Structure-activity relationships for the G-quadruplex-targeting experimental drug QN-302 and two analogues probed with comparative transcriptome profiling and molecular modeling

The tetrasubstituted naphthalene diimide compound QN-302 binds to G-quadruplex (G4) DNA structures. It shows high potency in pancreatic ductal adenocarcinoma (PDAC) cells and inhibits the transcription of cancer-related genes in these cells and in PDAC animal models. It is currently in Phase 1a clinical evaluation as an anticancer drug. A study of structure-activity relationships of QN-302 and two related analogues (CM03 and SOP1247) is reported here. These have been probed using comparisons of transcriptional profiles from whole-genome RNA-seq analyses, together with molecular modelling and molecular dynamics simulations. Compounds CM03 and SOP1247 differ by the presence of a methoxy substituent in the latter: these two compounds have closely similar transcriptional profiles. Whereas QN-302 (with an additional benzyl-pyrrolidine group), although also showing down-regulatory effects in the same cancer-related pathways, has effects on distinct genes, for example in the hedgehog pathway. This distinctive pattern of genes affected by QN-302 is hypothesized to contribute to its superior potency compared to CM03 and SOP1247. Its enhanced ability to stabilize G4 structures has been attributed to its benzyl-pyrrolidine substituent fitting into and filling most of the space in a G4 groove compared to the hydrogen atom in CM03 or the methoxy group substituent in SOP1247.

A small-molecule PI3Kα activator for cardioprotection and neuroregeneration

Harnessing the potential beneficial effects of kinase signalling through the generation of direct kinase activators remains an underexplored area of drug development1-5. This also applies to the PI3K signalling pathway, which has been extensively targeted by inhibitors for conditions with PI3K overactivation, such as cancer and immune dysregulation. Here we report the discovery of UCL-TRO-1938 (referred to as 1938 hereon), a small-molecule activator of the PI3Kα isoform, a crucial effector of growth factor signalling. 1938 allosterically activates PI3Kα through a distinct mechanism by enhancing multiple steps of the PI3Kα catalytic cycle and causes both local and global conformational changes in the PI3Kα structure. This compound is selective for PI3Kα over other PI3K isoforms and multiple protein and lipid kinases. It transiently activates PI3K signalling in all rodent and human cells tested, resulting in cellular responses such as proliferation and neurite outgrowth. In rodent models, acute treatment with 1938 provides cardioprotection from ischaemia-reperfusion injury and, after local administration, enhances nerve regeneration following nerve crush. This study identifies a chemical tool to directly probe the PI3Kα signalling pathway and a new approach to modulate PI3K activity, widening the therapeutic potential of targeting these enzymes through short-term activation for tissue protection and regeneration. Our findings illustrate the potential of activating kinases for therapeutic benefit, a currently largely untapped area of drug development.

Abstract 4069: The potent quadruplex-binding compound SOP1812 shows anti-tumor activity in patient-derived in vivo models of pancreatic cancer

The compound SOP1812, a tetra-substituted naphthalene diimide derivative has been previously disclosed to have single-digit nM anti-proliferative activity in a panel of human pancreatic ductal adenocarcinoma (PDAC) cell lines (Ahmed et al., ACS Med Chem Lett, 2020, 11, 1634-1644). It also has significant anti-tumor activity in the MIA-PACA2 xenograft model for PDAC as well as in the more demanding KPC model. We now report that this compound also shows significant anti-tumor activity in three patient-derived xenograft (PDX) models for PDAC. One is from a primary PDAC tumor at stage I and the two others from patients with stage IV PDAC (PDX tumor studies undertaken under contract by Champions Oncology). Transcriptome studies on cellular responses to SOP1812 have previously demonstrated that expression of a number of oncogenes and related signaling pathways are down-regulated by this agent. The promoter regions of these genes have an over-representation of quadruplex-containing sequences and several have also been shown by us to be also down-regulated in treated tumor xenografts. Our working hypothesis that the mechanism of action of SOP1812 in vivo involves targeting of quadruplex-containing genes, is also supported by the PDX data since these tumors have elevated levels of several quadruplex-containing genes previously identified by us in cells and in vivo. SOP1812 is bio-available at therapeutic doses and is well tolerated at these levels in these animal models. It is currently being evaluated as a candidate for clinical development by Qualigen Therapeutics Inc.

Citation Format: Stephen Neidle, Ahmed Ahmed, Richard Angell, Sally Oxenford. The potent quadruplex-binding compound SOP1812 shows anti-tumor activity in patient-derived in vivo models of pancreatic cancer [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 4069.

