Turning and turning in the
widening gyre
The falcon cannot hear the
falconer…
In our small, annual counterweight to Yeats’ “mere anarchy," Practical Fragments looks back on 2025.
This year marked the thousandth
post on Practical Fragments, a milestone neither Teddy nor I imagined
when the blog launched back in 2008. In terms of conferences, I wrote about
CHI’s Drug Discovery Chemistry in San Diego here and Discovery on Target in
Boston here.
For the past decade I’ve
participated in annual J. Med. Chem. perspectives covering fragment-to-lead
success stories, two of which published this year. The first, spearhead by Rhian
Holvey at Astex, covers the year 2023, while Astex’s David Twigg took the lead
on covering the year 2024. In addition to the tabular summaries for which these
reviews are best known, both also include tables of “near misses,” none of
which made the main tables because the starting points were (sometimes just
slightly) too large. Four out of six of these heavyweights are covalent
fragments, suggesting that the rule of three may need to be relaxed for these.
The most recent paper also includes a table showcasing the eight approved
FBLD-derived drugs.
Two more general publications are
also of interest. In a brief (open-access) editorial in J. Med. Chem. Weijun Xu and
Congbao Kang at A*STAR summarize fragment-finding methods and approved drugs
and discuss future applications of FBLD in PROTACs and targeting RNA. And in Curr.
Res. Pharm. Drug Discov., Geoffrey Wells, Exequiel Porta, and colleagues at
University College London present a “graphical review” which covers library
design, screening strategies, hit validation, fragment optimization, and a few
case studies of approved drugs, along with current challenges.
In Drug Des. Devel. Ther.,
Bangjiang Fang and colleagues at Shanghai University of Traditional Chinese
Medicine present an open-access bibliometrics analysis of 1301 fragment-based
drug design papers published between 2015 and the end of 2024, which includes
top ten lists of institutions, authors, and papers as well as keyword trends
and analyses. Annual growth has averaged 1.4%, and the field is both global and
collaborative, with 35% of publications involving more than one country.
Targets
Two reviews focus on oncology. The
first, in Bioorg. Chem. by Milind Sindkhedkar and collaborators at Manipal
College of Pharmaceutical Sciences and Lupin Ltd., briefly covers the history
and practice of FBDD before providing short summaries of seven of the eight approved
drugs to come from it. The second, published open-access in Chem. Rev. by
Vanderbilt’s Steve Fesik, is a concise and highly readable introduction and
account of the author’s groundbreaking work on BCL-2 family proteins, KRAS, and
WDR5.
A much longer open-access review
in Chem. Rev. by Paramjit Arora and colleagues at New York University covers protein-protein
interactions (PPIs). Much of the focus is on larger molecules such as cyclic
peptides, peptide mimetics, and other macrocycles, but there are summaries of
fragment-based approaches against KRAS and 14-3-3 proteins.
The topic of 14-3-3 proteins is
treated more fully in an open-access Acc. Chem. Res. paper by Michelle
Arkin and colleagues at UCSF. While the focus of most efforts against PPIs is
to find inhibitors, for 14-3-3 the goal is to find stabilizers, or molecular
glues. The Arkin lab and others have been succeeding using various approaches,
particularly disulfide tethering. We wrote about these efforts most recently in
2023, and the new review provides a nice update.
Fragment finding methods and
libraries
Sahra St. John-Campbell and Gurdip
Bhalay, both at The Institute of Cancer Research, published a massive
open-access perspective on “target engagement assays in early drug discovery” in
J. Med. Chem., covering a host of biochemical, biophysical, and
cell-based assays. A table lists more than 50 different techniques, almost half
of which are applicable to FBLD. Each row shows what characteristic(s) are
measured as well as critical requirements for protein, sample, and equipment. The paper is
also beautifully illustrated with dozens of figures: one shows which techniques
are most useful for different types of targets, and each method gets its own diagram.
A more focused open-access review
is provided by Stefanie Freitag-Pohl and colleagues at Durham University in Biophys.
Rev. After surveying various biophysical techniques, the researchers focus
on spectral shift analysis, and in particular the Dianthus instrument from
NanoTemper Instruments. This plate-based, high-throughput microfluidics-free
instrument can detect changes in fluorescence caused by environment or
temperature. Examples demonstrate affinity measurements across several orders
of magnitude, up to double-digit millimolar, and a nice scheme shows use of the
Dianthus in a fragment-screening workflow.
Moving to specific techniques, Jia
Gao, Ke Ruan, and colleagues at University of Science and Technology of China
Hefei provide an open-access survey of “the rise of NMR-integrated
fragment-based drug discovery in China” in Mag. Res. Lett. After a brief
overview of NMR approaches, they cover case studies from China, most of which are
focused on fragment screening rather than optimization.
A less common biophysical method
is native mass spectrometry (nMS), the subject of an open-access opinion in RSC
Med. Chem. by Louise Sternicki and Sally-Ann Poulsen at Griffith
University. This is a good survey of the approach; we highlighted a more
fragment-focused review by the same authors last year.
The most common fragment-finding
approach, X-ray crystallography, is covered in two open-access reviews. The
first, in Acta Cryst. F by Sarah Bowman and collaborators at University
of Buffalo and Brookhaven National Laboratory, focuses on critical early
stages, from protein characterization to sample preparation and various crystallization
approaches. The second, in Curr. Opin. Strut. Biol. by Martin Noble and
colleagues at Newcastle University, starts by briefly reviewing crystallographic
fragment screening before turning to fragment libraries. The paper includes a
nice table summarizing publicly available libraries at major synchrotrons, with
the text describing these in more detail.
