Twentieth-Fourth Annual Discovery on Target Meeting

Cambridge Healthtech Institute held its annual Discovery on Target (DoT) meeting in Boston last week. Attendance may have set a record, with over 1000 participants. There were sessions on antibodies, conjugates, and radioligands, but I’ll just touch on some of the small molecule themes most relevant to this blog.

 

Covalent approaches

As with last year, covalent approaches to drug discovery were well-represented. Dhirendra Simanshu (Frederick National Laboratory) described several drugs birthed in the NCI RAS Initiative, including ones targeting the G12C mutant of KRAS and C242 on the RAS-binding domain of PI3Kα. He also described how various KRAS mutants cause resistance to drugs, finding that most of them affect the K_I term (binding) more than the k_inact term (bonding). Continuing on the KRAS theme, Jack Sloan discussed efforts at BMS to discover inhibitors targeting both the on- and off-states of KRAS G12C.

 

Kasia Handing (Tango Therapeutics) presented both covalent and non-covalent approaches against VRK1, a synthetic lethal target for glioblastoma. A biochemical screen yielded covalent inhibitors that were characterized crystallographically, but they turned out to be too non-selective to progress. In the meantime, an in-cell DNA-encoded library (DEL) screen led to more advanceable molecules.

 

DEL was indeed a major topic of the conference, and here too covalent approaches are being explored. Elizabeth D’ambrosio described how GSK is identifying covalent binders from DEL screens, a process which includes testing for time-dependence as well as aggressive washing steps under denaturing conditions to quench unreacted molecules and wash away any sticky, non-covalently bound compounds. And Xiaojie Bruce Lu (Chinese Academy of Sciences) described applying DEL to a variety of targets, including some covalently targeting non-cysteine residues.

 

One of the advantages of DEL is being able to screen large libraries, and increasing throughput is also of interest to Harvard’s Steve Gygi, who is screening covalent fragments against cells and cell lysates. In 2024 we described how he was using tandem mass tag (TMT) multiplexing to analyze 18 samples in a single mass-spectrometry run, and he has now extended this to 35 samples. What’s more, Steve is combining 16 different fragments in each sample and introducing clever deconvolution approaches to further accelerate the process.

 

Not everyone is targeting cysteine residues. Mark Tye described the discovery of Revolution Medicines’ zoldonrasib, which uses an aziridine warhead to target the G12D mutant of KRAS. And Balyn Zaro (University of California San Francisco) described using ninhydrin derivatives to target arginine. Most organic chemists are familiar with ninhydrin’s reaction with primary amines such as the N-termini of peptides, but Balyn has been able to optimize selectivity for arginine and has used the resulting chemical probes to identify more than 7000 arginine residues in cells, about 5% of which are hyperreactive. Interestingly, some cell lines seem to have a greater proportion of reactive arginine residues than others.

 

Direct-to-Biology (D2B) approaches

Another recurring theme was direct-to-biology, in which crude reaction mixtures are screened directly in various assays without purification. Indeed, Nicholas Bland of Domainex said that after looking at the agenda of the meeting he considered skipping the introductory slides – and this was on the first official day of the conference. Nicholas described using D2B for optimizing PROTACs as well as for improving fragment hits against the GPCR A_2A receptor.

 

Jack Sadowsky, who also presented at DDC this past spring, described how he and his colleagues at Kimia are using D2B in combination with machine learning to develop selective inhibitors of kinases while also improving their in vitro ADME properties. This effort entailed making and testing tens of thousands of compounds from a virtual space of some 80 million molecules.

 

But even small-scale D2B can be valuable. Trevor Sherwood described how he and his colleagues at BMS used D2B to make and test 663 molecules to improve the potency of an EP4 agonist identified from a high-throughput screen. This involved multiple reaction types, including photoredox chemistry, for which they built a custom-designed reactor to evenly heat and illuminate the microtiter plates. The D2B work was done in parallel with medicinal chemistry, but interestingly the development candidate BMS-986526 came directly from the D2B work and has entered a phase 1/2a trial for rheumatoid arthritis.

 

There were other talks and posters on D2B that I missed, but I did attend two breakfast roundtables on the topic that were quite lively despite happening at 7:30 – a testament to the interest in the topic.

 

“Traditional” fragment-based drug discovery

At a plenary panel moderated by Drug Hunter’s Dennis Hu on drugging difficult targets, Biogen’s Klaus Urbahns asked the other panelists if they were still doing fragment-based lead discovery. John Tallarico of Novartis and Ian Storer of AstraZeneca immediately said yes. And in a separate presentation, Kris Borzilleri described how she and her Pfizer colleagues used fluorine-detected NMR and fragment optimization to identify ligands for an orphan GPCR.