Regulation of metastasis suppressor NME1 by a key metabolic cofactor coenzyme A

The metastasis suppressor protein NME1 is an evolutionarily conserved and multifunctional enzyme that plays an important role in suppressing the invasion and metastasis of tumour cells. The nucleoside diphosphate kinase (NDPK) activity of NME1 is well recognized in balancing the intracellular pools of nucleotide diphosphates and triphosphates to regulate cytoskeletal rearrangement and cell motility, endocytosis, intracellular trafficking, and metastasis. In addition, NME1 was found to function as a protein-histidine kinase, 3′-5′ exonuclease and geranyl/farnesyl pyrophosphate kinase. These diverse cellular functions are regulated at the level of expression, post-translational modifications, and regulatory interactions. The NDPK activity of NME1 has been shown to be inhibited in vitro and in vivo under oxidative stress, and the inhibitory effect mediated via redox-sensitive cysteine residues. In this study, affinity purification followed by mass spectrometric analysis revealed NME1 to be a major coenzyme A (CoA) binding protein in cultured cells and rat tissues. NME1 is also found covalently modified by CoA (CoAlation) at Cys109 in the CoAlome analysis of HEK293/Pank1β cells treated with the disulfide-stress inducer, diamide. Further analysis showed that recombinant NME1 is efficiently CoAlated in vitro and in cellular response to oxidising agents and metabolic stress. In vitro CoAlation of recombinant wild type NME1, but not the C109A mutant, results in the inhibition of its NDPK activity. Moreover, CoA also functions as a competitive inhibitor of the NME1 NDPK activity by binding non-covalently to the nucleotide binding site. Taken together, our data reveal metastasis suppressor protein NME1 as a novel binding partner of the key metabolic regulator CoA, which inhibits its nucleoside diphosphate kinase activity via non-covalent and covalent interactions.

•

NME1 is a major CoA-binding protein.

•

CoA can bind NME1 through covalent and non-covalent interactions.

•

NME1 CoAlation is induced by oxidative and metabolic stress in mammalian cells.

•

CoA inhibits the NDPK activity of NME1 in vitro.

Asymmetrically Substituted Quadruplex-Binding Naphthalene Diimide Showing Potent Activity in Pancreatic Cancer Models

Targeting of genomic quadruplexes is an approach to treating complex human cancers. We describe a series of tetra-substituted naphthalene diimide (ND) derivatives with a phenyl substituent directly attached to the ND core. The lead compound (SOP1812) has 10 times superior cellular and in vivo activity compared with previous ND compounds and nanomolar binding to human quadruplexes. The pharmacological properties of SOP1812 indicate good bioavailability, which is consistent with the in vivo activity in xenograft and genetic models for pancreatic cancer. Transcriptome analysis shows that it down-regulates several cancer gene pathways, including Wnt/β-catenin signaling.

Substituted Naphthalenediimide Compounds Bind Selectively to Two Human Quadruplex Structures with Parallel Topology

Interactions are reported of three representative naphthalenediimide derivatives with three quadruplex targets, from the promoter region of the telomerase (hTERT) gene, a human telomeric DNA quadruplex, and a telomeric RNA quadruplex (TERRA). Thermal melting studies showed that these compounds strongly stabilize the quadruplexes, with weak stabilization of a duplex DNA. Binding studies by surface plasmon resonance and fluorescence spectroscopy found that the compounds bind to the quadruplexes with nanomolar equilibrium dissociation constants. Plausible topologies for the quadruplex complexes were deduced from CD spectra, which together with the surface plasmon resonance data indicate that the quadruplexes with parallel quadruplex folds are preferred by two compounds, which was confirmed by qualitative molecular modeling.

Identification of Broad-Spectrum Antiviral Compounds by Targeting Viral Entry

Viruses are a major threat to human health and economic well-being. In recent years Ebola, Zika, influenza, and chikungunya virus epidemics have raised awareness that infections can spread rapidly before vaccines or specific antagonists can be made available. Broad-spectrum antivirals are drugs with the potential to inhibit infection by viruses from different groups or families, which may be deployed during outbreaks when specific diagnostics, vaccines or directly acting antivirals are not available. While pathogen-directed approaches are generally effective against a few closely related viruses, targeting cellular pathways used by multiple viral agents can have broad-spectrum efficacy. Virus entry, particularly clathrin-mediated endocytosis, constitutes an attractive target as it is used by many viruses. Using a phenotypic screening strategy where the inhibitory activity of small molecules was sequentially tested against different viruses, we identified 12 compounds with broad-spectrum activity, and found a subset blocking viral internalisation and/or fusion. Importantly, we show that compounds identified with this approach can reduce viral replication in a mouse model of Zika infection. This work provides proof of concept that it is possible to identify broad-spectrum inhibitors by iterative phenotypic screenings, and that inhibition of host-pathways critical for viral life cycles can be an effective antiviral strategy.