The provider of one of these
libraries, EU-OPENSCREEN, is the subject of an open-access review in SLAS
Discov. by Robert Harmel and collaborators at EU-OPENSCREEN ERIC and
Fraunhover ITMP. As we wrote last year, EU-OPENSCREEN is a broad consortium
whose mission is to advance early drug discovery by providing access to
technology and expertise. The new paper summarizes the four compound
collections, including the European Fragment Screening Library (EFSL), and surveys
progress to date. It also lays out ambitious plans, including expanding to
>30 sites in nine countries.
Computational approaches and cryptic
sites
Despite the hype about artificial
intelligence in the broader world, AI in fragment-based drug discovery has been
less common. In Curr. Opin. Struct. Biol., Woong-Hee Shin and colleagues
at Korea University College of Medicine summarize applications to fragment growing,
merging, and linking. The open-access paper includes a handy table of 13
programs, and includes GitHub links where available.
Cryptic binding sites, defined by
Ehmke Pohl and collaborators at Durham University and Cambridge
Crystallographic Data Centre “as binding pockets that exist in the ligand-bound
state of a protein but not in its apo form,” are the focus of an open-access
review in Bioinform. Adv. The researchers cover earlier computational
approaches for finding these, especially molecular dynamics (MD) and machine
learning (ML). They note that a key challenge for ML is the limited quantity and quality
of experimental data: undiscovered cryptic sites would be misclassified as non-binding
sites.
Yowen Dong, Ge-Fei Hao, and
colleagues at Guizhou University review “computational methods for identifying
cryptic pockets” in Drug Discov. Today. As with the previous review,
these are divided between molecular dynamics and AI-based techniques, which are
discussed individually and then compared. The researchers apply six approaches
to the model bacterial protein TEM-1 β-lactamase
and find that, for this highly studied single protein, the AI-based methods are much faster (seconds
instead of days) and just as accurate, though MD-based methods provide more
insight into formation mechanisms of cryptic pockets.
Covalent ligands
Allosteric sites are an important
sub-class of cryptic pockets, and in J. Med. Chem. Jianing Li and colleagues
at Purdue University discuss covalent allosteric inhibitors. After
briefly discussing advantages of covalent molecules, they review examples
targeting protein phosphatases, kinases, and GTPases, such as KRAS.
Of course, covalent molecules are
not limited to allosteric sites. An open-access review in Bioorg. Med. Chem.
Lett. by Walaa Bedewy, John Mulawka, and Marc Adler at Toronto Metropolitan
University summarizes published covalent protein ligands, grouping them by
target site: active sites, residues adjacent
to an active site, protein-protein interfaces, cofactor binding sites, and
allosteric sites.
Chem. Rev. published two
massive reviews on covalent ligands, each with more than 300 references. The
first, by Tomonori Tamura, Masaharu Kawano, and Itaru Hamachi at Kyoto
University, covers a wide range of topics, from covalent drugs, to peptide- and
protein-based covalent inhibitors, to chemical biology labeling and target
engagement strategies, to covalent bifunctional molecules such as PROTACs and
radionucleotide-based molecules, and even covalent modification of DNA and RNA.
The paper includes 68 figures, many reproduced from the original publications.
The second (open-access) Chem.
Rev. paper, by Ku-Lung Hsu and colleagues at University of Texas at Austin,
focuses on covalent ligands targeting protein residues other than cysteine,
particularly lysine and tyrosine; we highlighted some of Hsu’s work recently.
The paper also discusses naturally occurring molecules that bind to lysine,
such as pyridoxal phosphate and aldose sugars.
Methods for finding covalent ligands
are the focus on an open-access review in JACS Au by Mengke You, Hong
Liu, and Chunpu Li at Shanghai Institute of Materia Medica. Specifically, they
review disulfide tethering, activity-based protein profiling (ABPP), covalent
DEL, phage and mRNA display, and sulfur(IV) fluoride exchange (SuFEx), with
examples for each.
The last paper on this topic, in J.
Med. Chem., offers a brief but important overview of all covalent FDA-approved small molecule drugs through 2023. Samuel Dalton and collaborators at Isomorphic Laboratories
and Merck counted 128 covalent drugs, about 7% of all small molecule drugs.
More than half are antibiotics, and more than 85% target serine or
cysteine. Only 10% are reversible, but this number is rapidly increasing, with
11 of the 13 reversible covalent drugs approved since 2010. Importantly, the
names, chemical structures, indication, target and target residue, warhead, and
key references for all the drugs are provided in the supporting information.
Miscellaneous
Deconstruction of ligands to
smaller fragments that are then “reconstructed” into new leads is a venerable
approach in FBLD and the subject of an open-access perspective in J. Med.
Chem. by J. Henry Blackwell, Iacovos Michaelidies, and Floriane Gibault at AstraZeneca.
Multiple examples dating as far back as the late 1990s are provided, along with
appropriate caveats about potential changes in fragment binding modes and protein
conformations.
Finally, an open-access perspective
in J. Med. Chem. by Dean Brown (Jnana Therapeutics) examines the 104
oral drugs approved from 2020 through 2024, including structures, dosing,
pharmacokinetics, and safety. Roughly a third of these drugs are dosed more
than once per day, and almost a quarter have a black box warning, while 42%
have at least one contraindication. Dean warns that “overly prescriptive [development
candidate] criteria may inadvertently stifle the development of innovative
drugs,” and that it is difficult but important “to be the champion for a
compound that others perceive as ‘un-drug like.’” The growing success of
covalent drugs illustrates that some organizations are taking this to heart.
And that’s it for 2025. Thanks
for reading and special thanks for commenting. And in 2026, may the best of us
be filled with passionate intensity.
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