 

Debanu Das described using high-throughput crystallography screening at XPose Therapeutics, now part of Mid-Atlantic BioTherapeutics, to identify inhibitors of DNA damage response pathway proteins. Although the initial hits had no detectable activity, SAR by catalog was able to get to nanomolar inhibitors of the protein APE1, which is overexpressed in ovarian cancer, in a matter of weeks.

 

But perhaps the most robust validation of FBDD was provided by Steve Fesik of Vanderbilt, who described a decades-long effort to drug the MYC pathway, which is probably dysregulated in almost all cancers. We described some of his published work on WDR5 here, but he is now making progress against MYC itself. This has not been easy: MYC is intrinsically disordered, and SAR-by-NMR screens against both the transactivation domain and the DNA-binding domain failed. However, MYC forms a structured leucine-zipper heterodimer with the protein MAX, and screening this complex yielded hits at the DNA binding interface. (Earlier this year we described work from Novartis on a different leucine zipper.) The hits have been optimized to low nanomolar binders that disrupt DNA binding, unlike a slide full of other (alleged) MYC inhibitors, including high-profile commercially available compounds such as MYCi361 and MYCi975.

 

I’ll close – hopefully before you stop reading. If you attended, what talks or posters stood out? And if you wish you had attended, mark your calendar for Oct. 18-21 next year, when DoT returns to Boston in time for peak leaf-peeping season.

Twenty-First Annual Fragment-Based Drug Discovery Meeting

Last week some 875 people attended the CHI Drug Discovery Chemistry (DDC) meeting in San Diego. I can’t do justice to the 40 or so presentations I attended over four days but can highlight some of the main themes.

 

Reversible fragments

Membrane targets such as G protein-coupled receptors (GPCRs) pose a challenge for biophysical methods, but three talks presented progress. Matthew Eddy (University of Florida Gainesville) described high-resolution magic angle spinning (HRMAS) NMR, which entails spinning isolated cellular membranes containing GPCRs at high speed (4 kHz!), which miraculously yields sharp NMR signals for bound ligands. Matthew demonstrated applications with the human adenosine A_2A receptor and weak (mM) ligands. He noted that the technique can work with native, poorly expressed proteins, though data collection times can be upwards of 30 minutes.

 

Kris Borzilleri described using ¹⁹F NMR to find ligands against an orphan GPCR at Pfizer. The 2287 fragments screened yielded 87 hits, of which 38 confirmed by SPR. SAR studies eventually yielded low micromolar ligands, but these were difficult to advance in the absence of structure (see here for a more successful example from Merck).

 

Vanessa Porkolab (Eurofins Cerep) described using the Nanotemper Spectral Shift technology to screen 826 fragments against the adenosine A_2A receptor at 300 µM, with a 9.2% hit rate. Many of these ligands stabilized the GPCR in a thermal shift assay and seven were even active (as antagonists) in a cellular assay.

 

Turning to soluble proteins, Paola Di Lello presented a case study from Genentech and Vernalis applying ligand-observed NMR to the protein phosphatase PTPN22. Subsequent protein-observed NMR revealed that most of the 16 validated hits bound to two pockets some distance from the active site. The fragments were optimized to mid-micromolar affinity but showed no functional activity.

 

And Charlotte Hodson presented the eIF4E story from Astex. As we discussed last year, this yielded a low nanomolar ligand that did not have the desired cellular effects. Charlotte noted that subsequent genetic experiments were consistent with the limited efficacy. Still, the target was sufficiently interesting that a chemical probe would have been pursued even knowing it would be high-risk.

 

Covalent ligands

Covalent approaches made appearances throughout the conference. Keriann Backus (UCLA) described chemoproteomic approaches to find cysteine-targeting ligands; she noted that gain of cysteine residues (such as G12C in KRAS) are the most common missense variants in cancer. Keriann also warned how covalent compounds can cause potentially misleading effects in cells, as she described in Nat. Chem. Biol. last year.

 

In 2021 we wrote about the SpotXplorer fragment library from György Keserű (Hungarian Research Centre for Natural Sciences). György has now prepared a PhotoXplorer library, which uses diazirine tags for photochemical screening, which we described here. The new library has produced high hit rates across a variety of targets. György also described a new sulfozone-based photoprobe that is easier to prepare than diazirines.

 

Kelly Craft recounted a DNA-encoded library (DEL) screen at AbbVie against the target BCL2A1, also known as BFL1. This produced an aldehyde-containing low micromolar binder that formed an imine with buried lysine 102. Uncomfortable progressing an aldehyde, the researchers sought to covalently engage cysteine 55, the same cysteine targeted by AstraZeneca, as we wrote about here. The progression included at least one dual-warhead molecule which was crystallographically confirmed to bind both the lysine and cysteine. The effort ultimately yielded cysteine-selective leads.

