About

Jonathan Sachs is a Professor and Department Head of the Department of Biomedical Engineering at the University of Minnesota Twin Cities. His research focuses on making innovative discoveries at the molecular scale by combining experimental biophysics and cell biology with sophisticated computational modeling using some of the world’s fastest supercomputers. His work aims to explain how molecules malfunction in inflammatory diseases such as arthritis and neurodegenerative diseases like Parkinson’s. He uses this knowledge to develop cutting-edge approaches for discovering new therapeutic strategies, including small molecule drug discovery and protein engineering. Sachs has a background in Mathematical Biochemistry from the University of Michigan and holds a PhD in Biomedical Engineering from Johns Hopkins University. His postdoctoral fellowship was supported by the NIH NRSA at Yale University. His research has contributed significantly to understanding membrane remodeling, receptor conformational dynamics, and protein interactions relevant to disease mechanisms.

Research topics

• Chemistry
• Biology
• Computer Science
• Biochemistry
• Genetics
• Physics
• Crystallography
• Computational biology
• Biophysics
• Bioinformatics

Selected publications

• Multiplexed Dark FRET Biosensors: An Accessible Live-Cell Platform for Target- and Cell-Specific Monitoring of Protein–Protein Interactions in 2D and 3D Model Systems

  ACS Sensors · 2026-02-06 · 2 citations

  articleSenior authorCorresponding

  Simultaneous monitoring of multiple protein-protein interactions in live cells remains a key challenge in biology and drug discovery. While multiplexed FRET enables parallel molecular readouts, existing approaches are often constrained by spectral overlap, complex instrumentation, or incompatibility with live-cell models. To overcome these limitations and increase accessibility to the broader biological community, we present multiplexed dark FRET (MDF), a genetically encoded platform that uses spectrally distinct donors (mNeonGreen, mScarlet-I3) paired with nonemissive acceptors (ShadowY, ShadowR). We first establish that MDF fluorophores exhibit minimal background FRET under co-expression, enabling clean separation of donor lifetimes under multiplexed conditions. Using fluorescence lifetime (FLT) detection, we demonstrate MDF's versatility through three biologically and translationally relevant examples: (1) cell-type-specific biosensing in organoids, as exemplified in 3D neuro-glial spheroids; (2) target specificity for drug discovery through discrimination of TNFR1 versus TNFR2 receptor conformations and selective FLT modulation by receptor-specific small molecules; and (3) protein misfolding, as exemplified through simultaneous monitoring of alpha-synuclein oligomerization and misfolding. We further show that MDF can be applied within a single cellular environment, demonstrating the feasibility of same-cell multiplexing under optimized transient transfection conditions. MDF provides a scalable framework for real-time, live-cell biosensing across high-throughput, target-specific, and tissue-level applications in complex biological systems.

  PublisherDOI

• Engineering Murine Cross‐Reactivity Into an Affibody to Human Death Receptor 5

  Biotechnology and Bioengineering · 2026-05-06

  articleOpen access

  ABSTRACT Interspecies cross‐reactive protein therapeutics that target conserved epitopes across species are critical for translational research. The present study showcases the engineering of an affibody molecule, originally discovered for binding to human death receptor 5 (hDR5) with 94 nM affinity, to simultaneously acquire cross‐reactivity to murine DR5 and enhance its binding affinity to human DR5. DR5 plays a pivotal role in metabolic dysfunction‐associated steatohepatitis (MASH) by mediating hepatocyte apoptosis and inflammation. Utilizing a rationally designed library guided by enrichment information and a helix‐walking mutagenesis strategy, combined with alternating binding selections between human and murine DR5, we evolved affibody variants exhibiting significantly improved binding to both receptors. Deep sequencing revealed amino acid preferences in the paratope, and the dominant variant, ABY DR5‐A , demonstrated over 1000‐fold and 16‐fold affinity improvements to murine and human DR5, respectively, with equilibrium dissociation constants of 15 and 5.8 nM. ABY DR5‐A exhibited nanomolar IC 50 values for antagonism of TRAIL‐induced DR5 signaling, measured via caspase 8 activation, in both murine and human cells, albeit with incomplete inhibition. This engineered affibody provides a promising candidate for therapeutic development targeting DR5‐mediated liver disease. Further functional characterization and pharmacokinetic optimization are required to advance these findings toward preclinical evaluation in murine MASH models and, ultimately, clinical applications.

  PublisherDOI

• Engineering Affibody Binders to Death Receptor 5 and Tumor Necrosis Factor Receptor 1 With Improved Stability

  Biotechnology and Bioengineering · 2025-03-05

  articleOpen access

  ABSTRACT Protein developability is an important, yet often overlooked, aspect of protein discovery campaigns that is a key driver of utility. Recent advances have improved developability screening capacity, making it an increasingly viable option in early‐stage discovery. Here, we engineered one component of developability, stability, of two affibody proteins—one that targets death receptor 5 and another that targets tumor necrosis factor receptor 1—previously evolved to bind receptor and non‐competitively inhibit signaling via conformational modulation. Starting from an error‐prone PCR library of each affibody, variants were screened via yeast surface display binder selections, including depletion of non‐specific binders, followed by developability assessment using the on‐yeast protease and yeast display level assays. Multiplex deep sequencing identified variants for further evaluation. Purified variants exhibited elevated stability—8°C to 14°C increase in T m,app —with maintained 1–2 nM affinity for the TNFR1 affibody and 30‐fold improvement in the DR5 affibody affinity to 0.8 nM.

