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Stomach cancer causes the third-highest cancer-related deaths worldwide. Limited availability of anticancer measures with higher efficiency and low unwanted toxicities necessitates the development of better cancer chemotherapeutics. Naphthalene diimide (NDI) derivatives have gained significant attention owing to their excellent anticancer potential. We evaluated the anticancer properties of NDI derivatives, 1a and 2a in cancer cell lines and found that 1a showed higher efficacy as compared to 2a exhibiting a remarkable difference in activity upon single atom substitution of C with N. Particularly, NDI 1a showed potent inhibitory activity against gastric cancer cell line AGS with IC

DNA-encoded chemical libraries are increasingly used in pharmaceutical research because they enable the rapid discovery of synthetic protein ligands. Here we explored whether target-class focused DNA-encoded chemical libraries can be cost-effective tools to achieve robust screening productivity for a series of proteins. The study revealed that a DNA-encoded library designed for NAD+-binding pockets (NADEL) effectively sampled the chemical binder space of enzymes with ADP-ribosyltransferase activity. The extracted information directed the synthesis of inhibitors for several enzymes including PARP15 and SIRT6. The high dissimilarity of NADEL screening fingerprints for different proteins translated into inhibitors that showed selectivity for their target. The discovery of patterns of enriched structures for six out of eight tested proteins is remarkable for a library of 58 302 DNA-tagged structures and illustrates the prospect of focused DNA-encoded libraries as economic alternatives to large library platforms.

Purpose: About 500,000 people each year worldwide die from metastatic breast cancer. More than 70% of these metastatic breast cancer patients have bone metastases and median survival time from diagnosis of bone metastasis is only 2-3 years. As breast cancer bone metastases are primarily osteolytic, patients suffer from significant morbidities, including severe pain, pathological fractures, nerve compression, and hypercalcemia. Previously, it was shown that RON receptor tyrosine kinase mediates breast cancer outgrowth at metastatic sites, promotes osteolytic bone destruction, and induces systemic immune suppression. We hypothesized that inhibition of RON in specialized resident macrophages and/or osteoclasts will eliminate metastasis through dual effects of blocking osteolysis and enhancing anti-tumor immunity. In this study, we have developed several bis(phosphonate) or phosphate conjugates of BMS-777607 and LY2801653, and report their accumulation in the bone microenvironment along with effects on osteolysis and tumor burden. Methods: We have utilized novel synthetic schemes for synthesis of the drug conjugates. In vitro kinase assays were performed using ADP-Glo RON kinase assay kit (Promega). Hydroxyapatite binding assay was used to determine binding of drug conjugates to the bone mineral. Changes in phosphorylation of RON was demonstrated by Western blotting. Plasma pharmacokinetics and bone accumulation of lead drug conjugates in mice was assessed by mass-spectrometry. An intratibial bone metastasis model in which MSP-expressing MMTV-PyMT tumor cells are injected into the tibia of mice was used to assess the effect of treatment with lead drug conjugates. Results: Seven novel drug conjugates were synthesized and inhibited RON kinase activity with an IC50 of 0.060-2.4 µM. Three drug conjugates demonstrated better hydroxyapatite binding when compared with BMS-777607. In agreement with the in vitro kinase activity, a variable decrease in the phosphorylation of RON was observed in cells treated with the drug conjugates. ZB-28, a monophosphonate derivative of BMS-777607, showed higher accumulation in the bone when compared with BMS-777607 but failed to block tumor-mediated bone osteolysis in an intratibial bone metastasis mouse model. Currently, a cleavable phosphate conjugate of BMS-777607 (ZB-32) is undergoing testing in the same mouse model. We have confirmed that ZB-32 and its hydrolyzed product ZB-33 accumulate in the bone to a significantly higher level than BMS-777607. These results along with preliminary ADME will be presented. Conclusion: Targeting RON kinase in the bone microenvironment is a promising approach to alleviate morbidities observed in breast cancer patients with bone metastases. We present novel bone-targeting conjugates of BMS-777607 and highlight the potential for clinical development. Citation Format: Trason Thode, Jaime Fornetti, Ryan Rodriguez del Villar, Alexis Weston, Serina Ng, Srikanta Dana, Raffaella Soldi, Mohan Kaadige, Hariprasad Vankayalapati, Srinivas Kasibhatla, Alana Welm, Sunil Sharma. Development of bone-targeted Ron inhibitors to treat osseous metastases from breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3948.

