Biology subjects

Varricchio, C.

Publications and source records attributed to Varricchio, C..

4 recordsLinked to original sources

bioRxiv2026

Protein Folding Interference Enables Selective Cyclin D1 Degradation

Cyclin D1 is a central regulator of cell-cycle progression and a compelling therapeutic target in cancer, yet its non-enzymatic function, limited ligandability, and rapid turnover have hindered direct pharmacological intervention. Here we show that these limitations can be overcome by targeting a transient conformational state populated during protein folding. Computational reconstruction of the Cyclin D1 folding landscape enabled the identification of a ligandable folding intermediate that served as the basis for structure-guided discovery of small molecules inducing selective degradation of nascent Cyclin D1. Orthogonal computational, biophysical, and cellular studies support the proposed mechanism, linking engagement of the folding intermediate to selective degradation of newly synthesized Cyclin D1. Pharmacological folding interference suppressed Cyclin D1 signaling, inhibited tumor cell proliferation, produced antitumor activity in vivo, and retained efficacy in a model of acquired resistance to CDK4/6 inhibition. Together, our findings establish a rational strategy for directly targeting Cyclin D1. More broadly, they suggest that the conformational landscape explored during protein folding represents an untapped reservoir of therapeutic opportunities, expanding small-molecule discovery beyond the native structures that have traditionally defined the druggable proteome.

biochemistry↗

bioRxiv2025

Structure-Activity Relationship and Target Investigation of Thiophen-2-yl-Pyrimidines against Schistosoma species

Chemotherapeutic options for schistosomiasis, a prevalent infectious disease of poverty, are limited to just one drug, praziquantel (PZQ), and alternatives are needed. Our previous studies identified thiophen-2-yl pyrimidines (TPPs), which are structurally derived from microtubule (MT)-active phenylpyrimidines, as potent paralytics of Schistosoma mansoni. Although relatively non-toxic to mammalian cells, the progenitor compound, 3, had poor aqueous solubility and was lipophilic potentially hindering preclinical advancement. To address these issues and expand on the structure-activity and structure-property relationships, 43 new TPP analogs were designed and synthesized, their lipophilicity calculated (cLogP), and their anti-schistosomal activity evaluated in culture. This effort yielded compound 38, which possessed an oxetane-containing amine moiety at C5, and an ortho, ortho-difluoroaniline at C6 of the TPP scaffold. Compared to 3, compound 38 had better aqueous solubility (46 vs. < 0.5 {micro}M) and decreased lipophilicity (logP calc. 4.48 vs. 6.81), with toxicity CC50 values > 20 {micro}M against three mammalian cell lines. Further, paralytic potency, as measured by the EC50 value for adult S. mansoni motility, was increased 14.5-fold (538 vs. 37 nM), and plasma half-life (t1/2) was improved 3-fold, from 0.48 to 1.51 h for a 40% loss in maximum plasma concentration (Cmax). In washout experiments, 38 produced a sustained paralysis of both juvenile and adult S. mansoni, possibly suggesting a broader in vitro efficacy spectrum compared to PZQ, which is inactive against the juvenile parasite. Also, the two other medically important species, Schistosoma haematobium and Schistosoma japonicum, were susceptible to 38. Finally, to identify potential protein targets, we synthesized a TPP photoaffinity labeling (PAL) probe that labeled several S. mansoni proteins by SDS-PAGE fluorescence analysis, although, notably, not tubulin, suggesting that the antischistosomal activity of 38 is a function of engaging other targets. Future work with the TPP series will aim to decrease toxicity further while improving PK properties to better support in vivo efficacy testing.

microbiology↗

bioRxiv2023

Structure-Activity Relationships, Tolerability and Efficacy of Microtubule-Active 1,2,4-Triazolopyrimidines as Potential Candidates to Treat Human African Trypanosomiasis

Tubulin and microtubules (MTs) are potential protein targets to treat parasitic infections and our previous studies have shown that the triazolopyrimidine (TPD) class of MT- active compounds hold promise as antitrypanosomal agents. MT-targeting TPDs include structurally related but functionally diverse congeners that interact with mammalian tubulin at either one or two distinct interfacial binding sites; namely, the seventh and vinca sites, which are found within or between ,{beta}-tubulin heterodimers, respectively. Evaluation of the activity of 123 TPD congeners against cultured Trypanosoma brucei enabled a robust quantitative structure-activity relationship (QSAR) model and the prioritization of two congeners for in vivo pharmacokinetics (PK), tolerability and efficacy studies. Treatment of T. brucei-infected mice with tolerable doses of TPDs 3 and 4 significantly decreased blood parasitemia within 24 h. Further, two once-weekly doses of 4 at 10 mg/kg significantly extended the survival of infected mice relative to infected animals treated with vehicle. Further optimization of dosing and/or the dosing schedule of these CNS-active TPDs may provide alternative treatments for human African trypanosomiasis.

microbiology↗

bioRxiv2022

Geneticin shows selective antiviral activity against SARS-CoV-2 by targeting programmed -1 ribosomal frameshifting

SARS-CoV-2 is currently causing an unprecedented pandemic. While vaccines are massively deployed, we still lack effective large-scale antiviral therapies. In the quest for antivirals targeting conserved structures, we focused on molecules able to bind viral RNA secondary structures. Aminoglycosides are a class of antibiotics known to interact with the ribosomal RNA of both prokaryotes and eukaryotes and have previously been shown to exert antiviral activities by interacting with viral RNA. Here we show that the aminoglycoside geneticin is endowed with antiviral activity against all tested variants of SARS-CoV-2, in different cell lines and in a respiratory tissue model at non-toxic concentrations. The mechanism of action is an early inhibition of RNA replication and protein expression related to a decrease in the efficiency of the -1 programmed ribosomal frameshift (PRF) signal of SARS-CoV-2. Using in silico modelling, we have identified a potential binding site of geneticin in the pseudoknot of frameshift RNA motif. Moreover, we have selected, through virtual screening, additional RNA binding compounds, interacting with the same site with increased potency.

microbiology↗