Practical Fragments

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

14 July 2025

The importance of specific reactivity for covalent drugs

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As we noted in our thousandth post , covalent drugs are becoming increasingly popular, particularly for tackling tough targets. But finding ...
1 comment:
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...
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