In innovative drug discovery, identifying compounds for "difficult-to-drug" targets remains an ongoing challenge. Recently, Roche Group published a study in ACS Medicinal Chemistry Letters that systematically analyzed 21 projects targeting such difficult-to-drug targets completed within a three-year period. The study evaluated the effectiveness of various hit-finding strategies, with particular emphasis on the role of DNA-encoded library (DEL) technology, providing the industry with a reference framework based on real-world project data.

Key Finding 1: Correlation Between Target Classification and Project Success Rates
The study categorizes difficult-to-drug targets into two classes:

• Difficult-to-Drug (D2D) Targets: Targets with known or identifiable binding pockets, where it remains unclear whether binding will lead to the desired functional modulation (e.g., allosteric modulation, inhibition of protein-protein interactions).
• Difficult-to-Ligand (D2L) Targets: Targets lacking reliable structural information or assessed computationally as having no clearly druggable pocket (D-score < 0.7).

Figure 1. A diverse set of 21 difficult-to-drug targets and modes of action were analyzed.

Data analysis indicates that D2D targets show higher project advancement success rates. Among 7 D2D projects, 86% successfully yielded advanceable lead series, compared to 50% among 14 D2L projects. This suggests that target classification at the project outset can help predict technical success and guide resource allocation.

Key Finding 2: Performance Comparison of Screening Technologies
The study evaluated a total of 70 screening experiments across six common technologies. Figure 2 illustrates the frequency of each method's use across actual projects.

Figure 2. Multiple diverse screening methods were employed for a total of 70 screens on 21 projects. The graphic depicts the number of individual screens, color-coded by method.

In terms of breadth of application (Figure 3), DNA-encoded library technology was used in all 21 projects, high-throughput screening in 76% of projects, fragment screening in approximately half, while other methods were used less frequently.

Figure 3. Different hit finding methods were used with different frequency across the research units. Depicted is the percentage of projects for which a specific screen was used, e.g. a fragment screen was used on almost 50% of all projects.

Significant differences were observed in the performance of each method across two critical stages: "producing validated hits" and "conversion to lead series" (Figure 4 and table below):

Figure 4. Screening methods varied in their ability to produce validated hits and lead series. Plotted is the percentage of screens for each method that delivered validated hits (left columns) and lead series (right columns).

Data analysis reveals:

• DEL is widely applicable and demonstrates predictive value. This technology was used in all projects, achieved the highest success rate in yielding validated hits, and showed high positive predictive value (92%). This indicates that DEL can not only be used for hit identification but also serves as a reference tool for assessing target ligandability and guiding subsequent experimental strategies.
• High-throughput, covalent, and peptide screening show consistent performance in applicable contexts. These three methods each achieved a 50% success rate in advancing to lead series in applicable projects, demonstrating good reproducibility. They respectively offer advantages in functional activity screening, high-affinity binding, and large interface coverage.
• Fragment and virtual screening face challenges in the optimization phase. Although both performed reasonably well in initial hit identification, their success rates in optimizing hits into drug-like, advanceable lead series were low (<10%), suggesting they are more suitable for early exploratory phases.

Key Finding 3: Strategic Choices for Integrated Screening
The study identifies two common strategic approaches:

• "Broad Platform" Parallel Approach: Employing multiple screening technologies simultaneously to expand coverage of chemical space.
• "Focused" Sequential Approach: Concentrating resources on a limited combination of high-potential methods (e.g., DEL combined with HTS).

Data suggest that using more screening methods is not necessarily better. If three or more consecutive different screens on the same target fail to yield advanceable compounds, the likelihood of subsequent success may decrease significantly. Therefore, dynamically adjusting strategy based on target characteristics and early screening results can enhance R&D efficiency.

Conclusion
Roche's study not only provides strong evidence for the effectiveness of DEL technology but, more importantly, establishes an actionable decision-making framework. In an environment of rising drug development costs and increasing target difficulty, "informed integrated hit discovery" represents a strategic shift from experience-driven to data-driven thinking.

Looking ahead, with advancements in DEL technology itself (e.g., integrating machine learning for hit expansion), wider adoption of AI-based structure prediction tools, and the emergence of novel screening paradigms, we can anticipate the development of more intelligent and efficient integrated discovery platforms. These advancements hold the potential to transform more previously "undruggable" targets into revolutionary therapies for patients.

1. Gampe, C. M.; Worsdorfer, B.; Zou, G.; Ricci, A. Analyses of Recent Hit-Finding Campaigns for Difficult Targets Provides Guidance for Informed Integrated Hit Discovery. ACS Med. Chem. Lett. 2026. https://doi.org/10.1021/acsmedchemlett.5c00676

Christian M. Gampe , Bigna Wörsdörfer , Ge Zou , Antonio Ricci

ACS Medicinal Chemistry Letters

DOI: 10.1021/acsmedchemlett.5c00676

Abstract

Despite advancements in hit-finding technologies, many drug targets are considered difficult-to-drug (D2D) or difficult-to-ligand (D2L). Here, we present an analysis of 21 hit-finding campaigns across three research organizations within the Roche group, focusing on D2D and D2L targets. DNA-encoded library technology (DELT) was the most successful method in providing validated hits and lead series. High-throughput, covalent, and peptide screens also yielded progressable chemical matter in a substantial number of cases. In contrast, fragment and virtual screens, while effective in generating validated hits, demonstrated lower success rates. Stratifying targets into D2D and D2L categories provided a useful framework for estimating the likelihood of project success and informing additional screening strategies, with D2D targets showing higher rates of chemical enablement. Our findings indicate DELT as a valuable experimental tool for assessing ligandability and highlight the importance of informed integrated hit discovery by tailoring hit-finding strategies to target characteristics.