Development and validation of RdRp Screen, a crystallization screen for viral RNA-dependent RNA polymerases

Members of the Flaviviridae family constitute a severe risk to human health. Whilst effective drugs have been developed against the hepacivirus HCV, no antiviral therapy is currently available for any other viruses, including the flaviviruses dengue (DENV), West Nile and Zika viruses. The RNA-dependent RNA polymerase (RdRp) is responsible for viral replication and represents an excellent therapeutic target with no homologue found in mammals. The identification of compounds targeting the RdRp of other flaviviruses is an active area of research. One of the main factors hampering further developments in the field is the difficulty in obtaining high-quality crystal information that could aid a structure-based drug discovery approach. To address this, we have developed a convenient and economical 96-well screening platform. We validated the screen by successfully obtaining crystals of both native DENV serotype 2 and 3 RdRps under several conditions included in the screen. In addition, we have obtained crystal structures of RdRp3 in complex with a previously identified fragment using both soaking and co-crystallization techniques. This work will streamline and accelerate the generation of crystal structures of viral RdRps and provide the community with a valuable tool to aid the development of structure-based antiviral design.

Summary: We have developed a 96-well crystallization screen for viral RNA-dependent RNA polymerases (RdRps). The screen provides a convenient platform for streamlining the crystallisation of RdRps and implementing structure-based drug discovery programs.

Progress towards a public chemogenomic set for protein kinases and a call for contributions

Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.

Tetrahydroisoquinolines affect the whole-cell phenotype of Mycobacterium tuberculosis by inhibiting the ATP-dependent MurE ligase

Objectives

(S)-Leucoxine, isolated from the Colombian Lauraceae tree Rhodostemonodaphne crenaticupula Madriñan, was found to inhibit the growth of Mycobacterium tuberculosis H₃₇Rv. A biomimetic approach for the chemical synthesis of a wide array of 1-substituted tetrahydroisoquinolines was undertaken with the aim of elucidating a common pharmacophore for these compounds with novel mode(s) of anti-TB action.

Methods

Biomimetic Pictet–Spengler or Bischler–Napieralski synthetic routes were employed followed by an evaluation of the biological activity of the synthesized compounds.

Results

In this work, the synthesized tetrahydroisoquinolines were found to inhibit the growth of M. tuberculosis H₃₇Rv and affect its whole-cell phenotype as well as the activity of the ATP-dependent MurE ligase, a key enzyme involved in the early stage of cell wall peptidoglycan biosynthesis.

Conclusions

As the correlation between the MIC and the half-inhibitory enzymatic concentration was not particularly strong, there is a credible possibility that these compounds have pleiotropic mechanism(s) of action in M. tuberculosis.

The crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the mechanism of action for dimeric HCV inhibitors

New direct acting antivirals (DAAs) such as daclatasvir (DCV; BMS-790052), which target NS5A function with picomolar potency, are showing promise in clinical trials. The exact nature of how these compounds have an inhibitory effect on HCV is unknown; however, major resistance mutations appear in the N-terminal region of NS5A that include the amphipathic helix and domain 1. The dimeric symmetry of these compounds suggests that they act on a dimer of NS5A, which is also consistent with the presence of dimers in crystals of NS5A domain 1 from genotype 1b. Genotype 1a HCV is less potently affected by these compounds and resistance mutations have a greater effect than in the 1b genotypes. We have obtained crystals of domain 1 of the important 1a NS5A homologue and intriguingly, our X-ray crystal structure reveals two new dimeric forms of this domain. Furthermore, the high solvent content (75%) makes it ideal for ligand-soaking. Daclatasvir (DCV) shows twofold symmetry suggesting NS5A dimers may be of physiological importance and serve as potential binding sites for DCV. These dimers also allow for new conformations of a NS5A expansive network which could explain its operation on the membranous web. Additionally, sulfates bound in the crystal structure may provide evidence for the previously proposed RNA binding groove, or explain regulation of NS5A domain 2 and 3 function and phosphorylation, by domain 1.

