Biology subjects

Fine, E. J.

Publications and source records attributed to Fine, E. J..

5 recordsLinked to original sources

bioRxiv2026

Distinct activation mechanisms underlie ligand efficacy at a GPCR

Ligands that bind to the same G protein-coupled receptor (GPCR) can produce widely different levels of signaling. These differences in efficacy are central to pharmacology, yet how a receptor sequence determines signaling level remains incompletely understood. Here we develop a deep mutational pharmacology approach to measure how each residue in the -opioid receptor (OR) shapes responses to 15 opioids, yielding ~400,000 measurements of variant effects on signaling and expression, including full concentration-response series for three agonists. Mutational effects on potency are strongest near the orthosteric pocket, whereas effects on efficacy extend through the transmembrane core and intracellular face. Ligands share many functional determinants, but sensitivity to mutation differs with efficacy. As efficacy decreases, the residues required for signaling shift from the binding pocket towards the intracellular face; partial agonists therefore depend on residues that are dispensable for full agonists. Mutations can broadly increase receptor responses, allowing antagonists such as naloxone to produce signaling comparable to a full agonist and increasing the efficacy of partial agonist ligands. Combined mutations can also reorder the relative efficacies of ligands, showing that sequence changes reshape pharmacological differences rather than simply increasing or decreasing all responses together. These findings support a model in which ligands of different efficacy activate the receptor through distinct allosteric mechanisms which are determined by residues distributed across the receptor. Mapping these contributions across diverse ligands with deep mutational pharmacology provides a way to understand how one receptor converts molecular recognition into a range of signaling outputs.

biophysics↗

bioRxiv2026

Conformational Basis of Functionally Selective Allosteric Modulation of the Angiotensin II type 1 Receptor by Small Molecules

Blockade of signaling through the angiotensin II type 1 receptor (AT1R), a prototypical G protein-coupled receptor (GPCR), by angiotensin receptor blockers (ARBs) is a major therapeutic approach to treating a wide variety of cardiovascular and renal diseases1. Like most GPCRs, the AT1R signals through two transducers, G proteins and {beta}-arrestins2,3. Previous reports have described {beta}-arrestin-biased peptide orthosteric agonists for the AT1R with potential therapeutic advantages over currently available unbiased ARBs4-6. Here we report the DNA- encoded library screening-guided isolation and pharmacological characterization of the first small molecule AT1R allosteric ligands. We use cryo-electron microscopy, double electron- electron resonance spectroscopy, molecular dynamics simulations, and targeted mutagenesis to determine their binding sites, binding modes and conformational mechanisms driving their unique and divergent modulatory effects on G protein and {beta}-arrestin pathways. Our findings uncover new mechanisms for precisely controlling the dynamic behavior of the AT1R with implications for drug development targeting this pathophysiologically important receptor family.

biochemistry↗

bioRxiv2023

Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids

We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for {Delta}F/F0 vs [nicotine] ({delta}-slope, 2.7 M-1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the "candle snuffer" mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.

bioengineering↗

bioRxiv2021

Inhibition of cancer cells in culture. The effects of treatment with ketone bodies and/or rapamycin treatment

BackgroundThe potential for ketogenic diets or administration of exogenous ketone bodies to treat or prevent to cancer remains encouraging. Of particular interest is the possibility that, whatever the effect of a nutritional intervention alone, the diet might enhance the effect of existing cancer drugs, thereby requiring lower doses and a reduction in toxicity and side effects. MethodsSW480, a human cell line derived from colon, was treated with ketone bodies (sodium 3-hydroxy butyrate (common name, {square}-hydroxy butyrate) or with sodium acetoacetate in the presence or absence of rapamycin. Cells were incubated for 96 hours in DMEM with 10 mM glucose medium. HSF2617, a human epithelial fibroblast line served as control and cells were subjected to similar treatment as the SW480 cells. Cell proliferation and glucose consumption were determined with standard reagents. ResultsThe ketone bodies inhibited proliferation of SW480 cells in culture. Rapamycin also inhibited proliferation and its action was enhanced by the ketone bodies although there was little synergistic effect under these conditions. Human fibroblast controls were not inhibited by the ketone bodies. Both SW480 and control lines showed consumption of glucose during a 96 hour incubation period, suggesting that normal controls can switch to ketogenic metabolism while the cancer cells, which proliferate poorly, cannot. Results are consistent with recent reports of a mouse model showing the synergy of rapamycin and a ketogenic diet (Zou Y, et al. (2020) PLoS ONE 15 (5)) as well as earlier publications describing additive or synergistic effects of ketogenic diets with other modalities of cancer treatment. ConclusionsThe results show that the growth of a cancer cell line in culture can be inhibited by the addition of ketone bodies or rapamycin to the growth medium. The combination of treatments was found to be additive, consistent with results from a previously published mouse model. The data demonstrate the potential for a strategy whereby doses of anti-cancer agents that have detrimental or toxic side-effects can be reduced if coupled to an appropriate source of ketone bodies.

cancer biology↗

bioRxiv2020

The Effect of a Ketogenic Diet and Synergy with Rapamycin in a Mouse Model of Breast Cancer.

BackgroundThe effects of diet in cancer, in general, and breast cancer in particular, are not well understood. Insulin inhibition in ketogenic, high fat diets, modulate downstream signaling molecules and are postulated to have therapeutic benefits. Obesity and diabetes have been associated with higher incidence of breast cancer. Addition of anti-cancer drugs together with diet is also not well studied. MethodsTwo diets, one ketogenic, the other standard mouse chow, were tested in a spontaneous breast cancer model in mice. The diets were implemented either with or without added rapamycin, an mTOR inhibitor and potential anti-cancer drug. ResultsBlood glucose and insulin concentrations in mice ingesting the ketogenic diet (KD) were significantly lower, whereas beta hydroxybutyrate (BHB) levels were significantly higher, respectively, than in mice on the standard diet (SD). Growth of primary breast tumors and lung metastases were inhibited, and lifespans were longer in the KD mice compared to mice on the SD (p<0.005). Rapamycin improved survival in both mouse diet groups, but when combined with the KD was more effective than when combined with the SD. ConclusionsThe study provides proof of principle that a ketogenic diet a) results in serum insulin reduction and ketosis in a spontaneous breast cancer mouse model; b) can serve as a therapeutic anti-cancer agent; and c) can enhance the effects of rapamycin, an anti-cancer drug, permitting dose reduction for comparable effect. Further, the ketogenic diet in this model produces superior cancer control than standard mouse chow whether with or without added rapamycin.

cancer biology↗