[Image: see text] Antimalarial drug resistance is a serious obstacle in the persistent quest to eradicate malaria. There is a need for potent chemical agents that are able to act on drug-resistant Plasmodium falciparum populations at reasonable concentrations without any related toxicity to the host. By rational drug design, we envisaged to address this issue by generating a novel hybrid drug possessing two pharmacophores that can act on two unique and independent targets within the cell. We synthesized a new class of ciprofloxacin-based hybrid molecules, which have been integrated with acridine, quinolone, sulphonamide, and cinnamoyl pharmacophores (1–4). We realized a potent chloroquinolone-ciprofloxacin-based antimalarial hybrid (2, CQ-CFX) whose mechanism of action is unlike that of its parent molecules indicating a unique biological target. CQ-CFX is not only potent against CQ-resistant and susceptible strains of Plasmodium falciparum at low nanomolar concentrations (IC(50) values are 63.17 ± 1.2 nM and 25.52 ± 4.45 nM, respectively) but is also not toxic to mammalian and bacterial systems up to 20 μM and 1 μM, respectively.

DNA-encoded chemical libraries are increasingly used in pharmaceutical research because they enable the rapid discovery of synthetic protein ligands. Here we explored whether target-class focused DNA-encoded chemical libraries can be cost-effective tools to achieve robust screening productivity for a series of proteins. The study revealed that a DNA-encoded library designed for NAD

Purpose: Tumor genetic heterogeneity can lead to dysregulation of transcriptional programs and cause cancer cells to become highly dependent on certain regulators of gene expression. Super-enhancers (SEs) are a class of regulatory regions that are associated with a strong enrichment of transcriptional coactivators (MED1, BRD4) and chromatin marks (H3K27Ac). It has been shown that tumor cells can acquire SEs at oncogenic driver genes (MYC, TERT, BCL2, GFI1, MED1, OCT4, and SOX2), activate their expression, and induce transcriptional reprogramming. Importantly, the majority of super-enhancers depend on the ability of cyclin-dependent kinase 7 (CDK7) to initiate transcription by phosphorylating the C-terminal domain of RNA Pol II. Recent reports have shown that high level of CDK7 is associated with poor prognosis in breast, gastric, ovarian, pancreatic, SCLC, ATC, and AML cancers. We have embarked on developing a novel therapeutic that specifically targets the CDK7 catalytic ATP pocket. Previously, we reported the discovery of TGN-1062 as a potent inhibitor of CDK7. In this study, we report the development of TGN-1076, an analog of TGN-1062, as a selective and reversible inhibitor of CDK7 due to its ideal candidate criteria. Methods: With structure-guided and iterative medicinal chemistry approaches, the previous lead candidate TGN-1062 was further optimized to improve potency, target selectivity, and desirable drug-like properties. In vitro kinase assays were performed using ADP-GloTM kinase assay kit (Promega). Cell viability assays were performed in a panel of cancer cell lines using CellTiter-Glo assay kit (Promega). RNA Pol II phosphorylation and total MYC protein levels were determined by Western Blotting. Results: TGN-1076 inhibited CDK7 activity with an IC50 of 20 nM and showed 10-500 fold selectivity against the closest members of the CDK family. TGN-1076 blocked growth of multiple cancer cells, among these pancreatic cancer cells were most sensitive with an GI50 of 5 µM) against hERG and multiple P450 isozymes. The results from these studies along with ADME-Tox and pharmacokinetics will be presented. Conclusion: In summary, we have developed a novel selective and reversible inhibitor of CDK7. Our current efforts are focused on further optimization and nomination of a preclinical candidate for ADME-Tox and tumor efficacy studies. Citation Format: Trason Thode, Zhaoliang Li, Alexis Weston, Srikanta Dana, Sherin Daniel Ampanattu, Raffaella Soldi, Mohan Rao Kaadige, Hariprasad Vankayalapti, Vincent Chung, Joseph Chao, Daniel D Von Hoff, Sunil Sharma. Development of TGN-1076, a selective and reversible small molecule inhibitor of CDK7 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5221.

