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Welcome to ChemJam! A science blog with a bad name but great topics from a med chem perspective!

My name is John Widen, a medicinal chemist. I have >5 years of experience in biotech working on small molecule programs in oncology and neurodegeneration. I thought the world could use one more blog. I'm going to focus on aspects of drug discovery from a medicinal chemistry prespective. I'm planning to cover patent literature, biotech, target landscapes, and topics related to drug discovery. If you have any ideas on what you'd like to read about or have any feedback please email me at jwiden@chemjam.com. Thanks for stopping by.

Part 2: Free Drug Principle and Potency

By John Widen • October 5th, 2025

Tags: Medicinal Chemistry • potency • free fraction • Free Drug Principle • SAR

Often times free fraction corrected potency values are not reported in the literature. However, protein or matrix binding can have drastic effects on potencies and should be considered when interpreting data. This article discusses why correcting potencies with free fraction measurements is important.

Patent Busting: Move a nitrogen, file a patent

By John Widen • September 26th, 2025

Tags: Medicinal Chemistry • Patents • Patent Busting • TRPML1 • Casma Therapeutics • Caraway Therapeutics

Casma Therapeutics recently disclosed a patent application focused on TRPML1 agonists, a lysosomal ion channel involved in lysosomal storage diseases. Their patent application is an iteration from prior art by Caraway Therapeutics (now Merck) where they moved one nitrogen on the molecules' core.

Identifying small molecule RNA binders using covalent tethering

By John Widen • September 21st, 2025

Tags: Medicinal Chemistry • Covalent Small Molecules • RNA • Covalent Fragments • Screening • Mustards

A publication from the Disney Lab at UF Scripps Institute identifies a new mustard-like RNA reactive electrophile and applies covalent fragment-based screening to identify small molecule RNA binders. Could this approach be used more broadly to discover non-covalent RNA and protein binders?

Maze stock increases 55% in one day after reporting favorable phase 1 data for MZE782 and private investment of $150 million

By John Widen • September 12th, 2025

Tags: Medicinal Chemistry • Biotech News • Maze Therapeutics • Kidney Disease • Drug Discovery

Maze Therapeutics focuses on treating kidney disorders with two clinical assets. Maze reported yesterday favorable phase 1 data for MZE782, a small molecule inhibitor of a neutral amino acid transporter, SLC6A19.

Putting the free drug principle into practice to calculate brain penetrance and other PK/PD parameters

By John Widen • September 11th, 2025

Tags: Medicinal Chemistry • Free Drug Hypothesis • Free Drug Principle • Blood-brain barrier • BBB • DMPK • Drug Discovery

The free drug hypothesis principle is often ignored in publications. This article is a crash course on how to apply the free drug principle to calculate free (unbound) concentrations to correct for non-specific protein binding. I swear it is easy and requires very limited math!

Violet therapeutics are targeting EphB3 for neurodegenerative diseases including Alzheimer's

By John Widen • September 2nd, 2025

Tags: Medicinal Chemistry • Patents • Covalent small molecules • Cysteine • EphB3 • neurodegeneration • Alzheimer's Disease • Violet Therapeutics • Biotech • Drug Discovery

Violet Therapeutics is a platform biotech company that identified EphB3 as a cell receptor involved in neuroinflammation. This article discusses their development of covalent small molecule inhibitors of EphB3.

Part 3: Patent Busting A Literature-based Approach

By John Widen • August 27th, 2025

Tags: Medicinal Chemistry • Patents • Literature-based Approach • Information-driven Approach • How To

Part 3 of the patent busting Literature-based Approach series focuses on identifying GAPS in a patent focused on STING antagonists and discusses how to differentiate to design novel chemical matter.

Vinyl sulfonimidamides as a new cysteine reactive electrophile

By John Widen • August 19th, 2025

Tags: Covalent small molecules • electrophiles • warheads • screening libraries • covalency • cysteine reactivity • vinylsulfonimidamides

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Sanofi completes buyout of Vigil Neurosciences for a small molecule TREM2 agonist program

By John Widen • August 14th, 2025

Tags: TREM2 • buyouts • biotech deals • agonists • antibodies • small molecules • Vigil Neurosciences • Sanofi

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ChemUI Seek: Download this cool chemical structure search application

By John Widen • August 12th, 2025

Tags: Chemistry • Software • Application • Chemical Searches • Structure Search

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Part 2: The case for CD47-SIRPα small molecule inhibition

By John Widen • August 8th, 2025

Tags: CD47 • Cardivascular Disease • Cancer • Check-point inhibitors • Immunity • PD-1 • PD-L1 • SIRPalpha • small molecules • macrocyclic peptides

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The case for CD47-SIRPα small molecule inhibition

By John Widen • July 22nd, 2025

Tags: CD47 • Cardivascular Disease • Cancer • Check-point inhibitors • Immunity • PD-1 • PD-L1 • SIRPalpha

The other day I was perusing Arch Venture’s company portfolio and landed on...

Orthosteric versus allosteric SARM1 inhibitors

By John Widen • August 4th, 2025

Tags: SARM1 • Nura Bio • patents • covalent inhibitors • peripheral neuropathy • neurodegeneration

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APOE4 increases inflammation related pathways

By John Widen • July 18, 2025

Tags: Publication • Commentary Perspective • ApoE • Alzheimer's Disease • Parkinson's Disease • Dementia

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Patent Busting A Literature-based Approach

By John Widen • July 19th, 2025

Tags: Medicinal Chemistry • Patents • Literature-based Approach • Information-driven Approach • How To

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Part 2: Patent Busting A Literature-based Approach

By John Widen • July 28th, 2025

Tags: Medicinal Chemistry • Patents • Literature-based Approach • Information-driven Approach • STING • How To • Stimulator of Interferon Genes

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My First Article! Allow me to introduce myself

By John Widen • July 14, 2025

Tags: Introduction • First Article • Personal

Welcome to my first ever blog post! I know the name ChemJam might seem like a terrible choice to many people, but the domain name was supremely cheap, and I currently don’t have a consistent income right now (Hire me!). So, you will just have to deal with it...