 

Earlier this year I described the dDRTC method we developed at Frontier Medicines for determining k_inact/K_I, and Svetlana Kholodar presented a nice overview of its scope and utility. My colleague Johannes Hermann spoke in more detail about our covalent technologies, particularly those using AI.

 

Chemical space and the exploration thereof

Brian Shoichet (UCSF) gave an entertaining and wide-ranging account of “directed and random walks in chemical space.” Brian has consistently been on the bleeding edge of high-throughput in silico screens, from 67,000 compounds in 2009 to 138 million molecules in 2019 to 4 billion molecules today. When docking artifacts are avoided (as we discussed here), bigger libraries consistently produce more potent hits for more targets – an observation strikingly consistent with Alex Shaginian’s in 2023 as HitGen expanded their DEL libraries from billions to more than a trillion molecules. Brian is developing methods to computationally screen the >4 trillion make-on-demand molecules now available from companies such as Enamine.

 

Direct-to-biology (DTB) approaches, which rely on microscale chemical reactions screened without purification, have become increasingly popular methods for exploring chemical space. Jack Sadowsky correctly stated that Carmot was the first company formed around this approach; we previously wrote about the role Chemotype Evolution played in the discovery of sotorasib. Jack described how Kimia, which spun out of Carmot, has continued to advance the technology, applying it to find inhibitors selective for single members of closely related kinase families.

 

Allan Jordan described how Sygnature Discovery is applying DTB in a variety of assays including microsome stability and crystallography. (We wrote about crude reaction screening by crystallography earlier this year.) Expanding beyond DTB, Allan called their platform direct-to-discovery, and discussed how it led to a preclinical candidate with STORM Therapeutics in just 18 months.

 

WuXi Apptec is also using DTB. Peichuan Zhang described starting with ligands derived from fragment and DEL screens against the E3 ligase GID4 to make PROTACs to degrade BRD4; DTB was used to explore a wide range of different linkers. And Daniel Blair (St. Jude) described using DTB and affinity selection-mass spectrometry (AS-MS) to find new molecular glues for the oncology target LCK.

 

Computers, DEL, and DTB are not the only way to explore chemical space. Last year we covered Tom Kodadek’s bead-based screening approach at University of Florida Scripps, and Tom presented two talks on the topic, one using macrocycles to find binders to difficult targets such as PTP1B and one using small molecules to find molecular glues.

 

Speaking of PROTACs and glues, plenary keynote speaker Alessio Ciulli (University of Dundee) discussed the “evolution and future of targeted protein degradation.” Alessio noted that there are >25 PROTAC degraders and >10 glues in the clinic, though these collectively target only a small number of E3 ligands, so there is plenty of opportunity for the area to expand.

 

For many of us in industry, drugs represent the most privileged points in chemical space, and these often look quite different than we assume, as Dean Brown (Jnana) noted in his recent analysis of 104 oral small molecule drugs approved by the FDA from 2020 to 2024 (which we mentioned here). Some drugs contain eye-raising moieties such as acetylenes, styrenes, N-O bonds, and nitro groups. Indeed, it is worth remembering that venetoclax, arguably the most successful fragment-derived drug, sports a nitro group.

 

But before getting too complacent, Jonathan Baell (Manas) warned about frequent hitters in libraries of FDA-approved drugs. He notes in Eur. J. Med. Chem. earlier this year that many commercial libraries are actually enriched for molecules that cause spurious biological activity. Jonathan calls on library vendors to remove particularly egregious compounds, though I’d settle for world peace.

 

I’ll close on that pleasant thought, but please feel free to comment. I hope to see you in San Diego next year April 19-22 for the twenty-second iteration of DDC.

Twelfth Novalix Biophysics in Drug Discovery Conference

Last week the Twelfth Novalix Biophysics in Drug Discovery Conference was held for the first time in La Jolla, California. It’s been several years since I wrote about one of these, and I was happy to see that they’ve maintained their reputation for excellent science and convivial conversation. There’s no way to cover the two-dozen talks, but here are a few highlights.

 

One of the things I most enjoy about these meetings is learning about new and emerging methods, and these were well represented. Chris Brosey (AbbVie) discussed time-resolved high-throughput small-angle X-ray scattering (TR-HT-SAXS). As I discussed a couple years ago, the approach can be used to measure the kinetics of protein dimerization in response to fragment-sized ligands.

 

SAXS-based approaches typically require access to a synchrotron, but Takashi Sato (Rigaku) described a related approach, electron density tomography (EDT), using an in-house instrument. Using machine learning, EDT can provide more detailed structural information than standard SAXS, and Takashi provided examples for samples ranging in size from viruses to single-chain variable fragments (scFvs) smaller than 30 kD.

