Biology subjects

Saji, A.

Publications and source records attributed to Saji, A..

3 recordsLinked to original sources

bioRxiv2026

Discovery of a pathway-selective platelet P2Y1R inverse agonist that suppresses inflammation while preserving hemostasis

The platelet P2Y1 receptor (P2Y1R) is necessary for inflammation, signalling via Rho-GTPase pathways to elicit functions that are distinct from aggregation (PLC-dependent canonical signalling pathway). Whether these distinct platelet inflammatory functions can be selectively suppressed to preserve hemostasis through the rational design of P2Y1R antagonists has not been explored. In silico molecular docking analysis examined biased nucleotide interactions within the P2Y1R binding pocket. The identified possible key amino acid residues guided rational design to synthesize compounds for pathway selective inhibition, evolving from nucleotide to non-nucleotide structures. The nucleotide analogue KMR-82-13 was predicted to engage distinct regions of the binding pocket and selectively inhibited platelet chemotaxis while preserving aggregation. These findings informed the design of a non-nucleotide compound KSN-159-27, aiming to retain key KMR-82-13-like interactions while improving drug-like properties. Docking and molecular dynamics simulation supported a stable but dynamic binding mode for KSN-159-27 within the P2Y1R pocket, consistent with pathway-selective inhibition. KSN-159-27 displayed characteristics of a pathway selective inverse agonist at P2Y1R towards G12/13-mediated pathways, but not those associated by Gq activation in P2Y1R-transfected HEK293T cells. KSN-159-27 showed functionally selective inhibition for platelet P2Y1R-mediated functions. In vivo, KSN-159-27 suppressed inflammatory cell recruitment, whilst preserving bleeding time and ADP-induced thromboembolic responses, in contrast to the neutral P2Y1R antagonist MRS2500. This first demonstration for the rational design of a pathway selective inverse agonist at platelet P2Y1Rs has significant implications for novel therapeutic strategies developed to safely target platelet activation during inflammation, in contrast to current anti-platelet drugs used in the prevention of thrombosis. Key PointsO_LIBiased inverse platelet P2Y1R agonists selectively supress inflammation whilst preserving hemostasis and the ability of platelets to aggregate. C_LIO_LIBiased inverse agonism selectively inhibited P2Y1R G12/13 (Rho-GTPAse functions) but not Gq activities (PLC functions). C_LI

pharmacology and toxicology↗

bioRxiv2025

Reducing Foetal Bovine Serum Culture Conditions does not affect GPCR Signalling

Animal use in research extends beyond the use of animal models to study physiology and disease. Many aspects of in vitro research use reagents derived from animals, most prolifically the use of foetal bovine serum (FBS) in growth media for cellular models. With the aim to reduce animal use, we investigated the effect of reduced FBS culture conditions on cell growth, as well as different stages of G protein-coupled receptor (GPCR) signalling, a wide area of research which might therefore impact many groups. We identified little differences on cell growth or GPCR signalling when reducing culture FBS percentage from 10% to 5%, using assays ranging from receptor activation to downstream transcription factors stimulation. In addition to diminishing animal use, the reduction of FBS use will also have economic and environmental benefits, which we hope will be of benefit to the wider research community.

pharmacology and toxicology↗

bioRxiv2024

Evolutionary approaches predicted changes in transcription factors and cis-elements that associate with Kranz anatomy development in maize

C4 plants exhibit higher photosynthetic efficiency under high temperatures and low water availability due to their unique anatomical and biochemical adaptations, but the evolutionary mechanisms and regulatory components underlying their Kranz development remain partly known. If C4 traits evolved through adaptive changes, its developmental regulators should show detectable evolutionary signatures in C4 lineages. We investigated the adaptive evolutionary changes in both protein sequences and cis-motifs upstream of candidate genes differentially expressed during Kranz anatomy establishment in C4 grasses. We identified signatures of convergent evolution in candidate genes and their upstream regions by comparing C4 orthologs with their C3 counterparts, and enriched non-syntenic motifs present upstream of C4 orthologs through phylogeny-aware analysis. Out of 191 candidate genes analyzed, ten orthogroups containing maize orthologs of EREB160, DOF11, bHLH116, MADS9, bHLH33/bHLH105, SCRO1/SCR2, CADTFR3, THX8, C3H28, and SHR1/SHR2 showed positive selection pressure specific to C4 orthologs. Among them, DOF11, SCRO1/SCR2, and SHR1/SHR2 have previously been implicated in Kranz regulation by previous studies. Additionally, we identified a conserved position mutation present in bHLH116 across C4 lineages, which may influence its DNA-binding domain. Moreover, we identified 39 annotated non-syntenic/C4-shifted DNA motifs, upstream of 28 gene orthologs, enriched in C4 species. Notably, genes with these motifs did not intersect with the genes under positive selection, suggesting these pathways evolved separately without much crosstalk, nevertheless, a few putative regulatory-network-motifs were observed. These motifs are potential additions to the limited Kranz-specific motifs and can aid in predicting new putative regulators after experimental validation. Significance statementC4 plants evolved as an adaptive response through anatomical and biochemical changes in their C3 relatives. Unlike the biochemical changes, the regulators/drivers of anatomical changes and the nature of underlying changes remains only partially understood. Using signatures of adaptive evolution, the current study screened candidate regulatory factors and sequences, including a few previously known and many novel candidates. These findings complement the existing experimental knowledge and advance the discovery of the gene regulatory network underlying the anatomical changes associated with C4 evolution.

plant biology↗