Medicinal Chemists Workbench (MedChem Workbench, or MCW for short) provides a simple and easy-to-use web page for drug chemists to log in and manage compound lists, collect compound information, and perform common calculation tasks. The web-based work platform is developed based on the Pipeline Pilot platform, allowing simulation experts and IT experts to deploy common workflows in a unified web interface for daily use by pharmaceutical chemists and experimenters.
In the past drug design work mode, pharmacological experimenters need to use molecular simulation experts to achieve the calculation of routine tasks. This mode of work wastes a lot of precious time for experimenters. They need to spend time on compound data collection and structure sorting, and they need to constantly seek simulators to use software to obtain calculation results; at the same time, simulators also need to repeat each day Tired of computing work. On the other hand, due to the rapid development of drug design projects, pharmaceutical chemists are often unable to analyze information in a timely manner because they cannot quickly access calculation tools, such as:
• For a batch of compounds, what are their physical and chemical properties and ADMET properties?
• What are the trends in the structure-activity relationship of a batch of compounds?
• Which compounds are the latest screening results?
• What literatures are reported on the compounds currently in hand?
• For compounds to be synthesized, which ones contain harmful groups and need to be modified?
• What are the drug-like properties of the currently synthesized compounds?
• How to centrally manage the structure of compounds synthesized or collected every day?
• How to select and print out the structure and properties of a batch of compounds in an intuitive arrangement?
The emergence of MedChem Workbench has revolutionized the working mode of pharmaceutical companies, providing the simplest one-stop-shop service for drug experimenters, putting all the calculation problems that drug experimenters need to solve in a unified Web interface The following tasks can be achieved in the web page:
• Quick and easy collection of different batches of compound data sets.
• Convenient to calculate various physical and chemical properties and ADMET properties of a given compound.
• Display the two-dimensional structure-activity relationship of a given compound set.
• Perform cluster analysis on a given set of compounds.
• Search for compound names in the literature and convert them into corresponding compound structures.
• Enumerate similar structures of a given compound.
• Enumerate possible metabolites of a given compound.
• Screen a batch of compounds by a given pharmacophore and sort to give the screening results.
• Print labels with structure and properties for existing compounds.
• Export existing compounds to SDF files, Excel files, PDF files, PPT files, etc.
MedChem Workbench task example
Create 2D SAR table
Create a 2D SAR table of the relationship between the R group and the activity of the compound by entering the core structure and the selected compound. The vertical axis represents the R1 group and the horizontal axis represents the R2 group. The blue color is low, and the complete structure of the compound can be displayed when hovering the mouse.
Screening of five principles for quasi-drugs
By calculating the molecular weight, AlogP, hydrogen bond acceptor, hydrogen bond donor and other properties, the compound is subjected to Lipinski Rule of 5 screening. Pharmacists can customize the scope of the property screening. The result will display the current compound Rule of 5 statistical information, and A detailed distribution interval chart for each property.
Pharmacophore Screening
A batch of compounds are screened by a given pharmacophore model, the screening results are displayed in a list of successful screening and failed screening, and the successful screening compounds are sorted from high to low by Fit value, and can be viewed directly on the web interface 3D structure and matching degree with pharmacophore.
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