Biology subjects

Shafi, T.

Publications and source records attributed to Shafi, T..

5 recordsLinked to original sources

bioRxiv2025

Structural basis of Drosophila insulin receptor activation by DILP2 hormone

Insulin-related hormones regulate key life processes in the animal kingdom, from metabolism to growth, lifespan and aging, through an evolutionarily conserved insulin and insulin-like hormones signalling axis (IIS). In humans the IIS axis is controlled by insulin, two Insulin-like Growth Factors, two isoforms of the insulin receptor (hIR-A and -B), and its homologous IGF-1R. In Drosophila, this signalling engages seven insulin-like hormones (DILP1-7) and a single receptor (dmIR) that follows the blueprint of hIR/hIGF-1R. This report describes two cryo-EM structures of the dmIR ectodomain dmIR-ECD:DILP2 complex, revealing their structural homology with dmIR:DILP5 complex. The high excess of DILP2 yielded two dmIR-ECD complexes in asymmetric conformations, similar to that observed in some complexes of hIR and in the dmIR-ECD:DILP5 complex. This stoichiometric and structural heterogeneity, yielding one- and two-DILP2:receptor complexes - were not observed in DILP5:dmIR-ECD assembly. Also, the resistance of dmIR-ECD to form more DILP2 saturated complexes, despite very high excess of this hormone, suggest that the specificities of DILPs may lie in their kon/koff kinetic parameters. This work expands understanding of the dmIR conformational flexibility, suggesting also that insect dmIR follows more hIR rather than hIGF-1R receptor signal transduction pattern induced by various DILPs.

biochemistry↗

bioRxiv2023

Structural Conservation of Insulin/IGF Signalling Axis at the Insulin Receptors Level in Drosophila and Humans

The insulin-related hormones regulate key life processes in Metazoa, from metabolism to growth, lifespan and aging, through an evolutionarily conserved insulin signalling axis (IIS). In humans the IIS axis is controlled by insulin, two insulin-like growth factors, two isoforms of the insulin receptor (hIR-A and -B), and its homologous IGF-1R. In Drosophila, this signalling engages seven insulin-like hormones (DILP1-7) and a single receptor (dmIR). This report describes the cryoEM structure of the dmIR ectodomain:DILP5 complex, revealing high structural homology between dmIR and hIR. The excess of DILP5 yields dmIR complex in an asymmetric T conformation, similar to that observed in some complexes of human IRs. However, dmIR binds three DILP5 molecules in a hitherto-unseen arrangement, showing also dmIR-specific features. This work adds structural support to evolutionary conservation of the IIS axis at the IR level, underpinning also a better understanding of an important model organism.

biochemistry↗

bioRxiv2021

Structure of ABCB1/P-glycoprotein bound to the CFTR potentiator ivacaftor.

ABCB1 (P-glycoprotein) is an ATP binding cassette transporter that is involved in the clearance of xenobiotics and it affects the disposition of many drugs in the body. Here we have studied ABCB1 in the drug-bound and drug-free states, simultaneously, using high contrast cryo-electron microscopy imaging and a Volta phase plate. The binding of the potent CFTR potentiator, ivacaftor, at a site in the central aqueous cavity is mediated by transmembrane -helices 3,6,10,11 & 12. Binding is associated with a wider separation of the two halves of the transporter in the inward-facing state. Induced-fit changes the nucleotide binding domains in a way that may explain their increased affinity for ATP when drug is bound. Comparison of ivacaftor-bound structures of CFTR and ABCB1 suggests common features in the binding modes.

biochemistry↗

bioRxiv2021

Kite-shaped molecules block SARS-CoV-2 cell entry at a post-attachment step

Anti-viral small molecules are currently lacking for treating coronavirus infection. The long development timescales for such drugs are a major problem, but could be shortened by repurposing existing drugs. We therefore screened a small library of FDA-approved compounds for potential severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antivirals using a pseudovirus system that allows a sensitive read-out of infectivity. A group of structurally-related compounds, showing moderate inhibitory activity with IC50 values in the 1-5{micro}M range, were identified. Further studies demonstrated that these kite-shaped molecules were surprisingly specific for SARS-CoV and SARS-CoV-2 and that they acted early in the entry steps of the viral infectious cycle, but did not affect virus attachment to the cells. Moreover the compounds were able to prevent infection in both kidney- and lung-derived human cell lines. The structural homology of the hits allowed the production of a well-defined pharmacophore that was found to be highly accurate in predicting the anti-viral activity of the compounds in the screen. We discuss the prospects of repurposing these existing drugs for treating current and future coronavirus outbreaks.

microbiology↗

bioRxiv2018

Novel features in the structure of P-glycoprotein (ABCB1) in the post-hydrolytic state as determined at 7.9A resolution

P-glycoprotein (ABCB1) is a ATP-binding cassette transporter that plays an important role in the removal of drugs and xenobiotic compounds from the cell. It is also associated with multi-drug resistance in cancer. Here we report novel features of the cryo-EM-derived structure of P-glycoprotein in the post-hydrolytic state: The cytosolic nucleotide-binding domains (NBDs) are separated despite ADP remaining bound to the NBDs. Gaps in the TMDs that connect to the inner hydrophilic cavity are back-filled by detergent head-groups from the annular detergent micelle and are close to two regions predicted to delineate two pseudo-symmetry-related drug-binding sites. In this conformation, the (newly-resolved) N-terminal extension, NBD-TMD linker region and gap-filling detergents all appear to impede NBD dimerisation. We propose a model for the mechanism of action of the exporter where ATP will be bound to the protein for most of the time, consistent with the high physiological ATP concentrations in vivo.

biochemistry↗