Biology subjects

Nesheva, D.

Publications and source records attributed to Nesheva, D..

5 recordsLinked to original sources

bioRxiv2026

The FDA-approved CDK4/6 inhibitor Abemaciclib is a potent agonist of the β-arrestin-biased atypical chemokine receptor ACKR3

Atypical chemokine receptor 3 (ACKR3/CXCR7) is an intrinsically {beta}-arrestin-biased family-A GPCR that controls chemokine availability by scavenging CXCL12 and CXCL11, and consequently plays a key role in cancer, chronic inflammation, autoimmunity, cardiovascular disease, and CNS repair. Despite its pathophysiological significance, the chemical space available to interrogate and therapeutically modulate this receptor remains limited. Here, by using a drug-repurposing strategy to screen 2,342 FDA-approved compounds in a NanoBRET-based fluorescent chemokine-binding competition assay, we identified the clinically used CDK4/6 inhibitor abemaciclib (Verzenios(R)) as a nanomolar ACKR3 ligand. Abemaciclib inhibited CXCL12 binding to ACKR3 with comparable affinity to the ACKR3-reference agonist VUF15485, whereas the related clinically used CDK4/6 inhibitors palbociclib, ribociclib, dalpiciclib and trilaciclib were inactive on this receptor. Binding and functional profiling across classical and atypical chemokine receptors revealed selectivity for ACKR3, including lack of detectable activity at the CXCL12 receptors CXCR4 and ACKR5. Abemaciclib acted as a potent ACKR3 agonist, recruiting both {beta}-arrestin-1 and 2 and promoting rapid receptor internalization with potencies and efficacies, like the reference ACKR3 agonist VUF15485. Major CYP3A4-derived abemaciclib metabolites retained ACKR3 binding and agonist activity, albeit with reduced potency. Methionine 13C-HSQC NMR confirmed direct receptor engagement and revealed a small-molecule-like ACKR3 conformational signature distinct from the CXCL12-bound state. Cryo-EM of the abemaciclib-ACKR3-CID24 complex at 3.2 [A] uncovered a unique, inverted U-shaped ligand binding pose in the orthosteric pocket and activation-associated rearrangements of TM6, TM7 and helix 8. Functionally, abemaciclib blocked ACKR3-mediated uptake of CXCL11 and CXCL12 in vitro. Moreover, oral administration of abemaciclib in mice resulted in a time-dependent increase in plasma CXCL12 levels, indicative of in vivo ACKR3 target engagement. These findings establish this FDA-approved kinase inhibitor as a potent ACKR3 modulator and reveal an unexpected pharmacological link of this CDK4/6 inhibitor to atypical chemokine receptor biology.

molecular biology↗

bioRxiv2026

Gothic Identity as Cultural Practice: Paleogenomic Evidence for Multi - Ethnic Assemblages Under Gothic Material Culture in Late Antique Bulgaria (4th - 6th centuries CE)

We report genome-wide ancient DNA from 38 individuals associated with Gothic-period mortuary contexts at two Bulgarian sites: the Aquae Calidae necropolis ([~]320 - 375 CE; n=23) and the Aul of Khan Omurtag (AKO; [~]350 - 489 CE; n=15). Although linked by closely similar Gothic-associated material culture and east - west Arian burial practices, the two assemblages are genetically distinct. Aquae Calidae individuals are modeled with predominantly Anatolian-related ancestry (50 - 85% in qpAdm), whereas AKO individuals are modeled with predominantly Wielbark/Chernyakhov-related northern ancestry (60 - 78%). Across the full assemblage, no single ancestry model fits all individuals, whose profiles range from nearly unadmixed Chernyakhov-like to predominantly Anatolian-related. DATES analysis places admixture between northern European and southern Balkan/Anatolian-related ancestry components approximately 11 - 13 generations before burial (point estimate [~]50 CE; 95% CI, 85 BCE - 183 CE; Z=5.26), raising the possibility that this mixture predated the earliest documented Gothic - Roman contacts ([~]170 CE). The convergence of dates across alternative southern proxies, together with reduced fit when Balkan and Anatolian sources are pooled into a single southern reference, favors admixture involving a pre-blended Balkan - Anatolian substrate over two temporally distinct southern admixture pulses. This signal was not recovered in the non-Gothic Roman-period Balkan populations tested as controls and is consistent with admixture in a trans-Danubian frontier setting, potentially including Roman Dacia after 106 CE. These findings support models in which Gothic affiliation in the Balkans operated as a cultural-political framework encompassing populations of diverse biological ancestry.