 

Another approach to examine protein complexes is microfluidic diffusional sizing (MDS), described by James Wilkinson of Fluidic Sciences. By assessing the amount of diffusion in disposable chip-based chambers, MDS can determine how the hydrodynamic radius changes in response to ligands. Each chip holds 24 samples, and data can be collected in less than an hour. The minimum observable size change is 5-10% so measuring small molecules directly is unlikely. Still, the technique is useful for observing induced proximity events such as those caused by molecular glues, and it is sufficiently robust that it can be run in pure serum.

 

Among solution-based methods, none have achieved such recent prominence as cryo-EM. Weiru Wang, my colleague at Frontier Medicines, described how this technique was used iteratively to design and characterize bivalent degrader molecules that covalently exploit the E3 ligase DCAF2. (We recently published this work in Structure.)

 

Cryo-EM has revolutionized the types of biological molecules that can be structurally characterized. According to Denis Zeyer (Novalix), the technique accounted for 40% of PDB entries last year. However, despite the “resolution revolution,” most structures are not as detailed as those from X-ray crystallography; Denis noted that only 20% of the new structures were solved to a resolution better than 3 Å, which may have negative implications for machine-learning methods trained on these lower resolution structures.

 

If cryo-EM is the new kid in town, NMR is the grizzled veteran. But proving that it is possible to find new applications for old methods, Matthew Eddy (University of Florida) described a clever ¹⁹F-labeling approach for GPCRs in nanodiscs to quantify the distribution of various states in response to anionic lipids and ligands. This has allowed him to distinguish between antagonists and inverse agonists, which can be difficult using cell-based assays.

 

Turning from solution-based to surface-based methods, SPR has moved into the number two slot for fragment-finding, as we noted in our recent poll. Just as there are new tricks for NMR, the same applies to SPR. Matthew Peterfreund (Bruker Biosensors) described switchSENSE, a fluorescence proximity assay built on an SPR chip that is useful for measuring the binding and kinetics of bifunctional ligands such as PROTACs to two or more proteins. He also introduced the Triceratops SPR#64 instrument, which as its name implies supports 64 sensor spots.

 

Kris Borzilleri (Pfizer) discussed SPR-microscopy (SPRm), which combines an optical microscope with an SPR instrument. This can be used to measure the affinities of ligands binding to receptors in cells grown on SPR chips, and Kris described applications to membrane proteins such as GPCRs and solute carriers. The technique is still quite slow though, at only 10-15 compounds in duplicate per week.

 

Another surface-based approach to screening cells was described by Volker Gatterdam of Lino Biotech. Focal molography relies on changes in diffraction from nanoengineered diffraction gratings, called molograms. Targets, which can include living cells, are immobilized to the molograms, and analyte is flowed over. The instrument contains 64 spots, and assays can be run in complex samples such as tissue lysates.

 

Covalent drug discovery also made an appearance, with talks by Landon Whitby (Lundbeck) and Ben Cravatt (Scripps). Landon provided an overview of chemoproteomics techniques to screen ligands in cells, such as those we wrote about in 2016. Ben continued the theme, including several success stories, and also discussed challenges for finding cryptic ligandable pockets. Despite impressive progress with machine learning, Ben noted that these methods often find only common solutions, while empirical chemoproteomics methods can find rare types of pockets.

 

Of course, as we’ve repeatedly emphasized, biophysics methods are best used in combination, as noted by Daniel Harki (University of Minnesota) and Ann Boriack-Sjodin (Takeda). Daniel presented a screen of 1056 fragments against the cancer target APOBEC3 using NMR and SPR. This yielded just a single validated hit, which interestingly turned out to be the same fragment found against KRAS in a paper we discussed in 2022. And Ann described how biophysics led to multiple clinical compounds against a variety of targets at Epizyme and Accent Therapeutics.

 

I’ll stop here, but please feel free to add your thoughts. And while the date for the next Novalix conference has not yet been scheduled, the location has, with a return to beautiful Strasbourg. Vive la biophysique!

Fragment events in 2026

Lots of interesting events coming up this year - hope to see you at one!

February 17-19:  The Twelfth NovAliX Conference will be held for the first time in San Diego! You can read my impressions of the 2018 Boston event here, the 2017 Strasbourg event here, and Teddy's impressions of the 2013 event here, here, and here. 

 

April 13-16: CHI’s Fragment-Based Drug Discovery turns 21, old enough to legally drink in the US! The longest-running annual fragment event returns as usual to San Diego. This is part of the larger Drug Discovery Chemistry meeting. You can read impressions of the 2025 meeting, the 2024 meeting, the 2023 meeting, the 2022 meeting, the 2021 virtual meeting, the 2020 virtual meeting, the 2019 meeting, the 2018 meeting, the 2017 meeting, the 2016 meeting; the 2015 meeting here, here, and here; the 2014 meeting here and here; the 2013 meeting here and here; the 2012 meeting; the 2011 meeting; and the 2010 meeting. 

