Practical Fragments

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

25 August 2025

Fragments vs KEAP1: Fragment growing this time

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Kelch-like ECH-associated protein 1 (KEAP1) binds to nuclear factor erythroid 2-related factor 2 (NRF2), targeting it for degradation. Block...
18 August 2025

Hundreds of crystallographic ligands for FABP4 – many not as expected

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The ten human fatty-acid binding proteins (FABPs) shuttle lipids around cells. As we noted several years ago, FABP4 and FABP5 are potential...
4 comments:
11 August 2025

Fragments vs CYP125 and CYP142 for M. tuberculosis

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Although 2020 and 2021 were baleful exceptions, tuberculosis is normally the world’s deadliest infectious disease. The pathogen Mycobacteriu...
1 comment:
04 August 2025

The Chemical Probes Portal turns ten. Use it!

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Last week we highlighted a new tool to computationally predict whether a molecule might aggregate, thereby causing false positives. This do...
28 July 2025

Can machine learning help you avoid SCAMs?

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Among the many types of artifacts that can fool screens and derail efforts to find leads, small colloidally aggregating molecules (SCAMs) a...
21 July 2025

How can we house our crystallographic data?

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Three years ago we highlighted a growing debate about how and where to house crystallographic fragment data. With the recent surge in high-...
1 comment:
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 ...
4 comments:
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:
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