Practical Fragments

This blog is meant to allow Fragment-based Drug Design Practitioners to get together and discuss NON-CONFIDENTIAL issues regarding fragments.

07 July 2025

Fragment events in 2025 and 2026

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For better or for worse, 2025 is half-way over. There are still some good conferences coming up, and 2026 is also starting to take shape. Se...
30 June 2025

Fragments vs HNF4: a chemical probe

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Driven by the spectacular success of diabetes and obesity drugs, metabolism is a hot therapeutic area. Much of the focus has been on GPCRs s...
23 June 2025

Playing fast and loose with electrostatic anchors on RNA

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Two weeks ago we discussed how to find ligand-binding sites in RNA. Last week we wrote about how difficult it is to find good ligands even...
16 June 2025

Targeting SARS-CoV-2 RNA – but not specifically

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Last week we highlighted work suggesting that small molecule binding sites in RNA are most likely to be found in complex structures. A new ...
09 June 2025

Identifying ligand-binding pockets in RNA, computationally and experimentally

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Most drugs bind to proteins, but RNA provides many interesting targets. Unfortunately, finding drug-like small molecules that bind to RNA is...
02 June 2025

Small and simple, but novel and potent

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Back in 2012 we wrote about GDB-17, a database of possible small molecules having up to 17 carbon, oxygen, nitrogen, sulfur, and halogen at...
19 May 2025

Crystallography first in fragment optimization: Binding-Site Purification of Actives (B-SPA)

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At FBLD 2024 , Frank von Delft (Diamond Light Source) announced the ambitious goal of taking a 100 µM binder to a 10 nM lead in less than a ...
12 May 2025

From fragment to macrocyclic Ras inhibitors

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At the Drug Discovery Chemistry meeting last month chemist John Taylor described efforts against the oncology target RAS. This story was re...
5 comments:
05 May 2025

Solving protein-ligand NMR structures without isotopic labeling

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Last week we highlighted a protein-detected NMR method that does not require expensive and sometimes difficult isotopic labeling of protein...
1 comment:
28 April 2025

Protein-detected NMR without isotopic labeling

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Protein-detected NMR was the first practical approach for finding fragments , and as we noted last week some still consider it the gold sta...
1 comment:
21 April 2025

Twentieth Annual Fragment-Based Drug Discovery Meeting

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Last week’s CHI Drug Discovery Chemistry (DDC) meeting was held as usual in San Diego. More than 850 people attended, 96% in person, with 7...
1 comment:
14 April 2025

A library of covalent fragments vs a library of kinases

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Protein kinases have proven to be a fruitful class of targets, as evidenced by more than 80 FDA-approved drugs, five of which came from fra...
07 April 2025

Do covalent fragments need to be larger?

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A few months ago we highlighted work out of AstraZeneca detailing how to build a covalent fragment library. One of the design features was ...
3 comments:
01 April 2025

Fragments meet crypto!

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Two years ago today, Practical Fragment$ launched  a line of non-fungible tokens. Unfortunately, the NFT craze didn't last much longer t...
3 comments:
24 March 2025

Fragments and nanodiscs: beware nonspecific binding

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Membrane proteins make up roughly a quarter of human proteins, including many important drug targets. Biophysical methods for fragment scree...
17 March 2025

Fragments vs eIF4E: a chemical probe

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Cancer cells are known for growing and multiplying quickly, and to do so they need to produce large amounts of protein. The rate determining...
10 March 2025

Crude success against the SARS-CoV-2 main protease: From covalent fragment to noncovalent lead

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With increased throughput and reliability of biophysical and other methods , finding fragments against most targets is now fast and easy. Ad...
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