Nahal Bagheri

All Publications

• Covalent Drug Binding in Live Cells Monitored by Mid-Infrared Quantum Cascade Laser Spectroscopy: Photoactive Yellow Protein as a Model System. Journal of the American Chemical Society Mukherjee, S., Fried, S. D., Hong, N. Y., Bagheri, N., Kozuch, J., Mathews, I. I., Kirsh, J. M., Boxer, S. G. 2025

  Abstract

  The detection of drug-target interactions in live cells enables analysis of therapeutic compounds in a native cellular environment. Recent advances in spectroscopy and molecular biology have facilitated the development of genetically encoded vibrational probes like nitriles that can sensitively report on molecular interactions. Nitriles are powerful tools for measuring electrostatic environments within condensed media like proteins, but such measurements in live cells have been hindered by low signal-to-noise ratios. In this study, we design a spectrometer based on a double-beam quantum cascade laser (QCL)-based transmission infrared (IR) source with balanced detection that can significantly enhance sensitivity to nitrile vibrational probes embedded in proteins within cells compared to a conventional FTIR spectrometer. Using this approach, we detect small-molecule binding in Escherichia coli, with particular focus on the interaction between para-Coumaric acid (pCA) and nitrile-incorporated photoactive yellow protein (PYP). This system effectively serves as a model for investigating covalent drug binding in a cellular environment. Notably, we observe large spectral shifts of up to 15 cm-1 for nitriles embedded in PYP between the unbound and drug-bound states directly within bacteria, in agreement with observations for purified proteins. Such large spectral shifts are ascribed to the changes in the hydrogen-bonding environment around the local environment of nitriles, accurately modeled through high-level molecular dynamics simulations using the AMOEBA force field. Our findings underscore the QCL spectrometer's ability to enhance sensitivity for monitoring drug-protein interactions, offering new opportunities for advanced methodologies in drug development and biochemical research.

  View details for DOI 10.1021/jacs.5c14498

  View details for PubMedID 41391174

• Covalent Drug Binding in Live Cells Monitored by Mid-IR Quantum Cascade Laser Spectroscopy: Photoactive Yellow Protein as a Model System. bioRxiv : the preprint server for biology Mukherjee, S., Fried, S. D., Hong, N. Y., Bagheri, N., Kozuch, J., Mathews, I. I., Kirsh, J. M., Boxer, S. G. 2025

  Abstract

  The detection of drug-target interactions in live cells enables analysis of therapeutic compounds in a native cellular environment. Recent advances in spectroscopy and molecular biology have facilitated the development of genetically encoded vibrational probes like nitriles that can sensitively report on molecular interactions. Nitriles are powerful tools for measuring electrostatic environments within condensed media like proteins, but such measurements in live cells have been hindered by low signal-to-noise ratios. In this study, we design a spectrometer based on a double-beam quantum cascade laser (QCL)-based transmission infrared (IR) source with balanced detection that can significantly enhance sensitivity to nitrile vibrational probes embedded in proteins within cells compared to a conventional FTIR spectrometer. Using this approach, we detect small-molecule binding in E. coli, with particular focus on the interaction between para-coumaric acid (pCA) and nitrile-incorporated photoactive yellow protein (PYP). This system effectively serves as a model for investigating covalent drug binding in a cellular environment. Notably, we observe large spectral shifts of up to 15 cm-1 for nitriles embedded in PYP between the unbound and drug-bound states directly within bacteria, in agreement with observations for purified proteins. Such large spectral shifts are ascribed to the changes in the hydrogen-bonding environment around the local environment of nitriles, accurately modeled through high-level molecular dynamics simulations using the AMOEBA force field. Our findings underscore the QCL spectrometer's ability to enhance sensitivity for monitoring drug-protein interactions, offering new opportunities for advanced methodologies in drug development and biochemical research.

