About

Brian M. Paegel, Ph.D., is a Principal Investigator at the Paegel Lab. His work focuses on defeating druggability and democratizing drug discovery. The lab's research involves innovative approaches to ligand discovery, including the use of DNA-encoded libraries (DEL) and cellular screening techniques. Dr. Paegel's contributions are centered on advancing methods that facilitate the identification of new therapeutic compounds, making the process more accessible and efficient.

Research topics

• Combinatorial chemistry
• Organic chemistry
• Chemistry
• Biochemistry
• Computer Science
• Programming language
• Nanotechnology
• Computational biology

Selected publications

• Hydrogel-Bead Particles Enable Activity-Based Identification of Nucleic Acid Aptamer Enzyme Inhibitors

  Analytical Chemistry · 2025-09-15

  articleOpen accessSenior authorCorresponding

  Nucleic acid aptamers bridge the gap between small molecules and antibodies as potentially nonimmunogenic, stable, selective, and potent ligands. Aptamer discovery starts with massively parallel affinity selection-driven directed evolution, which only identifies sequences based on target binding. We have developed an activity-based aptamer screening system using magnetic beads templated with aptamer-encoding DNAs and encapsulated in polyacrylamide hydrogel droplets. Magnetic bead-bound DNAs are copied to the oligonucleotide-functionalized gel periphery via transcription-reverse transcription amplification. A model enzyme (trypsin) in-gel activity assay was developed wherein tryptic hydrolysis of a gel-immobilized N-terminal-Cy5-labeled trypsin substrate peptide is inhibited in the presence of gel-immobilized trypsin inhibitor aptamers, leaving the bead with high Cy5 fluorescence for sorting. Proof-of-concept screens enriched positive controls 100,000-fold in multiround screens. Though this study used DNA, the technology could also be applied to non-natural nucleic acids and other encoded library formats.

  PublisherOA PDFDOI

• Solid-phase DNA-encoded Library Technology

  2025-02-21

  book-chapterOpen accessSenior author

  Solid-phase DNA-encoded library (DEL) technology introduces advanced activity-based screening capabilities by virtue of its “one-bead-one-compound” (OBOC) format. In this review, we first describe the design and construction of so-called “OBOC-DELs.” We then explore the engineering of a microfluidic screening platform that integrates and automates high-throughput bead-based screening, highlighting examples of fluorescence-based functional assay development and miniaturization to microfluidic droplets. Additionally, we detail the statistical framework of OBOC-DEL screening experimental design and data interpretation. Finally, we summarize the numerous applications that have spawned since OBOC-DEL technology’s inception, including screening by biochemical activity, dose-response, cellular activity, competition binding affinity, and pharmacokinetic properties. Looking forward, there are likely further opportunities to employ bead-based synthesis and screening strategies to other encoded library modalities.

  PublisherDOI

• Solid-phase DNA-encoded library synthesis: a master builder’s instructions

  Nature Protocols · 2025-05-22 · 4 citations

  reviewOpen accessSenior author
  PublisherOA PDFDOI

• Building Block-Centric Approach to DNA-Encoded Library Design

  Journal of Chemical Information and Modeling · 2024-06-11 · 7 citations

  articleOpen accessSenior authorCorresponding

  DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.

  PublisherOA PDFDOI

• Activity-Based DNA-Encoded Library Screening for Selective Inhibitors of Eukaryotic Translation

  ACS Central Science · 2024-10-04 · 12 citations

  articleOpen accessSenior authorCorresponding

  Small molecule probes exist for only ∼2% of human proteins because most lack functional binding pockets or cannot be assayed for high-throughput screening. Selective translation modulation circumvents canonical druggability and assay development constraints by using in vitro transcription–translation (IVTT) as a universal biochemical screening assay. We developed an IVTT activity assay by fusing a GFP reporter to various target gene sequences and screened the target sequences for inhibitors in microfluidic picoliter-scale droplets using a 5,348-member translation inhibitor DNA-encoded library (DEL). Screening a proof-of-concept PCSK9-GFP reporter yielded many hits; 6/7 hits inhibited PCSK9-GFP IVTT (IC50 1–20 μM), and the lead hit reduced PCSK9 levels in HepG2 cells. Preliminary selectivity was informed by counterscreening the DEL against a frameshift mutant PCSK9-GFP reporter. A plug-and-play approach to assay development and screening was demonstrated by scouting the DEL for activity using reporter genes of targets with difficult-to-assay or even unknown function (RPL27, KRASG12D, MST1, USO1). This microfluidic IVTT DEL screening platform could scale probe discovery to the human proteome and perhaps more broadly across the tree of life.