Purpose: In recent years, programs targeting the innate immune pathways alone and alongside the adaptive immune pathways have become increasingly popular. A main area of interest in innate immunity is the STING (STimulator of INterferon Genes) pathway. STING plays an integral role by activating type 1 interferons in response to detection of cytosolic nucleic acid by cGAS (Cyclic GMP-AMP Synthase). cGAS detects cytosolic DNA and converts it into 2′3′ cGAMP, which is the direct ligand of STING. Targeting the direct activation of this pathway using synthetic, non-hydrolyzable forms of this ligand has shown to be effective in preclinical efficacy models, but has failed to impress in phase 1 clinical trials. Another method of activating this pathway is to inhibit the direct negative regulator, ENPP1 (Ectonucleotide pyrophosphatase/phosphodiesterase 1). ENPP1 constitutively hydrolyzes 2′3′-cGAMP, suppressing the pathway both in the cancer cells and in the surrounding tumor microenvironment. Previously, we reported that SR-8314, a highly selective and potent ENPP1 inhibitor, induces the activation of the STING pathway via type I interferon response in both in vitro and in vivo models. In this study, we continue this research and present our nominated clinical candidate, SR-8541A, which shows improved physiochemical characteristics and increased immune response. Methods: Direct binding of SR-8541A to ENPP1 was evaluated using a thermal shift assay. Inhibition of ENPP1 enzymatic activity was shown using TMP or ATP as substrates in either cell free or cell based assays. RT-PCR, western blots, immune infiltration using peripheral blood mononuclear cells (PBMCs), and MesoScale Disovery (MSD) ELISA assays were performed to evaluate the effect of SR-8541A on the STING pathway. ENPP1 CRISPR knockout cells were generated to demonstrate on-target activity of SR-8541A. Pharmacokinetics, stability, and selectivity were completed with outside vendors. Results: SR-8541A exhibits strong binding to ENPP1 and shows inhibitory activity at an IC50 of 1.4 nM. STING pathway activation was confirmed by a significant increase in gene expression of IFNβ, ISG15 and CXCL10 in SR-8541A treated cells. An increase in secreted type 1 interferon and other cytokines was also observed in these treated cells. Using immune infiltration assays, we show that SR-8541A stimulates the migration and infiltration of immune cells (PBMC) into cancer spheroids. Importantly, depletion of dendritic cells results in loss of infiltration of remaining PBMCs into cancer spheroids. Additionally, natural killer (NK) cells do not infiltrate into SR-8541A treated cancer spheroids unless co-cultured with dendritic cells. ENPP1 CRISPR knockout cell models confirmed that the drug effect was dependent on the presence of ENPP1. SR-8541A was stable for >60 mins in liver microsomes and S9 fractions from various species. Rodent pharmacokinetics showed a strong oral bioavailability of ~50% and tumor efficacy studies are ongoing. Conclusions: In summary, we show that SR-8541A is a potent and selective inhibitor of ENPP1 that displayed strong immune response in 3D spheroid models. The results from these studies along with physiochemical properties and tumor model data will be presented. The promising physiochemical properties make it a strong candidate for clinical studies. Citation Format: ALEXIS S. WESTON, Trason G. Thode, Ryan Rodriguez del Villar, Srikanta Dana, Srinivas Kasibhatla, Mohan R. Kaadige, Sunil Sharma. SR8541A is a potent inhibitor of ENPP1 and exhibits dendritic cell mediated antitumor activity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-118.

Naphthalene diimide (NDI) derivatives have been shown to exhibit promising antineoplastic properties. In the current study, we assessed the anticancer and anti-bacterial properties of di-substituted NDI derivative. The naphthalene-bis-hydrazimide, 1, negatively affected the cell viability of three cancer cell lines (AGS, HeLa and PC3) and induced S phase cell cycle arrest along with SubG0/G1 accumulation. Amongst three cell lines, gastric cancer cell line, AGS, showed the highest sensitivity towards the NDI derivative 1. Compound 1 induced extensive DNA double strand breaks causing p53 activation leading to transcription of p53 target gene p21 in AGS cells. Reduction in protein levels of p21 and BRCA1 suggested that 1 treated AGS cells underwent cell death due to accumulation of DNA damage as a result of impaired DNA damage repair. β-catenin downregulation and consequently decrease in levels of c-Myc may have led to 1 induced AGS cell proliferation inhibition.1 induced AGS cell S phase arrest was mediated through CylinA/CDK2 downregulation. The possible mechanisms involved in anticancer activity of 1 includes ROS upregulation, induction of DNA damage, disruption of mitochondrial membrane potential causing ATP depletion, inhibition of cell proliferation and downregulation of antiapoptotic factors ultimately leading to mitochondria mediated apoptosis. Further compound 1 also inhibited H. pylori proliferation as well as H. pylori induced morphological changes in AGS cells. These findings suggest that NDI derivative 1 exhibits two-pronged anticancer activity, one by directly inhibiting cancer cell growth and inducing apoptosis and the other by inhibiting H. pylori.

This chapter describes some of the most extensively investigated π-conjugated scaffolds, which have the inherent ability to accept one or more electrons. Thus, the progress of the knowledge of well-known electron acceptors in recent times is deliberated. The focus of the chapter has been to highlight the new developments in the direction of design and synthesis of ambient stable open-shell, multi-anionic and multi-radical based systems and their new age applications. It is realized that weak intramolecular and intermolecular noncovalent interactions play pivotal role towards the delocalization of the unpaired electron and stability of the system. The significance of molecular and crystal engineering principles is discussed, which allow efficient transport of electrons in highly electron deficient systems to confer high charge mobility. The recent advances in molecular design approaches towards non-fullerene based electron acceptors for organic solar cells are illustrated. The photophysical properties of the excited doublet states of these radical anions have been discussed, which have shown that it is possible to control the movement of electrons within a multisite donor–acceptor array on a femtosecond time scale. In addition, the application of the photoexcited radical ions towards C–C bond formation reactions and aryl halide reduction is elucidated. Furthermore, the applications of the radical ions as probes to sense toxic analytes utilizing their attractive multi-channel absorption properties are explained. Finally, we examine the recent progress made en route to utilizing these π-conjugated electroactive materials for organic Li ion batteries.