May 10-12: Industrial Biostructures of America will be held in Cambridge, MA. The meeting covers all aspects of structural biology including FBLD, membrane proteins, allostery, cryo-EM, machine learning, and more. 

September 14-16: Fragments X, RSC-BMCS Tenth Fragment-based Drug Discovery Meeting, will be held in Cambridge, UK.  You can read my impressions of the 2024 meeting, the 2013 meeting, and the 2009 meeting.

September 28 to October 1: CHI’s Twenty-Fourth Annual Discovery on Target will be held as always in Boston. As the name implies this event is more target-focused than chemistry-focused, but there are always plenty of FBDD-related talks. You can read my impressions of the 2025 meeting, the 2024 meeting, the 2023 meeting, the 2022 meeting, the 2021 meeting, the 2020 virtual meeting, the 2019 meeting, and the 2018 meeting.

 

November 10-12: CHI holds its third Drug Discovery Chemistry Europe in beautiful Barcelona. This will likely include tracks on lead generation, protein-protein interactions, degraders and glues, and machine learning, with multiple fragment talks throughout. 

Know of anything else? Please leave a comment or drop me a note.

Review of 2025 reviews

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.

Twentieth-Third Annual Discovery on Target Meeting

The CHI Discovery on Target (DoT) meeting was held last week in Boston. More than 850 people from 24 countries attended, 75% from industry. As usual I’ll just touch on some broad themes.

 

Covalent approaches

Covalent approaches were prominent throughout the conference. One of the very first talks was by Stefan Harry (Harvard/MGH), who described screening 416 cancer cell lines with three reactive “scout probes,” identifying some 6000 cysteine residues that could be covalently liganded. There are some interesting cell and context-dependent differences, and all the data are publicly available and easily searchable through a free online portal called DrugMap. He is now profiling a library of dual-electrophile-containing compounds to identify molecular glues.

 

Knowing which cysteines can be targeted is the first step for covalent drug discovery, and Sherry Ke Li described how she and colleagues at Genentech go about finding ligands. They’ve experimentally determined the reactivity of more than 6400 compounds against free cysteine and used this to train a machine-learning model to predict chemical (as opposed to specific) reactivity. Mass spectrometry (MS) using isolated proteins is the workhorse screening approach, but Sherry also described using variable temperature surface plasmon resonance (SPR) to dissect the individual components of k_inact/K_I.

 

AstraZeneca has also been doing considerable covalent screening, and Hua Xu briefly described the BFL1 story we wrote about here. In addition to pure proteins, they are now also starting to screen their covalent library in cells. Hua also presented earlier work from Pfizer on the discovery of the covalent kinase inhibitor ritlecitinib, which started with a noncovalent binder. Proteomic studies revealed that in addition to the intended target JAK3, it hits other TEC-family kinases too.

 

Adding a covalent warhead to a reversible binder is also the approach taken by MOMA Therapeutics in the discovery of their clinical WRN inhibitor MOMA-341, as presented by Momar Toure. They ended up targeting the same cysteine as Vividion (see here), though the binding mode is somewhat different. MOMA is also pursuing covalent fragment screening using intact protein MS, and Brian Sosa-Alvarado described how they were able to identify nanomolar inhibitors of RAD54L within six months of starting the program, aided by DNA-encoded libraries (DEL).

 

Not everyone is pursuing cysteine: Ken Hsu described how he and his team at University of Texas Austin are using sulfur-triazole exchange chemistry (SuTEx) to target tyrosine residues across the proteome. He noted that although cysteine could react with this warhead, the resulting thiosulfonate would be unstable. This is true in general, but I wonder if, just like the reversible cyanoacrylamide warheads we wrote about more than a decade ago, they could be stabilized within folded proteins.

 

Noncovalent approaches

Covalency is not the only game in town, as exemplified in a talk by Emma Rivers on “integrated hit discovery” at AstraZeneca. I was tickled that she grouped FBLD with HTS as “traditional” approaches, onto which they’ve added DEL and peptide libraries. Importantly, they’re focused on generating and capturing as much high-quality data as possible to enable machine learning – a topic we’ll touch on more below.

 

Nor are proteins the only target; there was a whole track on RNA- and DNA-targeting small molecules, where Benjamin Brigham described the plate-based equilibrium dialysis-based approach taken at Atavistik to screen metabolites and metabolite-like molecules. This led to two fragment-sized hits against RNA encoding SERPINA1, and although the affinities are modest, they do inhibit translation in a cell-free system.