The Prophylaxis and Treatment with Antiviral Agents of Respiratory Syncytial Virus Infections

In this review, we consider recent advances in the discovery and development of antiviral agents for respiratory syncytial virus (RSV) infections. A background to the various manifestations of human RSV infection and current treatments is provided. The technical, clinical and commercial issues surrounding the development of such antiviral agents are discussed.

Re-induction of obese body weight occurs more rapidly and at lower caloric intake in beagles

For the purpose of investigating the mechanism of obesity-induction/re-induction including weight-cycling in beagles, a study was conducted using commercially available dog food combined with human food to mimic at home-snacking and diet-supplementation behaviours. Adult female beagles, which had free access to water and exercise, were used (n = 9). All dogs were initially offered two times their daily calculated number of calories using a dry extruded diet plus blend of canola and soybean oils and allowed to eat ad libitum. After 3 weeks, Pecan shortbread cookies were added to the diet mixture. Obesity was induced during a 19-week period with 1875-2250 kcal/day consumed, on average, during this period. The dogs were then subjected to a weight-loss regimen while consuming 490-730 kcal/day. After weight loss, a similar degree of obesity was re-induced for 17 weeks even though dogs consumed only 1125-1250 kcal/day. Body weight, body condition scores, kcal consumption and food efficiency were recorded. Results indicated that less time and fewer kcal were required to re-induce the same degree of obesity compared with the initial obesity induction. Human snack foods appeared to stimulate appetite and thus contribute to the obese state. Food efficiency was also increased during the obesity-reinduction period compared with the induction period. This information may help pet owners better understand the need to limit table scraps and human-type food snacks in dogs prone to obesity as well as weight maintenance after weight loss.

Biphenyl amide p38 kinase inhibitors 3: Improvement of cellular and in vivo activity

The biphenyl amides (BPAs) are a novel series of p38alpha MAP kinase inhibitor. The optimisation of the series to give compounds that are potent in an in vivo disease model is discussed. SAR is presented and rationalised with reference to the crystallographic binding mode.

Structures of S. aureus thymidylate kinase reveal an atypical active site configuration and an intermediate conformational state upon substrate binding

Methicillin-resistant Staphylococcus aureus (MRSA) poses a major threat to human health, particularly through hospital acquired infection. The spread of MRSA means that novel targets are required to develop potential inhibitors to combat infections caused by such drug-resistant bacteria. Thymidylate kinase (TMK) is attractive as an antibacterial target as it is essential for providing components for DNA synthesis. Here, we report crystal structures of unliganded and thymidylate-bound forms of S. aureus thymidylate kinase (SaTMK). His-tagged and untagged SaTMK crystallize with differing lattice packing and show variations in conformational states for unliganded and thymidylate (TMP) bound forms. In addition to open and closed forms of SaTMK, an intermediate conformation in TMP binding is observed, in which the site is partially closed. Analysis of these structures indicates a sequence of events upon TMP binding, with helix alpha3 shifting position initially, followed by movement of alpha2 to close the substrate site. In addition, we observe significant conformational differences in the TMP-binding site in SaTMK as compared to available TMK structures from other bacterial species, Escherichia coli and Mycobacterium tuberculosis as well as human TMK. In SaTMK, Arg 48 is situated at the base of the TMP-binding site, close to the thymine ring, whereas a cis-proline occupies the equivalent position in other TMKs. The observed TMK structural differences mean that design of compounds highly specific for the S. aureus enzyme looks possible; such inhibitors could minimize the transfer of drug resistance between different bacterial species.

First-meiotic-division nondisjunction in human oocytes

Reject oocytes from in vitro-fertilization patients are currently the only practical source of human oocyte material available for meiotic studies in women. Two hundred clearly analyzable second meiotic (MII) metaphase oocytes from 116 patients were examined for evidence of first meiotic (MI) division errors. The chromosome results, in which 67% of oocytes had a normal 23,X chromosome complement but none had an extra whole chromosome, cast doubt on the relevance, to human oocytes, of those theories of nondisjunction that propose that both chromosomes of the bivalent fail to disjoin at MI so that both move to one pole and result in an additional whole chromosome at MII metaphase. The only class of abnormality found in the MII oocytes had single chromatids (half-chromosomes) replacing whole chromosomes. Analysis of the chromosomally abnormal oocytes revealed an extremely close correlation with data on trisomies in spontaneous abortions, with respect to chromosome distribution, frequency, and maternal age, and indicated the likelihood of the chromatid abnormalities being the MI-division nondisjunction products that lead to trisomy formation after fertilization. The most likely derivation of the abnormalities is through a from of misdivision process usually associated with univalents, in which the centromeres divide precociously at MI, instead of MII, division. In the light of recent data that show that altered recombination patterns of the affected chromosomes are a key feature of most MI-division trisomies, the oocyte data imply that the vulnerable meiotic configurations arising from altered recombination patterns are processed as functional univalents in older women. Preliminary evidence from MI-metaphase oocytes supports this view.

