Provide Medicinal Chemistry Solutions, Focused on R&D Stages from Ideation to Lead Optimization
With Knowledge Gained from Practical Experiences, We Take on Challenges with Collaboration, Integrity and Speed
Professional Profile
- Program chemistry lead in cross-functional team.
- ADC payload and linker design.
- Designing and synthesizing small molecules ranging from heterocycles to natural products and cyclic dinucleotides.
- Expertise in structure-based drug design to address program challenges (potency, selectivity, metabolic stability, hERG, CYP, PK, in-vitro and in-vivo pharmacology, intellectual property).
- Extensive use of x-ray structure, Livedesign, Mastro and Lead discovery for CADD.
- Effective utilization of CRO to support chemistry needs.
- Good use of modern equipment in a medicinal chemistry lab.
- Efficient use of electronic notebooks.
Side Projects
- ChEMBL has >2 million compounds with >20 million assay datapoints. It is a good source to collect information and learn from previous examples.
- This project is about finding an efficient work flow to search for information needed.
- In the example, Zuranolone’s human hepatocyte stability data was used to illustrate how CHMEBL data might be useful.
- BatchVinaGUI provides a layer above docking engines like Vina and Vina-GPU etc..
- This program makes docking using Vina and its different forks (versions) very convenient.
- This project is about setting up a docking workflow that incorporates BatchVinaGUI, using redocking of Gleevec to 1iep as an example.
- US patents application are published every week and they are freely available to the public.
- All the chemical structures associated with the patents are nicely stored in zip files along with the patents in xml format.
- With StyleVision, a xml file software, we could extract and rearrange the patents’ contents, especially the chemical structures, so it is easier to grasp the patents’ contents related to chemical structures.
- Download and see an example, a reformatted patent in RTF format (The structure links in the file are hard coded and not active. It takes less than 10 mins to prepare the document after the work flow has been set up.)
- US patents application are published every week and they are freely available to the public.
- All the chemical structures associated with the patents are nicely stored in zip files.
- Using RDkit and Python, a SDF file of all the chemical structures can be assembled.
- This database is helpful for extracting all the chemical structures in a patent quickly. (Combined with previous project, this speeds up the extraction of SAR information in a Patent application.)
- The example is a SDF file of part of the chemical structures published in 2022 (~100k, 500 MB)
- Use chemdraw API to convert cdxml to sdf
- Create new table from parent table (Ironpython in spotfire)
- Combine mol files into sdf and add properties to each molecule, including the location of its tiff format, the code is used to construct US patent structure database
- DB browser code for assemble different tables
- Collection of substituents of bioactive scaffolds: original paper by Peter Ertl and text file of smiles, properties of those substituents (the example link below). This helps to determine how to decorate the scaffolds of interest during compound optimization