Practical Fragments

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

13 October 2025

Ivermectin postmortem: PAINful experiences with a good drug

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Ivermectin is a miracle drug. It cures infections caused by several types of parasitic roundworms, including those that cause river blindnes...
1 comment:
06 October 2025

Exploiting avidity for finding fragments

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As our poll last year demonstrated, there is no shortage of methods to find fragments. But that doesn’t mean new approaches aren’t welcome,...
29 September 2025

Twentieth-Third Annual Discovery on Target Meeting

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The CHI Discovery on Target ( DoT ) meeting was held last week in Boston. More than 850 people from 24 countries attended, 75% from industry...
4 comments:
22 September 2025

Fragment merging without crystallography for CGRP receptor antagonists

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Migraines are the third leading cause of disability worldwide. Although the pathology is complex, blocking the interaction of calcitonin gen...
15 September 2025

Covalent ligand efficiency

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Ligand efficiency ( LE ) was proposed more than two decades ago as “a useful metric for lead selection.” The concept is simple: divide the b...
2 comments:
08 September 2025

Fragment growing in three dimensions made easy

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Nearly a decade ago we highlighted a paper from Astex that exhorted chemists to develop new synthetic methodologies useful for fragment-bas...
2 comments:
02 September 2025

Keeping molecular dynamics cool for fragments

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Accurately and reliably predicting fragment binding modes would be preferrable to doing messy, expensive, and sometimes tedious experimental...
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...
5 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...
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