 

At FBLD 2018 Astex presented the first cryo-EM structure of a fragment-protein complex, noting that throughput was an issue. The company has leaned into that challenge and now has three microscopes, including a top-of-the-line Krios, with another on the way. Miguel Zamora-Porras described how they have now solved hundreds of structures. Their Krios can collect data on two compounds per day, and the full cycle time from protein-ligand preparation to structure is about a week. Miguel described how structures of ligands bound to the ion channel protein TRPML1 helped reveal why some were agonists and others antagonists.

 

Data and its discontents

On the subject of structures, Steve Burley (Rutgers) gave an eloquent history and defense of the “RCSB Protein Data Bank: an open access research resource that benefits all humanity.” From its humble beginnings with just seven structures in 1971, the PDB now contains more than 240,000. And these are not just of scientific interest: all 88 of the new molecular entities the FDA approved for oncology between 2010 and 2023 had PDB structures that informed the biology or druggability, and 75% of the efforts involved structure-based design. Steve also mentioned that the question of where and how to store large-scale crystallographic data will be discussed in a meeting sometime in the spring of next year. Finally, Steve is hoping to retire from his position as Director of the RCSB PDB, so if you’re looking to make an impact, please apply.

 

The dramatic advances in protein structure prediction exemplified by AlphaFold would not have been possible without the PDB, but unfortunately the same high-quality information on protein-ligand binding modes and affinities is not available, as noted by Woody Sherman of Psivant. To illustrate the importance of training data, Woody asked ChatGPT to produce a picture of an analog clock set to 6:32. The result? A clock with three hands, one at 10, one at 2, and one at 6, because most images of clocks are set to 10:10.

 

Woody asked whether machine-learning-based docking can extrapolate or just interpolate. Although impressive results have been reported for some protein-ligand complexes, it turns out that there are often similar ligands in the training data. For truly novel ligands, the predictions tend to fall flat. Similarly, allosteric ligands are often (mis)placed into an orthosteric site – just because the model has been trained that that’s where ligands should go. Indeed, although Psivant is heavily invested in computational approaches, Woody mentioned that they often use “wet” approaches for finding initial chemical matter.

 

On the subject of dubious data, Al Edwards (University of Toronto) noted that a third of all immunofluorescence images in the literature use antibodies that give signals in knockout cells. And as we wrote just last month, many reported small molecule “probes” are just as bad. Al is CEO of the Structural Genomics Consortium, whose ambitious Target 2035 aims to find a pharmacological probe for every target in the human genome. As a starter, they’re aiming for 2000 probes in the next five years. They’re using affinity-selected mass spectrometry (ASMS), screening pools of 500 compounds and 8 proteins at a time, and are getting micromolar hits against about 30% of targets. They’re accepting protein submissions, so if you’re looking for starting points against your favorite protein contact them.

 

I’ll end here, but please leave comments. And mark your calendar for Sep. 28 to Oct. 1 next year, when DoT returns to Boston.

Fragment events in 2025 and 2026

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.

September 21-24: FBLD 2025 will be held in the original Cambridge (UK),  where it was supposed to be held in 2020. This will mark the ninth in an illustrious series of conferences organized by scientists for scientists. You can read impressions of FBLD 2024, FBLD 2018, FBLD 2016, FBLD 2014, FBLD 2012, FBLD 2010, and FBLD 2009. 

 

September 22-25: You'll need to make a tough choice: FBLD 2025 or CHI’s Twenty-Third Annual Discovery on Target in Boston. As the name implies this event is more target-focused than chemistry-focused, but there are always plenty of FBDD-related talks. You can read my impressions of the 2024 meeting, the 2023 meeting, the 2022 meeting, the 2021 meeting, the 2020 virtual meeting, the 2019 meeting, and the 2018 meeting.

 

November 11-13: CHI holds its second Drug Discovery Chemistry Europe in beautiful Barcelona. This will include tracks on lead generation, protein-protein interactions, degraders and glues, and machine learning, with multiple fragment talks throughout. 

2026

February 17-19:  The Twelfth NovAliX Conference will be held for the first time in San Diego! (Please note the date and location change.) You can read my impressions of the 2018 Boston event here, the 2017 Strasbourg event here, and Teddy's impressions of the 2013 event here, here, and here. 

 

April 13-16: CHI’s Fragment-Based Drug Discovery turns 21, old enough to legally drink in the US! The longest-running annual fragment event returns as always to San Diego. This is part of the larger Drug Discovery Chemistry meeting. You can read impressions of the 2025 meeting, the 2024 meeting, the 2023 meeting, the 2022 meeting, the 2021 virtual meeting, the 2020 virtual meeting, the 2019 meeting, the 2018 meeting, the 2017 meeting, the 2016 meeting; the 2015 meeting here, here, and here; the 2014 meeting here and here; the 2013 meeting here and here; the 2012 meeting; the 2011 meeting; and the 2010 meeting. 

