Long winter is here in the global
north, with its dim days and gaping nights. As is tradition, Practical
Fragments looks back on the year almost done. 2024 was the best year for
conferences since the arrival of COVID. I wrote about CHI’s Drug Discovery
Chemistry in San Diego, FBDD-DU in Brisbane, FBLD 2024, and CHI’s Discovery on Target, both in Boston.
Another tradition is the annual J. Med. Chem.
fragment-to-lead success story review; the latest covers the year 2022 and was
written by Andrew Woodhead (Astex) and collaborators, including yours truly.
For a timely and accessible overview
of “how to find a fragment,” look no further than a review of that title in ChemMedChem
by Marcio Vinicius Bertacine Dias and collaborators at University of São Paulo
and University of Warwick. This covers crystallography, cryo-EM, NMR, SPR,
thermal shift, virtual screening, functional screening, ITC, mass spectrometry
(including HDX-MS), MST, and BLI, and concludes with a nice comparison table. Some twenty other reviews were also published throughout the year, and these are
discussed thematically.
Structure-based methods
Three reviews cover NMR. In J.
Med. Chem., Janet Caceres-Cortes and colleagues at Bristol-Myers Squibb
provide “perspectives on nuclear magnetic resonance spectroscopy in drug
discovery.” Ligand- and protein-detected screening are covered thoroughly, with
examples such as the discoveries of BI-2852 and venetoclax. Applications beyond
hit finding are also discussed, such as the characterization of atropisomers in
sotorasib, the identification and characterization of impurities and
metabolites, in-cell NMR, and much more.
“Perspectives on applications of 19F-NMR
in fragment-based drug discovery” is the title of an open-access review in Molecules
by Qingxin Li and CongBao Kang at Guangdong Academy of Sciences and A*STAR,
respectively. As we discussed in 2020, fluorine NMR is becoming increasingly
common in FBLD, and this paper covers the various methods, including using 19F-NMR
to measure ligand affinity. The authors also include a table summarizing 17 fragment
screens that used fluorine NMR.
The rise of powerful permanent
magnets has enabled low-maintenance benchtop NMR instruments that can be yours for as little
as $50,000, compared to upwards of $1 million for a 600 MHz superconducting machine.
Although sensitivity is at least 150-fold lower, hyperpolarization techniques
such as photo-CIDNP, which we wrote about here, can close the gap. The latest
developments are described (open access) in Chemistry–Methods by Felix
Torres and collaborators at NexMR and the ETHZ.
X-ray crystallography has retained the top position among fragment-finding methods according to our most recent poll.
In an open-access Applied Research paper, Daren Fearon, Frank von Delft,
and collaborators describe high-throughput crystallographic fragment screening
at the Diamond Light Source. As of August 2024 they have collected more than 240,000
academic data sets on hundreds of targets, and the paper distills some of the key
lessons, some of which were applied to the COVID Moonshot, which we last wrote
about here. The paper also describes future developments and needs, such as how
and where to house such massive quantities of data.
Another center for high-throughput
crystallographic screening is the Helmhotz-Zentrum Berlin (HZB) F2X-Facility at
the BESSY II synchrotron, and in an open-access Applied Research paper
Manfred Weiss and collaborators provide an overview of workflows and
capabilities. One unique offering is the F2X-GO kit, in which F2X fragment
libraries (which we wrote about here) as well other supplies are shipped to users
to do soaking experiments in their own laboratories prior to shipment to the synchrotron.
“Structure-based virtual screening
of vast chemical space” is the topic of an open-access review in Curr. Opin.
Struct. Biol. by Jens Carlsson (Uppsala University) and Andreas Luttens
(MIT). The Enamine REAL collection currently contains 40 billion compounds, and
the researchers predict that “make-on-demand chemical libraries will likely
reach more than one trillion compounds in the next few years,” which presents
both opportunities and challenges, particularly given the existence of the “virtual
cheaters” we recently discussed. Machine learning and fragment-based methods such
as V-SYNTHES could help.
Continuing the virtual theme, Li
Wang and collaborators at Nantong University discuss “molecular fragmentation
as a crucial step in the AI-based drug development pathway” in an open-access Commun.
Chem. paper. This summarizes 15 different computational methods for
dissecting larger molecules into fragments, and also includes a list of 11
library vendors.
Other methods
Among experimental methods, few
can match the throughput of fluorescence techniques, the subject of an
open-access Heliyon review by Neelagandan Kamariah and colleagues at
inSTEM & NCBS in Bangalore. It has short sections on “fluorescence
polarization (FP) and anisotropy (FA), Förster resonance energy transfer
(FRET), time-resolved Förster resonance energy transfer (TR-FRET),
fluorescence lifetime (FLT), protein-induced fluorescence enhancement (PIFE),
fluorescence thermal shift assay (FTSA) and microscale thermophoresis.” It also
describes applications to GPCRs, protein-protein interactions, and other biological
systems.
Native mass spectrometry (nMS),
which we wrote about most recently in 2022, is the subject of an RSC Med.
Chem. review by Louise Sternicki and Sally-Ann Poulsen at Griffith
University. Sally-Ann is a leading expert in nMS, and the paper describes the
technique and how it compares to other fragment-finding methods. It also includes
a nice table summarizing 17 studies published between 2013-2023 that used nMS
for FBLD; a 2013 review of nMS covered earlier examples.
Covalent Fragments
Mass spectrometry plays a
prominent role in finding covalent fragments, as discussed in an open-access SLAS
Discovery review by Simon Lucas and colleagues at AstraZeneca. “Covalent
hits and where to find them” also describes other biophysical, biochemical, cellular
approaches, and even DEL screening. It also discusses covalent libraries (which
we wrote about earlier this month) and successful examples such as the
discovery of sotorasib. In my opinion the researchers succeed in their “hope
that this review will help serve as a useful roadmap to those seeking to drug
the undruggable.”
