Zlatko Janeba

6-Oxopurine phosphoribosyltransferases (HGXPRTs) are essential enzymes in the purine salvage pathway of Plasmodium parasites and attractive antimalarial targets. However, the high conservation of their active sites with the human homolog complicates selective inhibitor development. Here, we report thiophene-linked nucleotide analogues as potent and selective inhibitors of plasmodial HG(X)PRTs. Structure-based modeling and conformational analysis guided the incorporation of a rigid thiophene core to control the orientation of phosphate-mimicking groups. C5 sulfonyl substitution markedly enhanced potency, yielding low- to single-digit nanomolar inhibitors of Plasmodium falciparum HGXPRT (PfHGXPRT). Compound 66 emerged as a lead inhibitor (Ki = 7 nM), showing up to ∼3300-fold selectivity over the human enzyme. Compound 63 was the most potent against Plasmodium vivax HGPRT (Ki = 30 nM), highlighting species-dependent linker length effects. Cellular activity remained limited, emphasizing intracellular delivery and/or prodrug activation as key remaining challenges. These compounds establish a promising selective chemotype for further antimalarial development.

Light-activated drugs are a promising way to treat localized diseases for which existing treatments have severe side effects. However, their development is complicated by the set of photophysical and biological properties that must be simultaneously optimized. Here we used computational techniques to find a set of promising candidates for the photoactive inhibition of the poly(ADP-ribose) polymerase 1 (PARP1) cancer target. Using our recently developed methods based on atomistic simulation and machine learning (ML), we screened a set of 5 million hypothetical photoactive ligands. Our workflow used protein–ligand docking to identify candidates with differential PARP1 binding under light and dark conditions; ML force fields and quantum chemistry calculations to predict pKa, absorption spectra, and thermal half-lives; graph-based surrogate models to screen additional compounds; excited-state nonadiabatic dynamics with ML force fields to estimate quantum yields; and free energy perturbation (FEP) to refine binding predictions. From these predictions, we prioritized a small set of synthetically feasible candidates expected to have red-shifted absorption spectra, thermal half-lives on the order of seconds to minutes, and isomer-dependent PARP1 binding under visible-light control. We synthesized 10 candidates and experimentally characterized their photobehavior and PARP1 inhibition constants. Among the validated compounds, 1 showed a 15-fold increase in inhibition of PARP1 upon green-light irradiation at 519 nm (208.8 ± 28.3 μM vs 14.4 ± 1.9 μM). These results validate the computation-guided screening strategy for identifying red-shifted PARP1 photoinhibitors, while also underscoring current limitations such as rapid thermal relaxation in aqueous media.

Figure S3 shows MYC-induced apoptosis and cell death in early and late timepoints, ectopic expression of BCL2 and its impact on MYC-induced RNA decay, gene expression changes upon DIS3L knockdown in MYC-hyperactivated conditions, and expression of exosome components upon MYC-induction.

Figure S4 shows DIS3L mutation in human tumors, evolutionary action score of tumor-derived mutation in DIS3L, genomic alteration of MYC and DIS3L in human breast cancer, expression of DIS3L mRNA in human breast tumors, and expression of genes in ribonucleotide catabolism and synthesis upon DIS3L knockdown.

Table S1 is the list of candidate facilitator genes of MYC-induced cell death. Table lists the candidate facilitators of MYC-induced cell death discovered through the MYC-specific loss of function genetic screen.

Table S4 shows predictions of hypothetical purine nucleotide flux.

Figure S1 shows PCA of human breast tumors, hallmark MYC signature score for human breast tumors, expression of MYC-target NECTIN4, schematic for purine ribonucleotide catabolism, concentrations of nucleotides in physiological conditions, prediction of hypothetical purine nucleotide flux, MYC-induced cell death in MYC-ER HMECs, and candidate facilitators of MYC-induced cell death.

Figure S5 shows expression of MCL1 upon DIS3L knockdown, effect of XDH inhibition on MYC-induced cell death, effect of xanthosine on TNBC apoptosis, ROS and MYC-induced cell death, MYC-induced cell death upon HPRT1 knockdown, and expression of HPRT1 upon knockdown, and effect of DIS3L knockdown on TNBC xenografts.