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Mass Spectrometry: Molecular Fragmentation Overview

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can...

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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

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Expanding Bioactive Fragment Space with the Generated Database GDB-13s.

Ye Buehler¹, Jean-Louis Reymond¹

¹Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.

Journal of Chemical Information and Modeling

|September 18, 2023

Summary

Medicinal chemists can discover novel drug design fragments by analyzing large molecule databases. This study identifies simple, synthetically accessible ring fragments (RFs) and acyclic fragments (AFs) enriched in bioactive compounds.

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Area of Science:

Medicinal Chemistry
Computational Chemistry
Drug Discovery

Background:

Classical molecular series have limitations in drug design.
Fragment-based drug discovery (FBDD) requires innovative molecular fragments.
Public databases offer vast chemical diversity for fragment identification.

Purpose of the Study:

To identify novel ring fragments (RFs) and acyclic fragments (AFs) for drug design.
To analyze the prevalence and bioactivity enrichment of RFs and AFs in chemical databases.
To explore the potential of novel fragments in advancing FBDD.

Main Methods:

Deconstruction of molecules into RFs (ring atoms + adjacent atoms) and AFs (acyclic atoms).
Analysis of RFs and AFs in public databases (ZINC, PubChem, COCONUT) and ChEMBL.
Enumeration and analysis of RFs and AFs within the GDB-13s database (99 million molecules).

Main Results:

RFs and AFs up to 13 atoms are prevalent in public molecule and natural product databases.
Many RFs and AFs are significantly enriched in bioactive compounds compared to inactive ones.
A substantial number of novel, simple, and synthetically accessible RFs and AFs were identified in GDB-13s.

Conclusions:

Novel RFs and AFs represent promising building blocks for innovative drug design.
These fragments offer opportunities for synthetic chemistry to contribute to FBDD.
The identified fragments can help overcome limitations of traditional drug discovery approaches.