A concise open-access review in Curr.
Opin. Struct. Biol. by Katrin Rittinger and collaborators at The Francis
Crick Institute and GSK focuses on using covalent fragments to assess target
tractability, specifically ligandability and functionality. Target-based, proteome-wide
and function-first approaches are summarized, and the researchers also discuss
the importance of negative control compounds such as inactive enantiomers.
Continuing the theme of “assayability,”
Micah Niphakis (Lundbeck) and Ben Cravatt (Scripps) review “ligand discovery by
activity-based protein profiling” (ABPP) in a Cell Chem. Biol. paper.
Because ABPP is usually conducted in cells or cell lysates, full-length proteins
are assayed in their native environment, facilitating the discovery of allosteric
ligands as in the case of WRN, which we wrote about earlier this year. The paper
summarizes multiple examples of finding covalent ligands for challenging
targets, and also highlights future challenges such as increasing throughput
and targeting residues beyond cysteine.
Reversible covalent inhibitors
are the topic of an open-access review by Dustin Duncan and colleagues at Brock
University in ACS Chem. Biol. The researchers argue that reversible covalent
inhibitors may cause less accumulation of the off-target adducts that could
form with irreversible inhibitors. The paper includes a figure showing reversible
covalent warheads, details on how to characterize them, a nice summary of
general considerations, and success stories for JAK3, BTK, and proteases.
Targets
Covalent ligands have been particularly
important for cancer targets, as reviewed by Xiaoyu Zhang (Northwestern
University) and Ben Cravatt (Scripps) in an open-access Annual Review of
Cancer Biology paper. The focus is on use of chemical proteomics “to expand
the druggability of cancer proteomes.” The paper presents examples of finding
and characterizing covalent ligands for a variety of oncology targets including
KRASG12C.
E3 ligases are briefly mentioned,
and this target class is the focus of an Expert Opin. Drug Discov. review
by Jongmin Park and colleagues at Kangwon National University. As we’ve discussed
recently, the 600 or so human E3 ligases are potentially valuable for targeted
protein degradation applications such as PROTACs. The review focuses on “fragment-based
approaches to discover ligands for tumor-specific E3 ligases.” In addition to summarizing
successes against targets such as BCL6 and XIAP, it includes a list of 113
tumor-specific E3 ligases and another list of 52 E3 ligases that are overexpressed
in certain tumors.
The “impact of fragment-based
drug design on PROTAC degrader discovery” is also the subject of a review in Trends in Analytical Chemistry by
Xiaoguang Lei and colleagues at Shenzen Bay Laboratory. Here, the focus is more
on using FBLD to discover ligands for target proteins rather than for E3s. For
example, the researchers describe how the fragment-derived drug navitoclax was
used as a starting point for developing DT2216, a clinical-stage BCL-xL
degrader.
As Vicki Nienaber noted more than
a decade ago, fragment-based drug discovery is ideally suited for targeting the
central nervous system, particularly when combined with a ruthless focus on
molecular properties. This is the topic of an open-access review in Front. Chem. by Michael Kassiou and collaborators at University
of Sydney, CSIRO, and Vast Bioscience. After a brief summary of FBLD the researchers
present case studies published since 2015, the last year this topic was
reviewed. We’ve covered quite a few on Practical Fragments, including
apoE4, Notum, and PDE10A.
Other
We mentioned allostery above, and
in an open-access FEBS Open Bio. article Andrea Bellelli and collaborators
at Sapienza University of Rome and elsewhere ask “is allostery a fuzzy concept?”
Digging into half-century old publications from Jacques Monod, the researchers
conclude that the concept was “born with an original sin: two definitions.” Indeed,
the first mathematical model did not even apply to monomeric proteins. Most
readers of this blog will probably be satisfied with the notion that an
allosteric ligand is one that binds outside of an active site, but it is worth
remembering that “allostery is an umbrella that covers more than a single
reaction mechanism and cannot be defined by a single mathematical expression.”
Structure comes up frequently on Practical
Fragments, but James Fraser (UCSF) and Mark Murcko (Disruptive Biomedical)
remind us in Cell that “structure is beauty, but not always truth.” We’ve written
multiple posts about getting misled by crystal structures, and in this brief
commentary the authors provide “four harsh truths: a structure is a model, not
experimental reality; representing wiggling and jiggling is hard; in vitro
can be deceiving; drugs mingle with many different receptors.” They conclude
that “truth is a molecule that transforms the practice of medicine.”
Stumbling towards truth is a
little easier with the help of a good chemical probe, and in Nucleic Acids
Res. Paul Workman (Institute of Cancer Research) and collaborators provide
an updated description of The Chemical Probes Portal. This free community
resource now contains 803 probes against 570 targets, including 28 covalent ligands
and 51 degraders. Moreover, 332 of the probes have structurally related
negative controls. Importantly, the Portal also includes 258 “Unsuitable” compounds
that are insufficiently potent or selective to serve as chemical probes. Checking
this list can save you valuable time when reading papers about unfamiliar
targets.
Finally, a brief open-access
interview with Nobel Laureate Katalin Karikó in Issues in Science and
Technology is an inspiring reminder that “you learn more from failure,” and
that the pleasure of doing science can be its own reward.
Thanks for reading. Good luck in
2025, and remember that the sun is always out there, even when you can neither
feel nor see it.
Posts
No comments:
Post a Comment