  PublisherOA PDFDOI

• Multiplexed Dark FRET Biosensors: An accessible live-cell platform for target- and cell-specific monitoring of protein-protein interactions in 2D and 3D model systems

  Research Square · 2025-05-12

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Fluorescence Lifetime-Based FRET Biosensors for Monitoring N Terminal Domain-Dependent Interactions of TDP-43 in Living Cells: A Novel Approach for ALS and FTD Drug Discovery

  ACS Chemical Neuroscience · 2025-06-10 · 5 citations

  articleOpen accessSenior authorCorresponding

  model. These findings establish both the biosensors and the HTS platform as innovative tools for TDP-43 drug discovery and support an exciting translational approach for targeting TDP-43 proteinopathies.

  PublisherDOI

• Post-translational modification sites are present in hydrophilic cavities of alpha-synuclein, tau, FUS, and TDP-43 fibrils: A molecular dynamics study

  Biophysical Journal · 2024-02-01

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Post‐translational modification sites are present in hydrophilic cavities of alpha‐synuclein, tau, <scp>FUS</scp>, and <scp>TDP</scp>‐43 fibrils: A molecular dynamics study

  Proteins Structure Function and Bioinformatics · 2024-03-08 · 3 citations

  articleOpen accessSenior authorCorresponding

  Hydration plays a crucial role in the refolding of intrinsically disordered proteins into amyloid fibrils; however, the specific interactions between water and protein that may contribute to this process are still unknown. In our previous studies of alpha-synuclein (aSyn), we have shown that waters confined in fibril cavities are stabilizing features of this pathological fold; and that amino acids that hydrogen bond with these confined waters modulate primary and seeded aggregation. Here, we extend our aSyn molecular dynamics (MD) simulations with three new polymorphs and correlate MD trajectory information with known post-translational modifications (PTMs) and experimental data. We show that cavity residues are more evolutionarily conserved than non-cavity residues and are enriched with PTM sites. As expected, the confinement within hydrophilic cavities results in more stably hydrated amino acids. Interestingly, cavity PTM sites display the longest protein-water hydrogen bond lifetimes, three-fold greater than non-PTM cavity sites. Utilizing the deep mutational screen dataset by Newberry et al. and the Thioflavin T aggregation review by Pancoe et al. parsed using a fibril cavity/non-cavity definition, we show that hydrophobic changes to amino acids in cavities have a larger effect on fitness and aggregation rate than residues outside cavities, supporting our hypothesis that these sites are involved in the inhibition of aSyn toxic fibrillization. Finally, we expand our study to include analysis of fibril structures of tau, FUS, TDP-43, prion, and hnRNPA1; all of which contained hydrated cavities, with tau, FUS, and TDP-43 recapitulating our PTM results in aSyn fibril cavities.

  PublisherOA PDFDOI

• Fluorescence lifetime-based FRET biosensors for monitoring N-terminal domain interactions of TDP-43 in living cells: A novel resource for ALS and FTD drug discovery

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-12 · 3 citations

  preprintOpen accessSenior authorCorresponding

  Abstract TAR DNA-binding protein 43 (TDP-43) pathological aggregates are widely implicated in Alzheimer’s disease, frontotemporal dementia and amyotrophic lateral sclerosis. While therapeutic platforms targeting TDP-43 have predominantly targeted its aggregation, recent findings suggest that loss of functional TDP-43 dimers and multimers — essential for RNA processing — occur upstream of aggregation and is driven through disruption of N-terminal domain (NTD) interactions. Here, we demonstrate that these interactions are targetable via cellular fluorescence lifetime-based FRET biosensors which we used to screen the FDA-approved Selleck library. Our NTD-specific hit ketoconazole rescues sorbitol-induced TDP-43 mislocalization and aggregation, and ameliorates TDP-43 induced downregulation of SREBP2, a TDP-43 mRNA binding target with known implication in ALS. In addition, ketoconazole improves neurite outgrowth in a TDP-43 overexpressing neuron model and motor dysfunction in TDP-43 overexpressing C. elegans. Taken together, our platform represents a novel approach for targeting NTD-dependent TDP-43 interactions, and the identification of ketoconazole validates an exciting translational premise for TDP-43 drug discovery.