  PublisherDOI

• Hydrogel-Encapsulated Beads Enable Proximity-Driven Encoded Library Synthesis and Screening

  ACS Central Science · 2023-07-13 · 5 citations

  articleOpen accessSenior authorCorresponding

  Encoded combinatorial library technologies have dramatically expanded the chemical space for screening but are usually only analyzed by affinity selection binding. It would be highly advantageous to reformat selection outputs to ”one-bead-one-compound” solid-phase libraries, unlocking activity-based and cellular screening capabilities. Here, we describe hydrogel-encapsulated magnetic beads that enable such a transformation. Bulk emulsion polymerization of polyacrylamide hydrogel shells around magnetic microbeads yielded uniform particles (7 ± 2 μm diameter) that are compatible with diverse in-gel functionalization (amine, alkyne, oligonucleotides) and transformations associated with DNA-encoded library synthesis (acylation, enzymatic DNA ligation). In a case study of reformatting mRNA display libraries, transcription from DNA-templated magnetic beads encapsulated in gel particles colocalized both RNA synthesis via hybridization with copolymerized complementary DNA and translation via puromycin labeling. Two control epitope templates (V5, HA) were successfully enriched (50- and 99-fold, respectively) from an NNK5 library bead screen via FACS. Proximity-driven library synthesis in concert with magnetic sample manipulation provides a plausible means for reformatting encoded combinatorial libraries at scale.

  PublisherOA PDFDOI

• Dose–Response Activity-Based DNA-Encoded Library Screening

  ACS Medicinal Chemistry Letters · 2023-08-21 · 9 citations

  articleOpen accessSenior authorCorresponding

  = 7 ± 2, 13 ± 2, and 1 ± 0.3 μM). Photochemical dose-response DEL screening data prioritized hits for synthesis, the rate-limiting step in DEL lead identification.

  PublisherDOI

• Translating the Genome into Drugs

  Accounts of Chemical Research · 2023-02-09 · 24 citations

  articleOpen accessSenior authorCorresponding

  The Human Genome Project ultimately aimed to translate DNA sequence into drugs. With the draft in hand, the Molecular Libraries Program set out to prosecute all genome-encoded proteins for drug discovery with automated high-throughput screening (HTS). This ambitious vision remains unfulfilled, even while innovations in sequencing technology have fully democratized access to genome-scale sequencing. Why? While the central dogma of biology allows us to chart the entirety of cellular metabolism through sequencing, there is no direct coding for chemistry. The rules of base pairing that relate DNA gene to RNA transcript and amino acid sequence do not exist for relating small-molecule structure with macromolecular binding partners and subsequently cellular function. Obtaining such relationships genome-wide is unapproachable via state-of-the-art HTS, akin to attempting genome-wide association studies using turn-of-the-millennium Sanger DNA sequencing.Our laboratory has been engaged in a multipronged technology development campaign to revolutionize molecular screening through miniaturization in pursuit of genome-scale drug discovery capabilities. The compound library was ripe for miniaturization: it clearly needed to become a consumable. We employed DNA-encoded library (DEL) synthesis principles in the development of solid-phase DELs prepared on microscopic beads, each harboring 100 fmol of a single library member and a DNA tag whose sequence describes the structure of the library member. Loading these DEL beads into 100 pL microfluidic droplets followed by online photocleavage, incubation, fluorescence-activated droplet sorting, and DNA sequencing of the sorted DEL beads reveals the chemical structures of bioactive compounds. This scalable library synthesis and screening platform has proven useful in several proof-of-concept projects involving current clinical targets.Moving forward, we face the problem of druggability and proteome-scale assay development. Developing biochemical or cellular assays for all genome-encoded targets is not scalable and likely impossible as most proteins have ill-defined or unknown activity and may not function outside of their native contexts. These are the dark undruggable expanses, and charting them will require advanced synthesis and analytical technologies that can generalize probe discovery, irrespective of mature protein function, to fulfill the Genome Project's vision of proteome-wide control of cellular pharmacology.