Yagong Wang , Huanqing Zhang , Fanming Zeng , Xue Zhao , Junyun Chen , Lijun Xue , Kexin Yang , Yun Jin Hu

DOI: 10.1002/asia.70611

Abstract

Dithiocarbamates (DTCs) are privileged scaffolds in medicinal chemistry, yet inaccessible via DNA-encoded libraries (DELs) due to a lack of robust on-DNA synthesis. We developed a general procedure for on-DNA DTC formation using a carbon disulfide (CS2) bridging strategy. This method efficiently links diverse aliphatic secondary amines and alkyl halides under mild conditions with high conversions and excellent DNA compatibility. The utility of this method was demonstrated by constructing a prototype DEL, thereby bridging a critical gap in chemical space and facilitating the rapid discovery of DTC-based therapeutics.

Sangeeta Pandey , Florent Samain , Omprakash Nacham , Jon D. Williams , Nathaniel L. Elsen

Expert Opinion on Drug Discovery

DOI: 10.1080/17460441.2026.2622373

Abstract

INTRODUCTION

Affinity selection mass spectrometry (AS-MS) is a powerful label-free technique for characterizing macromolecule-ligand interactions that has been used as a hit finding tool with significant success. Recent advances in MS and separation technology have positioned AS-MS to impact more areas of drug discovery.

AREAS COVERED

This manuscript provides a brief historical review of AS-MS and the recently developed technologies that have enabled AS-MS. The report also provides examples and references for how AS-MS has been used for high-throughput screening (HTS) to DNA-encoded library (DEL) screening hit confirmation, Direct-to-Biology, and natural product screens. The references for this work were collected from a broad range of sources, including Google Scholar, Scopus, review articles identified via Google Scholar, and the internal AI resource at AbbVie Inc.

EXPERT OPINION

AS-MS is a unique biophysical binding assay that does not rely on labels and can specifically detect binders from large pools of potential ligands based on molecular weight. There is still significant room for growth in areas of impact that will be driven by decreases in separation time and a move toward equilibrium conditions during separation. Increased use for driving rapid structure-activity relationships (SAR) has potential to decrease project cycle times in lead identification and optimization.

Francesco V Reddavide , Trine L Toft-Bertelsen , Ieva Drulyte , Aspen Rene Gutgsell , Dzung Nguyen , Sara Bonetti , Katerina Vafia , Anne-Sophie Tournillon , Stephan Heiden , Grosser Grosser , Katarina Iric , Veronica Diez , Nanna MacAulay , Stefan Geschwindner , Thompson Thompson , Jens Frauenfeld , Robin Loving

bioRxiv - Biochemistry

DOI: 10.64898/2026.01.27.701919

Abstract

Developing novel drugs against membrane proteins is a major challenge in drug discovery due to the difficulty of stabilizing these targets for high-throughput screenings. Pannexin 1 (PANX1) is a membrane channel protein involved in various physiological and pathological processes, making it a promising target for drug discovery. However, efforts to develop PANX1-targeting therapeutics have been hindered by the inherent challenges of stabilizing the protein channel and conducting effective pharmacological screening. Here, we report a proof-of-concept workflow that integrates the Salipro lipid nanoparticle platform with DNA-Encoded Library screenings in a detergent-free format. In this case study, the Salipro DirectMX method was used to generate functional PANX1 nanoparticles for drug discovery and characterisation. Using a high-stringency selection strategy and computational approaches, we identified a specific set of candidate compounds with selective PANX1 enrichment. Surface Plasmon Resonance analysis confirmed the identification of hit compounds. Cryo-Electron Microscopy of the Salipro-PANX1-Compound complex provided structural insights into a potential compound binding site. Electrophysiological recordings in PANX1-expressing Xenopus laevis oocytes demonstrated dose-dependent inhibition of PANX1-mediated ion conductance by the compounds. These findings establish a robust workflow for ligand discovery against challenging membrane protein targets and provide novel chemical starting points for the development of PANX1 modulators.

Baljit Kaur , Longfei Zhang , Hossam Nada , Laura Calvo-Barreiro , Moustafa Gabr

RSC Medicinal Chemistry

DOI: 10.1039/d5md00943j

Abstract

Chitinase-3-like protein 1 (CHI3L1, also known as YKL-40) has emerged as a central effector of astrocyte-mediated neuroinflammation and a promising biomarker for Alzheimer's disease (AD). However, small molecule CHI3L1 inhibitors that modulate neuroinflammation are limited. Here, we report the discovery of a CHI3L1-targeted small molecule, DEL-C1, identified through DNA-encoded library (DEL) screening and validated using orthogonal biophysical, computational, and cellular approaches. DEL-C1 demonstrated direct CHI3L1 binding in microscale thermophoresis (MST) and surface plasmon resonance (SPR) assays, with reversible and concentration-dependent association. Molecular docking and 100-ns molecular dynamics simulations revealed a stable binding mode within the CHI3L1 substrate groove, anchored by Tyr206 and flanked by Trp99 and Trp352, supporting a thermodynamically favorable interaction. In vitro ADME profiling indicated a balanced physicochemical profile, permeability, and metabolic stability, consistent with CNS drug-like properties. Functionally, DEL-C1 reversed CHI3L1-induced astrocyte dysfunction by restoring Aβ uptake, lysosomal acidification, and proteolytic activity, while reducing CHI3L1 and IL-6 secretion. DEL-C1 also suppressed CHI3L1-driven NF-κB transcriptional activation, highlighting its anti-inflammatory potential. Collectively, this study establishes DEL-C1 as a promising small molecule modulator of CHI3L1 and a chemical tool to interrogate astrocyte-driven neuroinflammation in AD.