Biology subjects

Ramadurai, S.

Publications and source records attributed to Ramadurai, S..

4 recordsLinked to original sources

bioRxiv2026

Nanobodies against the S2 region of the spike protein potently neutralize SARS-CoV-2 viruses and show resistance to virus escape

Entry of coronaviruses into cells is mediated by the viral spike (S) glycoproteins each consisting of S1 receptor binding and S2 membrane fusion subunits. The sequence of the S2 region is very highly conserved amongst variants of SARS-CoV-2 and compared to the S1 unit shares significant sequence identity amongst different beta-coronavirus lineages. By targeting the S2 of SARS-CoV-2 we have identified two selective and potent neutralizing nanobodies (BA.1-C2 and BA.1-D3) that bind to two different quaternary epitopes in the S2 formed by the Heptad Repeat 2 (HR2) trimer at the base of the spike protein. The HR2 sequence is identical in SARS-CoV and SARS-CoV-2 but differs in other beta-coronaviruses explaining the lack of binding to the spike proteins of MERS-CoV or HuCoV-OC43. No viral escape was observed following serial passaging of SARS-CoV-2 (JN.1) with a combination of BA.1-C2 and BA.1-D3 and the most potent of these nanobodies reduced viral load in the hamster model of COVID-19, following intranasal administration. Overall, the results show the value of nanobody technology for identifying novel neutralising epitopes in the S2 region of beta-coronaviruses with potential for the development of new selective anti-viral agents.

molecular biology↗

bioRxiv2025

High-throughput discovery of a dearomative cycloaddition enables dual photochemical-photophysical perturbative probing of protein function

Proteins exist in multiple conformations or states, often associated with different functional capacities. The ability to selectively identify and study these states is crucial for understanding the dynamic nature of proteins and their roles in cellular processes, yet can be currently limited by the artefacts of existing molecular labels and the lack of strategies to exploit them in diverse ways. Whilst i) methods for the photochemical perturbation of proteins and ii) photophysical protein probes and sensors are both known powerful tools, simultaneous methods for site- and context-specific photochemical modification of a protein side chain with concomitant modulation of photophysical properties would allow interrogation of protein function via diverse modes (potentially reporting simultaneously on structure and dynamics of ground- and reactive-state properties). Due to their mechanistic complexity, rational approaches for the design of suitable photochemical strategies can be difficult and non-intuitive. Here, we describe a high-throughput experimentation (HTE) strategy designed to allow the photochemical modification of a genetically-encoded, minimally disruptive ( zero-size), photophysically-active - yet typically unreactive and biologically-inert - unnatural amino acid (uAA) residue in proteins. The discovery of a novel dearomative, formal [4+3] photocycloaddition of imidazopyrimidine reagents which proceeds via photochemically generated C* intermediates with polyaromatic substrates enabled chemoselective application to the normally unreactive Trp-mimetic residue, 2-naphthylalanine (Npa). Npas site-selective installation allows dual photochemical and photophysical dearomative perturbation benignly and efficiently in proteins. Replacement of Trp in the archetypal apoptotic biosensor protein Annexin A5 (AnxV) enabled dual photochemical-photophysical determination of switched, conformationally-determined reactive states induced by Ca2+-binding, without any apparent functional perturbation of its in vitro or cellular recognition of phospholipids, indicating an ordered annexin mechanism. This ready and benign unification of photochemistry and photophysics suggests a general approach for using high-throughput light-mediated experimentation in artefact-free chemical biology to capture different functional states of proteins and to interrogate those states using combined photochemical-photophysical methods. HighlightsO_LIDevelopment of a general, high-throughput experimentation (HTE) approach enabled identification of an unprecedented photochemical reaction with potential for editing amino acid side chains within proteins. C_LIO_LIGenetic incorporation of 2-naphthylalanine, a minimally-disruptive ( zero-size) Trp mimic, enabled photochemical side chain editing with concomitant modulation of its distinctive photophysical properties in proteins. C_LIO_LIA naphthalene-tagged variant of the apoptotic biomarker protein AnxV enabled dual photochemical-photophysical exploration of its dynamic conformational states induced by Ca2+-binding whilst fully maintaining its functional capacity for in vitro or cellular recognition of phospholipids. C_LI

biochemistry↗

bioRxiv2025

Hypoxia induced lipid alterations in iPSC-derived human glial progenitor cells revealed by Matrix assisted laser desorption ionization mass spectrometry based cellular fingerprinting