Malaria continues to be a major health problem globally. There is an urgent need to find new antimalarials. Acriflavine (ACF) is known as an antibacterial agent and more recently as an anticancer agent. Here, we report that ACF inhibits the growth of asexual stages of both chloroquine (CQ) sensitive and resistant strains of human malarial parasite, Plasmodium falciparum in vitro at nanomolar concentration. ACF clears the malaria infection in vivo from the bloodstreams of mice infected with Plasmodium berghei. Interestingly, ACF is accumulated only in the parasitized red blood cells (RBCs) and parasite specific transporters may have role in this specific drug accumulation. We further show that ACF impairs DNA replication foci formation in the parasites and affects the enzymatic activities of apicoplast specific Gyrase protein. We thus establish ACF as a potential antimalarial amidst the widespread incidences of drug resistant Plasmodium strains.

A novel class of bifunctional molecules was synthesized integrating acridine (Ac) and redox-active naphthalenediimide (NDI) scaffolds directly and through a flexible linker (en). We evaluated in vitro antiplasmodial activity, physicochemical properties, and a possible mode of action. Theoretical studies suggested electronic segmentation between the electron-rich Ac and electron-deficient NDI scaffolds. Orthogonal Ac–NDI molecules showed activities in the micromolar to submicromolar range against a chloroquine (CQ)-sensitive strain of human malaria pathogen Plasmodium falciparum (maximum activity, IC50: 0.419 μM). The flexible Ac–en–NDI molecules were most potent and showed activity in the nanomolar range against both CQ-sensitive (with most effective compounds, IC50: 3.65 and 4.33 nM) as well as CQ-resistant (with most effective compounds, IC50: 52.20 and 28.53 nM) strains of P. falciparum. Significantly, with CQ-resistant strains, the activity of the most effective compounds was 1 order of magnitude better than that of standard drug CQ. Ac–en–NDI-conjugated molecules were significantly more potent than the individual NDI and Ac-based molecules. The structure–activity relationship (SAR) suggests that the flexible spacer (en) linking the Ac and NDI scaffolds plays a vital role in exhibiting improved potency. None of the molecules triggered hemolysis in culture, and the most potent compounds did not show cytotoxicity in vitro against mammalian fibroblast NIH3T3 cells at their respective IC50 values. The other significant outcome of this work is that some of the investigated molecules have the potential to affect multiple processes in the parasite including the hemozoin formation in digestive vacuoles (DVs), mitochondrial membrane potential, and the redox homeostasis of the parasite.

An electronically segmented amphiphile was created by conjugating two π-functional units hydroxyquinoline and naphthalenediimide (HQ/NDI) for the first time. The differential electrostatic potential of the π-surfaces, H-bonding units, etc. trigger a manifold response and direct the assembly of a unique collection of seven diverse nano-architectures. Chiral assembly, distinct classes of fibers, 3-D sheets, and metallo-spheres/fibrils with μM levels of Co/Cu/Zn(II) ions emerged from this new approach of assorted morphosynthesis under ambient conditions.

Apicoplast, an essential organelle of human malaria parasite Plasmodium falciparum contains a ∼35 kb circular genome and is a possible target for therapy. Proteins required for the replication and maintenance of the apicoplast DNA are not clearly known. Here we report the presence of single–stranded DNA binding protein (SSB) in P falciparum. PfSSB is targeted to the apicoplast and it binds to apicoplast DNA. A strong ssDNA binding activity specific to SSB was also detected in P. falciparum lysate. Both the recombinant and endogenous proteins form tetramers and the homology modelling shows the presence of an oligosaccharide/oligonucleotide-binding fold responsible for ssDNA binding. Additionally, we used SSB as a tool to track the mechanism of delayed death phenomena shown by apicoplast targeted drugs ciprofloxacin and tetracycline. We find that the transport of PfSSB is severely affected during the second life cycle following drug treatment. Moreover, the translation of PfSSB protein and not the transcription of PfSSB seem to be down-regulated specifically during second life cycle although there is no considerable change in protein expression profile between drug-treated and untreated parasites. These results suggest dual control of translocation and translation of apicoplast targeted proteins behind the delayed death phenomena.