  View details for DOI 10.1101/2025.08.15.670201

  View details for PubMedID 40894761

  View details for PubMedCentralID PMC12393337

• Magnetic resonance control of reaction yields through genetically-encoded protein:flavin spin-correlated radicals in a live animal. bioRxiv : the preprint server for biology Burd, S. C., Bagheri, N., Ingaramo, M., Condon, A. F., Mondal, S., Dowlatshahi, D. P., Summers, J. A., Mukherjee, S., York, A. G., Wakatsuki, S., Boxer, S. G., Kasevich, M. 2025

  Abstract

  Radio-frequency (RF) magnetic fields can influence reactions involving spin-correlated radical pairs. This provides a mechanism by which RF fields can influence living systems at the biomolecular level. Here we report the modification of the emission of various red fluorescent proteins (RFPs), in the presence of a flavin cofactor, induced by a combination of static and RF magnetic fields. Resonance features in the protein fluorescence intensity were observed near the electron spin resonance frequency at the corresponding static magnetic field strength. This effect was measured at room temperature both in vitro and in the nematode C. elegans , genetically modified to express the RFP mScarlet. These observations suggest that the magnetic field effects measured in RFP-flavin systems are due to quantum-correlated radical pairs. Our experiments demonstrate that RF magnetic fields can influence dynamics of reactions involving RFPs in biologically relevant conditions, and even within a living animal. These results have implications for the development of a new class of genetic tools based on RF manipulation of genetically-encoded quantum systems.

  View details for DOI 10.1101/2025.02.27.640669

  View details for PubMedID 40093161

  View details for PubMedCentralID PMC11908193

• Detection of covalent drug binding in live cells using a quantum cascade laser and nitrile-labeled amino acids Fried, S. D. E., Mukherjee, S., Bagheri, N., Hong, N. Y., Boxer, S. G. CELL PRESS. 2025

  View details for Web of Science ID 001461666900190

• Detection of covalent drug binding in live cells using a quantum cascade laser and nitrile-labeled amino acids Fried, S. D. E., Mukherjee, S., Bagheri, N., Hong, N. Y., Boxer, S. G. CELL PRESS. 2025

  View details for Web of Science ID 001510145400176

• Detection of covalent drug binding in live cells using a quantum cascade laser and nitrile-labeled amino acids Fried, S. D. E., Mukherjee, S., Bagheri, N., Hong, N. Y., Boxer, S. G. CELL PRESS. 2025

  View details for Web of Science ID 001461404400032

• A Fluorogenic Pseudoinfection Assay to Probe Transfer and Distribution of Influenza Viral Contents to Target Vesicles. Analytical chemistry Bhattacharya, A., Bagheri, N., Boxer, S. G. 2024

  Abstract

  Fusion of enveloped viruses with endosomal membranes and subsequent release of the viral genome into the cytoplasm are crucial to the viral infection cycle. It is often modeled by performing fusion between virus particles and target lipid vesicles. We utilized fluorescence microscopy to characterize the kinetic aspects of the transfer of influenza viral ribonucleoprotein (vRNP) complexes to target vesicles and their spatial distribution within the fused volumes to gain deeper insight into the mechanistic aspects of endosomal escape. The fluorogenic RNA-binding dye QuantiFluor (Promega) was found to be well-suited for direct and sensitive microscopic observation of vRNPs which facilitated background-free detection and kinetic analysis of fusion events on a single particle level. To determine the extent to which the viral contents are transferred to the target vesicles through the fusion pore, we carried out virus-vesicle fusion in a side-by-side fashion. Measurement of the Euclidean distances between the centroids of superlocalized membrane and content dye signals within the fused volumes allowed determination of any symmetry (or the lack thereof) between them as expected in the event of transfer (or the lack thereof) of vRNPs, respectively. We found that, in the case of fusion between viruses and 100 nm target vesicles, ∼39% of the events led to transfer of viral contents to the target vesicles. This methodology provides a rapid, generic, and cell-free way to assess the inhibitory effects of antiviral drugs and therapeutics on the endosomal escape behavior of enveloped viruses.

  View details for DOI 10.1021/acs.analchem.4c01142

  View details for PubMedID 39086018