneity, chronobiotics share the common ability to alter circadian dynamics. The concept of chronobiotic drugs has been recognized for over five decades, dating back to the discovery and detailed clinical characterization of the hormone melatonin. However, the field remains fragmented, lacking a unified classification system for these pharmacological agents. The current categorizations include natural chrononutrients, synthetic targeted circadian rhythm modulators, hypnotics, and chronobiotic hormones, yet no comprehensive repository of knowledge on chronobiotics exists. Addressing this gap, the development of the world's first curated and continuously updated database of chronobiotic drugs-circadian rhythm modulators-accessible via the global Internet, represents a critical and timely objective for the fields of chronobiology, chronomedicine, and pharmacoinformatics/bioinformatics. The primary objective of this study is to construct a relational database, ChronobioticsDB, utilizing the Django framework and PostGreSQL as the database management system. The database will be accessible through a dedicated web interface and will be filled in with data on chronobiotics extracted and manually annotated from PubMed, Google Scholar, Scopus, and Web of Science articles. Each entry in the database will comprise a detailed compound card, featuring links to primary data sources, a molecular structure image, the compound's chemical formula in machine-readable SMILES format, and its name according to IUPAC nomenclature. To enhance the depth and accuracy of the information, the database will be synchronized with external repositories such as ChemSpider, DrugBank, Chembl, ChEBI, Engage, UniProt, and PubChem. This integration will ensure the inclusion of up-to-date and comprehensive data on each chronobiotic. Furthermore, the biological and pharmacological relevance of the database will be augmented through synchronization with additional resources, including the FDA. In cases of overlapping data, compound cards will highlight the unique properties of each chronobiotic, thereby providing a robust and multifaceted resource for researchers and practitioners in the field.
时间生物学药物代表了一类药理学上多样的物质，包括实验性化合物和临床实践中使用的化合物，它们具有调节昼夜节律参数的能力。这些物质会影响各种生理和生化过程的波动，包括模式生物和细胞培养物中核心“时钟”基因的表达，以及时钟控制基因的表达。尽管它们在化学性质上具有异质性，但时间生物学药物具有改变昼夜节律动态的共同能力。时间生物学药物的概念已经被认可了五十多年，其可追溯到褪黑素的发现和详细的临床特征描述。然而，该领域仍然分散，缺乏针对这些药物制剂的统一分类系统。目前的分类包括天然时间营养物、合成靶向昼夜节律调节剂、催眠药和时间生物学激素，但尚未存在关于时间生物学药物的全面知识库。为填补这一空白，开发世界上第一个经过策划且不断更新的时间生物学药物——昼夜节律调节剂数据库，并可通过全球互联网访问，这对时间生物学、时间医学以及药物信息学/生物信息学领域来说是一个关键且及时的目标。本研究的主要目标是利用Django框架和PostGreSQL作为数据库管理系统构建一个关系数据库ChronobioticsDB。该数据库将通过专用的网络界面访问，并将填充从PubMed、谷歌学术、Scopus和科学网文章中提取并手动注释的时间生物学药物数据。数据库中的每个条目都将包括一张详细的化合物卡片，其中包含指向原始数据源的链接、分子结构图像、以机器可读的SMILES格式表示的化合物化学式，以及根据IUPAC命名法的名称。为了提高信息的深度和准确性，该数据库将与ChemSpider、DrugBank、Chembl、ChEBI、Engage、UniProt和PubChem等外部存储库同步。这种整合将确保包含每种时间生物学药物的最新和全面数据。此外，通过与包括美国食品药品监督管理局在内的其他资源同步，该数据库的生物学和药理学相关性将得到增强。在数据重叠的情况下，化合物卡片将突出每种时间生物学药物的独特特性，从而为该领域的研究人员和从业者提供一个强大且多方面的资源。