BackgroundIncreasing evidence suggests that the development of highly aggressive form of brain tumor "glioblastoma" contain cancer stem cells that closely resemble glial progenitor cells. The hypoxic microenvironment of tumors leads to metabolic reprogramming of cells, driving them towards more aggressive and treatment resistant state. To identify better targets for the effective removal of hypoxia adaptive cells, it is crucial to understand how these cells alter metabolism in hypoxic conditions. MethodsWe have used confocal microscopy to visualize mitochondrial morphology which confirmed hypoxia, and matrix assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) to decipher lipid metabolic changes in iPSC-derived human glial progenitor cells induced by that hypoxia. ResultsOur findings revealed that hypoxia induced changes in mitochondrial morphology, interaction of mitochondria with lysosomes, and the expression of oxidized lipid species in iPSC-derived human glial progenitor cells. Hypoxic cells showed elongated mitochondria that resembled strings. MALDI-MSI based finger printing showed upregulation of oxidized phosphatidylethanolamine (PE): m/z 716.484 PE(33:1)+O, m/z 730.01 PE(34:1)+O, m/z 766.497 PE(37:5)+O, m/z 768.510 PE(37:4)+O, and oxidized phosphatidylcholine (PC): m/z 742.500 PC(32:2)+O, m/z 744.513 PC(33:2)+O, m/z 770.531 PC(34:2)+O), m/z 794.534 PC(34:1)+O, m/z 888.523 PC(42:11)+OH, and oxidized phosphatidic acid (PA): m/z 673.444 PA(33:2)+O, m/z 699.466 PA(35:3)+OH, m/z 725.531 PA(37:4)+OH in hypoxic cells. ConclusionsGiven the importance of glial progenitor cells in the central nervous system, as a precursor of glioblastoma, and their structural reliance on lipids, the molecular perturbations in the cell as a result of oxygen deficiency (hypoxia) remains unclear. The change in mitochondrial morphology showed that the cells were under hypoxic stress and mass spectrometry imaging unveiled important lipid metabolic changes in hypoxic iPSC-derived human glial progenitor cells as byproducts of oxidative stress, and provided insights that could lead to better treatment strategies for hypoxia-resistant cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/672639v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@873267org.highwire.dtl.DTLVardef@1fe4810org.highwire.dtl.DTLVardef@12d1aa3org.highwire.dtl.DTLVardef@30048f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Graphical abstract was created in BioRender https://app.biorender.com/illustrations/6822efb6aadd8c37669dd403

biochemistry↗

bioRxiv2022

CineFinch: An animated female zebra finch for studying courtship interactions

Dummies, videos and computer animations have been used extensively in animal behaviour to study simple social interactions. These methods allow complete control of one interacting animal, making it possible to test hypotheses about the significance and relevance of different elements of animal displays. Recent studies have demonstrated the potential of videos and interactive displays for studying more complex courtship interactions in the zebra finch, a well-studied songbird. Here, we extended these techniques by developing an animated female zebra finch and showed that ~40% of male zebra finches (n=5/12) sing to this animation. To study real-time social interactions, we developed two possible methods for closed loop control of animations; (1) an arduino based system to initiate videos/animations based on perch hops and (2) a video game engine based system to change animations. Overall, our results provide an important tool for understanding the dynamics of complex social interactions during courtship. SUMMARY STATEMENTWe develop and test an animation of a female zebra finch to study song and courtship interactions in the male zebra finch.

animal behavior and cognition↗