September 14-16: RSC-BMCS Tenth Fragment-based Drug Discovery Meeting will be held in Cambridge, UK.  You can read my impressions of the 2024 meeting, the 2013 meeting, and the 2009 meeting.

 

Know of anything else? Please leave a comment or drop me a note.

Twentieth Annual Fragment-Based Drug Discovery Meeting

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 70% from industry and 28% from outside the US. I personally attended more than three dozen talks over the four days and will just touch on some broad themes.

 

Noncovalent approaches

Steve Fesik (Vanderbilt) gave two talks, the first of which was focused on “FBDD tips for success.” This opinionated and entertaining romp revealed lessons learned across several projects on difficult targets such as KRAS. Another holy grail oncology target is MYC, which is largely disordered. A two-dimensional NMR screen against the protein failed to yield any hits, but a screen of the MYC:MAX heterodimer provided hits which have been optimized to high nanomolar potency and are able to block DNA binding.

 

The second talk was focused on E3 ligases, a target class Steve has been pursuing for the past decade. Steve is particularly interested in E3 ligases such as CBL-C, TRAF4, and KLHL12 that are differentially expressed in certain tissues. In the case of KLHL12, which is not found in heart tissue, an NMR-based screen led to fragment hits that were ultimately optimized to mid-nanomolar binders and could be turned into bivalent degraders for Bcl-xL and β-catenin.

 

When asked about his second favorite fragment-finding method after protein-detected NMR, Steve mentioned SPR. The throughput for SPR has historically been modest, but John Quinn (Genentech) described the new Carterra Ultra, which is capable of screening 96 proteins simultaneously while retaining good sensitivity. John screened 3000 fragments at 500 µM against multiple proteins in just two weeks, which provided an immediate assessment of both protein ligandability and fragment selectivity. Interestingly, and in contrast to some other analyses, shapelier fragments had similar hit rates to flatter fragments.

 

Several talks focused on fragment-to-lead success stories, some of which we’ve covered on Practical Fragments, such as RIP2 kinase inhibitors that started from flat fragments and were evolved to more three-dimensional leads as described by Mark Elban (GSK). John Taylor discussed pan-RAS inhibitors discovered at Cancer Research Horizons, the subject of an upcoming post. Andrew Judd (AbbVie) described the discovery of ABBV-973, a potent STING agonist that could be useful for certain types of cancer. And Justyna Sikorska described the discovery of a non-covalent WRN inhibitor at Merck. This is a nice complement to Vividion’s covalent WRN inhibitor, which we wrote about here and which was presented by Shota Kikuchi. Interestingly, structural biology was not enabled until late in this project.

 

One of the earliest arguments for fragment linking was the concept of avidity, and this underlies the basis of a technology discussed by Tom Kodadek and Isuru Jayalath at University of Florida Scripps. The idea is to immobilize fragments onto TentaGel beads, each the size of a red blood cell. These can be screened against multivalent proteins using either simple plate-based assays or FACS, the idea being that even if an individual protein-ligand interaction is weak, a multimeric protein can interact with several ligands on a single bead for enhanced binding. The researchers validated the concept with streptavidin, and also used it to find millimolar binders to the proteasome subunit Rpn13.

 

Last year we wrote about using photoaffinity crosslinking with fully functionalized fragments (FFFs) to identify non-covalent ligands to thousands of proteins in cells, and this was the subject of several talks. Chris Parker (Scripps) has mapped more than 7000 binding sites and described the discovery of an inhibitor against the inflammatory target SLC15A4. Interestingly, the molecule binds what appears to be a disordered region, though Chris speculated that it adopts a more defined structure in cells.

 

Belharra has gone all in on using FFFs, and Jarrett Remsberg and Andrew Wang described the construction of a diverse >11,000-membered FFF library, 88% of which consists of enantiomers. This has been screened against 13 different oncology and immunology cell lines to identify enantioselective or chemoselective hits against >4000 proteins including STAT3, IRF3, and AR.

 

Covalent approaches

The FFF approach uses covalent bond formation to trap a noncovalent ligand, but of course covalent ligands are all the rage these days, as we noted just last week. Dan Nomura (UC Berkeley) described the identification of stereoselective covalent ligands against a disordered region of cMYC that seem to work by destabilizing the protein in cells. Similarly, covalent ligands against the largely disordered AR-V7 also seem to destabilize the protein. It will be interesting to explore the mechanism of these molecules to see whether the proteins are more ordered inside cells.

 

Jin Wang (Baylor College of Medicine) described a chemoproteomic approach called Fragment Probe Protein Enrichment (FraPPE) which entails linking covalent fragments to a desthiobiotin tag. Labeled proteins are then pulled down, proteolyzed, and analyzed by mass spectrometry. In contrast, competition methods such as those described last year pull down labeled peptides after proteolysis. The advantage of FraPPE is that it can capture multiple peptides from each pulled-down protein, leading to fewer false negatives.