  PublisherOA PDFDOI

• Liposomal Permeation Assay for Droplet-Scale Pharmacokinetic Screening

  Journal of Medicinal Chemistry · 2023-04-19 · 6 citations

  articleOpen accessSenior authorCorresponding

  Combinatorial library screening increasingly explores chemical space beyond the Ro5 (bRo5), which is useful for investigating ”undruggable” targets but suffers compromised cellular permeability and therefore bioavailability. Moreover, structure–permeation relationships for bRo5 molecules are unclear partially because high-throughput permeation measurement technology for encoded combinatorial libraries is still nascent. Here, we present a permeation assay that is scalable to combinatorial library screening. A liposomal fluorogenic azide probe transduces permeation of alkyne-labeled molecules into small unilamellar vesicles via copper-catalyzed azide–alkyne cycloaddition. Control alkynes (e.g., propargylamine, various alkyne-labeled PEGs) benchmarked the assay. Cell-permeable macrocyclic peptides, exemplary bRo5 molecules, were alkyne labeled and shown to retain permeability. The assay was miniaturized to microfluidic droplets with high assay quality (Z′ ≥ 0.5), demonstrating excellent discrimination of photocleaved known membrane-permeable and -impermeable model library beads. Droplet-scale permeation screening will enable pharmacokinetic mapping of bRo5 libraries to build predictive models.

  PublisherOA PDFDOI

• Highly Parallelized Screening of Functionally Enhanced XNA Aptamers in Uniform Hydrogel Particles

  ACS Synthetic Biology · 2023-07-06 · 11 citations

  article

  Xeno-nucleic acid (XNA) aptamers based on evolvable non-natural genetic polymers hold enormous potential as future diagnostic and therapeutic agents. However, time-consuming and costly procedures requiring the purification of individual XNA sequences produced by large-scale polymerase-mediated primer extension reactions pose a major bottleneck to the discovery of highly active XNA motifs for biomedical applications. Here, we describe a straightforward approach for rapidly surveying the binding properties of XNA aptamers identified by in vitro selection. Our strategy involves preparing XNA aptamer particles in which many copies of the same aptamer sequence are distributed throughout the gel matrix of a polyacrylamide-encapsulated magnetic particle. Aptamer particles are then screened by flow cytometry to assess target binding affinity and deduce structure-activity relationships. This generalizable and highly parallel assay dramatically accelerates the pace of secondary screening by allowing a single researcher to evaluate 48-96 sequences per day.

  PublisherDOI

Recent grants

• NIH Grant DP2OD008535

  NIH · $3.0M · 2016

• NIH Grant F32GM073438

  NIH · $93k · 2007

• High-Throughput Droplet-Scale Functional Screening of DNA-Encoded Combinatorial Libraries

  NIH · $1.4M · 2017–2022

• NIH Grant R00GM083155

  NIH · $740k · 2011

• CAREER: A Route to Synthetic Cells

  NSF · $797k · 2013–2018

Frequent coauthors

• Richard A. Mathies

  University of California, Berkeley

  35 shared

• Alison M. Skelley

  12 shared

• V. Cavett

  University of California, Irvine

  11 shared

• Robert G. Blazej

  11 shared

• James R. Scherer

  10 shared

• Ryan A. Shenvi

  Scripps (United States)

  10 shared

• Wesley G. Cochrane

  Salk Institute for Biological Studies

  8 shared

• R. A. Street

  Palo Alto Research Center

  8 shared

Labs

• Paegel LabPI

Education

• Ph.D., Chemistry

  UC Berkeley

  2003

• B.S., Chemistry

  Duke University

  1998

Awards & honors

• NIH NRSA Postdoctoral Fellow
• NIH Pathway to Independence Award
• NIH Director's New Innovator Award
• NSF CAREER Award