Treatment of Tourette's syndrome with transdermal clonidine: a pilot study

Nine patients with mild Tourette's syndrome completed a cross-over, placebo-controlled study of clonidine administered transdermally. Although the subjects showed no improvement on objective measures of symptom severity, most subjects felt they had improved. Seven subjects chose to continue taking clonidine. Larger, blinded studies of transdermal clonidine are indicated.

A three-year follow-up of Cambodian young people traumatized as children

Twenty-seven Cambodian young people, who were severely traumatized at ages 8 to 12, were followed up 3 years after an original study. A structured interview and self-rating scales showed that post-traumatic stress disorders (PTSD) were still highly prevalent (48%). Depression existed in 41%. Those with PTSD differed significantly from those without PTSD on the Global Adjustment Scale, the Social Adjustment Scale, the Beck Depression Inventory, and the Impact of Event Scale. Eight subjects had PTSD at both interviews, while 11 had none at either time. Eight showed a variable course. Avoidance behavior was highly prevalent, even among those without PTSD diagnosis. Although functioning relatively well, these youths continued to show symptoms related to their trauma of 8 to 12 years before.

A comparison of fixed regimens for obtaining human cleaving oocytes for research purposes

A fixed schedule for ovarian stimulation and follicular aspiration, previously used in our department for research purposes, was modified in an attempt to increase the recovery and cleavage rates of the oocytes. Three different clomiphene regimens were used to stimulate the ovaries of normal volunteer women requesting laparoscopic sterilization (50 mg and 150 mg daily for 5 days, and 50 mg daily for 10 days). Oocytes were recovered from 83% of the aspirated follicles, i.e. 1.6 oocytes/patient: 65% of the oocytes cleaved after in-vitro fertilization and, on average, 1.0 cleaving egg was obtained per patient. There were no differences in the recovery and cleavage rates between the three clomiphene regimens. It is concluded that a sufficient number of cleaving embryos for research purposes can be generated with the present fixed regimen, which offers little inconvenience to the volunteers as the day of egg recovery can be predicted some time in advance.

Meiosis-inducing substances in human preovulatory follicular fluid related to time of follicle aspiration and to the potential of the oocyte to fertilize and cleave in vitro

Meiosis-inducing substance (MIS) and steroid and gonadotropic hormones were investigated in 41 preovulatory follicular fluids (FFs) aspirated at either 0, 12, or 36 hours after human chorionic gonadotropin (hCG) administration in 25 women with clomiphene citrate-stimulated cycles. Twenty-one oocytes were recovered from these FFs and subjected to in vitro fertilization. MIS activity was present in 25 (61%) of the FFs. The frequency of MIS-active FFs increased from 11% (1 of 9) at 0 hours and 40% (2 of 5) at 12 hours to 81% (22 of 27) at 36 hours after hCG administration (P less than 0.001). The concentration of hormones in MIS-active FFs was not significantly different from that of MIS-inactive FFs. Twelve (86%) of 14 oocytes that fertilized and cleaved in vitro were recovered from MIS-active FFs. By contrast, all seven oocytes that remained unfertilized in vitro were recovered from MIS-inactive FFs. These findings support the notion that resumption of meiosis in the preovulatory oocyte is triggered by MIS in FF and suggest that follicular MIS production may be one of the factors that determines the success of in vitro fertilization and early embryonic development.

The recovery of pre-ovulatory oocytes using a fixed schedule of ovulation induction and follicle aspiration

Thirty-two volunteer women, scheduled for laparoscopy, were subjected to a fixed regimen of ovulation induction and ovarian follicle aspiration, following manipulation of the previous menstrual cycle with oral contraceptive pills or norethisterone. This allowed the time of oocyte recovery to be planned several weeks in advance. The recovery rate of mature oocytes (loosely dispersed cumulus) in the patients who had their cycles adjusted with norethisterone was comparable to that in a group of women treated in an embryo-transfer programme who were being individually monitored, although there was evidence from cleavage rates and concentration of sex steroids in follicular fluid that further follicular maturation could have occurred. It is suggested that a modification of this schedule could provide an acceptable recovery rate of pre-ovulatory oocytes for research purposes, and possibly by simplifying the monitoring technique could be applicable to a wider range of patients seeking embryo transfer.