 

Of course, not every application of covalent discovery involves chemoproteomics. Joe Patel, who co-organized FBLD 2016, described the Nexo Therapeutics platform. They’ve built from scratch a library of >12,000 fragments, a third of which contain stereocenters. Each member is rule-of-three compliant before adding the warhead, meaning that the final molecules can be larger, which as we noted earlier this month is probably a good idea. To date Nexo has successfully screened more than a dozen targets using intact protein mass spectrometry.

 

The Nexo library targets not only cysteines but other residues as well, and Maurizio Pellecchia (UC Riverside) described using sulfonyl fluorides and fluorosulfates to target histidine residues. He and his group screened a library of 600 fluorosulfate-containing fragments (MW 250-350 Da) against the oncology target MCL1 and found several that stabilized the protein towards thermal denaturation. Crystallography confirmed covalent bond formation.

 

Most covalent fragments are electrophilic so that they can react with nucleophilic protein residues, but as we noted in 2022 it is possible to do the reverse. Megan Matthews (University of Pennsylvania) described how she used chemoproteomics to discover the mechanism of action for hydralazine, a drug that has been used since 1949 to treat hypertension. This fragment-sized (MW 160 Da!) molecule irreversibly alkylates a histidine residue within the active site of the enzyme ADO, a target that has also been implicated in gliobastoma.

 

Plenary Keynotes

The approval of the covalent BTK inhibitor ibrutinib in 2013 arguably marks the start of the modern era of covalent drug discovery, and Chris Helal described Biogen’s efforts against this target using reversible inhibitors, irreversible inhibitors, and degraders. Chris traced the origin of their phase-2 BIIB091 to a collaboration with Sunesis that used Tethering, so perhaps we should include this molecule in our list of fragment-derived clinical compounds.

 

Phil Baran of Scripps, who last spoke at the conference in 2020, gave the secondary plenary keynote. After stating that “medicinal chemists are the backbone of society,” he then detailed multiple examples of how they’ve been doing things wrong. Fortunately, he provided useful chemistry solutions, with “useful” defined as reactions that are operationally simple, have wide scope, and require only readily available reagents. Rather than deploying tedious protecting group installations and deprotections, Phil uses radical chemistry to directly generate carbon-carbon bonds between or within complicated molecules. His goal is to make the chemistry so simple and practical as to be boring, and he illustrated the point by showing his teenage daughter successfully running a reaction.

 

I’ll end here, but please leave comments. And mark your calendar for April 13-16 next year, when DDC returns to San Diego.

Fragment events in 2025

After a bumper year for conferences in 2024, this year is also shaping up to be eventful. 

April 14-17: CHI’s Twentieth Annual Fragment-Based Drug Discovery, the longest-running annual fragment event, returns as always to San Diego. This is part of the larger Drug Discovery Chemistry meeting. You can read impressions of the 2024 meeting here, the 2023 meeting here, the 2022 event here, the 2021 virtual meeting here, the 2020 virtual meeting here, the 2019 meeting here, the 2018 meeting here, the 2017 meeting here, the 2016 meeting here; the 2015 meeting here, here, and here; the 2014 meeting here and here; the 2013 meeting here and here; the 2012 meeting here; the 2011 meeting here; and 2010 here. 

 

May 5-6: Returning after a five year hiatus, Industrial Biostructures of America will be held in Cambridge, MA and includes a session on FBLD. 

June 2-4:  The Eleventh NovAliX Conference returns to the stunning city of Strasbourg. You can read my impressions of the 2018 Boston event here, the 2017 Strasbourg event here, and Teddy's impressions of the 2013 event here, here, and here.

September 21-24: FBLD 2025 will be held in the original Cambridge (UK),  where it was supposed to be held in 2020. This will mark the ninth in an illustrious series of conferences organized by scientists for scientists. You can read impressions of FBLD 2024, FBLD 2018, FBLD 2016, FBLD 2014, FBLD 2012, FBLD 2010, and FBLD 2009. 

 

September 22-25: You'll need to make a tough choice: FBLD 2025 or CHI’s Twenty-Third Annual Discovery on Target. As the name implies this event is more target-focused than chemistry-focused, but there are always plenty of FBDD-related talks. You can read my impressions of the 2024 meeting here, the 2023 meeting here, the 2022 meeting here, the 2021 event here, the 2020 virtual event here, the 2019 event here, and the 2018 event here.

 

Finally, from November 11-13 CHI holds its second Drug Discovery Chemistry Europe in beautiful Barcelona. This will include likely tracks on lead generation, protein-protein interactions, degraders, machine learning, and probably several fragment talks. 

   

Know of anything else? Please leave a comment or drop me a note.

Review of 2024 reviews

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 KRAS^G12C.

 

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-x_L 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.