  PublisherOA PDFDOI

• Data from HuR Contributes to TRAIL Resistance by Restricting Death Receptor 4 Expression in Pancreatic Cancer Cells

  2023-04-03

  preprintOpen access

  &lt;div&gt;Abstract&lt;p&gt;Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal cancers, in part, due to resistance to both conventional and targeted therapeutics. TRAIL directly induces apoptosis through engagement of cell surface Death Receptors (DR4 and DR5), and has been explored as a molecular target for cancer treatment. Clinical trials with recombinant TRAIL and DR-targeting agents, however, have failed to show overall positive outcomes. Herein, we identify a novel TRAIL resistance mechanism governed by Hu antigen R (HuR, ELAV1), a stress-response protein abundant and functional in PDA cells. Exogenous HuR overexpression in TRAIL-sensitive PDA cell lines increases TRAIL resistance whereas silencing HuR in TRAIL-resistant PDA cells, by siRNA oligo-transfection, decreases TRAIL resistance. PDA cell exposure to soluble TRAIL induces HuR translocation from the nucleus to the cytoplasm. Furthermore, it is demonstrated that HuR interacts with the 3′-untranslated region (UTR) of DR4 mRNA. Pre-treatment of PDA cells with MS-444 (Novartis), an established small molecule inhibitor of HuR, substantially increased DR4 and DR5 cell surface levels and enhanced TRAIL sensitivity, further validating HuR's role in affecting TRAIL apoptotic resistance. NanoString analyses on the transcriptome of TRAIL-exposed PDA cells identified global HuR-mediated increases in antiapoptotic processes. Taken together, these data extend HuR's role as a key regulator of TRAIL-induced apoptosis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Implications:&lt;/b&gt; Discovery of an important new HuR-mediated TRAIL resistance mechanism suggests that tumor-targeted HuR inhibition increases sensitivity to TRAIL-based therapeutics and supports their re-evaluation as an effective treatment for PDA patients. &lt;i&gt;Mol Cancer Res; 14(7); 599–611. ©2016 AACR.&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;

  PublisherDOI

• Zafirlukast Is a Promising Scaffold for Selectively Inhibiting TNFR1 Signaling

  ACS Bio & Med Chem Au · 2023-04-07 · 14 citations

  articleOpen accessSenior authorCorresponding

  Tumor necrosis factor (TNF) plays an important role in the pathogenesis of inflammatory and autoimmune diseases such as rheumatoid arthritis and Crohn's disease. The biological effects of TNF are mediated by binding to TNF receptors, TNF receptor 1 (TNFR1), or TNF receptor 2 (TNFR2), and this coupling makes TNFR1-specific inhibition by small-molecule therapies essential to avoid deleterious side effects. Recently, we engineered a time-resolved fluorescence resonance energy transfer biosensor for high-throughput screening of small molecules that modulate TNFR1 conformational states and identified zafirlukast as a compound that inhibits receptor activation, albeit at low potency. Here, we synthesized 16 analogues of zafirlukast and tested their potency and specificity for TNFR1 signaling. Using cell-based functional assays, we identified three analogues with significantly improved efficacy and potency, each of which induces a conformational change in the receptor (as measured by fluorescence resonance energy transfer (FRET) in cells). The best analogue decreased NF-κB activation by 2.2-fold, IκBα efficiency by 3.3-fold, and relative potency by two orders of magnitude. Importantly, we showed that the analogues do not block TNF binding to TNFR1 and that binding to the receptor's extracellular domain is strongly cooperative. Despite these improvements, the best candidate's maximum inhibition of NF-κB is only 63%, leaving room for further improvements to the zafirlukast scaffold to achieve full inhibition and prove its potential as a therapeutic lead. Interestingly, while we find that the analogues also bind to TNFR2 in vitro, they do not inhibit TNFR2 function in cells or cause any conformational changes upon binding. Thus, these lead compounds should also be used as reagents to study conformational-dependent activation of TNF receptors.

  PublisherDOI

Recent grants

• NIH Grant R21CA152668

  NIH · $329k · 2013

• Understanding the structural dynamics of TNF receptors

  NIH · $2.0M · 2019–2024

• Dynamics of transmembrane dimers in TNF-Receptors by EPR and molecular simulation

  NIH · $1.3M · 2014–2019

• Engineering synthetic ligands with potent allosteric inhibition of tumornecrosis factor receptors

  NIH · $1.5M · 2019–2024

• NIH Grant F32GM071134

  NIH · $106k · 2007

Frequent coauthors

• Anthony R. Braun

  University of Minnesota

  53 shared

• Thomas B. Woolf

  Johns Hopkins University

  47 shared

• Horia I. Petrache

  Indiana University – Purdue University Indianapolis

  35 shared

• Andrew K. Lewis

  University of Minnesota

  31 shared

• David D. Thomas

  University of Minnesota

  30 shared

• Christopher C. Valley

  New Mexico Cancer Center

  27 shared

• Jonathan R. Brody

  21 shared

• Chih Hung Lo

  Nanyang Technological University

  21 shared

Labs

• Tissue Mechanics LaboratoryPI

Awards & honors

• NIH NRSA Postdoctoral Fellowship, Yale University (2004-2006…