genomics↗

bioRxiv2024

Inhibition of constitutive activity of the atypical chemokine receptor ACKR3 by the small-molecule inverse agonist VUF16840

The atypical chemokine receptor 3 (ACKR3) has emerged as a promising drug target for the treatment of cancer, cardiovascular, and autoimmune diseases. In this study, we present the pharmacological characterization of VUF16840, the first small-molecule inverse agonist of ACKR3. VUF16840 effectively displaces CXCL12 binding to ACKR3 and inhibits chemokine-induced {beta}-arrestin2 recruitment in a concentration-dependent manner. Furthermore, VUF16840 stabilizes the inactive conformation of ACKR3, as demonstrated by its ability to suppress constitutive {beta}-arrestin2 recruitment. This inverse agonism alters ACKR3 constitutive trafficking, leading to receptor enrichment at the plasma membrane and inhibition of intracellular CXCL12 uptake. Importantly, VUF16840 exhibits high selectivity for ACKR3 over a broad panel of human chemokine receptors. These findings establish VUF16840 as a potent and selective ACKR3 inverse agonist capable of modulating constitutive and chemokine-induced signaling and internalization events. As such, VUF16840 represents a valuable pharmacological tool for exploring the molecular and translational roles of ACKR3 in both physiological and pathological contexts.

pharmacology and toxicology↗

bioRxiv2024

ACKR5/GPR182 is a scavenger receptor for the atypical chemokine CXCL17, GPR15L and various endogenous peptides

GPR182/ACKR5, the most recently deorphanized chemokine receptor, is mainly expressed on endothelial cells and was proposed to act as a scavenger regulating the availability of a large set of chemokines. In this study, we first established the exact profiles and ranking of the chemokines binding to the human and mouse GPR182. We confirmed the high promiscuity of GPR182 towards XC, CC and CXC chemokines and a clear difference in the chemokine repertoires of the human and mouse orthologues. We next demonstrated that, beyond classical chemokines, GPR182 exhibits potent binding to the chemoattractant protein GPR15L/C10orf99, the atypical chemokine CXCL17 and various endogenous peptides, mainly from the opioid, apelin, and PACAP families. We also showed that these newly identified ligands engage GPR182 through varied binding modes. While GPR15L, just like classical chemokines, predominantly engages GPR182 via its N terminus, conversely to the C terminus-dependent binding to its cognate receptor GPR15, CXCL17 exhibits a more complex interaction, relying on both the N and C terminus. The binding mode of the newly identified peptide ligands also differ from the interactions with their cognate receptors. Our findings establish the first scavenger receptor for CXCL17 and GPR15L and advance the understanding of GPR182 ligand interactions, suggesting a regulatory role beyond chemokines.

pharmacology and toxicology↗

bioRxiv2020

Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease

Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. In addition, ten variants designated as possibly or likely pathogenic were detected. The oldest of these were two variants in the MT-TD gene, m.7543A>G and m.7554G>A, from Neolithic samples dated 8205-7700 BCE. A novel mutation in contemporary populations, m.4440G>A in the MT-TM gene, is established in 12 ancient mtDNA samples from different periods ranging from 2800 BCE to 920 CE. The pathogenic effect of these possibly/likely pathogenic mutations is not yet well established, and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Seven mutations are located in CS-Anticodon stem, 4 are located in AS-Acceptor stem, 2 in TS-T{Psi}C stem, and single mutations are found in DL-Dihydrouridine Loop, CL-Anticodon Loop and DS-Dihydrouridine stem. Exposing pathogenic variants in ancient human populations expands our understanding of their origin.

genetics↗