Enhanced Oral Bioavailability of 2-(Phosphonomethyl)-pentanedioic Acid (2-PMPA) from its (5-Methyl-2-oxo-1,3-dioxol-4-yl)methyl (ODOL)-Based Prodrugs

2-(Phosphonomethyl)-pentanedioic acid (2-PMPA) is a potent (IC₅₀ = 300 pM) and selective inhibitor of glutamate carboxypeptidase II (GCPII) with efficacy in multiple neurological and psychiatric disease preclinical models and more recently in models of inflammatory bowel disease (IBD) and cancer. 2-PMPA (1), however, has not been clinically developed due to its poor oral bioavailability (<1%) imparted by its four acidic functionalities (c Log P = -1.14). In an attempt to improve the oral bioavailability of 2-PMPA, we explored a prodrug approach using (5-methyl-2-oxo-1,3-dioxol-4-yl)methyl (ODOL), an FDA-approved promoiety, and systematically masked two (2), three (3), or all four (4) of its acidic groups. The prodrugs were evaluated for in vitro stability and in vivo pharmacokinetics in mice and dog. Prodrugs 2, 3, and 4 were found to be moderately stable at pH 7.4 in phosphate-buffered saline (57, 63, and 54% remaining at 1 h, respectively), but rapidly hydrolyzed in plasma and liver microsomes, across species. In vivo, in a single time-point screening study in mice, 10 mg/kg 2-PMPA equivalent doses of 2, 3, and 4 delivered significantly higher 2-PMPA plasma concentrations (3.65 ± 0.37, 3.56 ± 0.46, and 17.3 ± 5.03 nmol/mL, respectively) versus 2-PMPA (0.25 ± 0.02 nmol/mL). Given that prodrug 4 delivered the highest 2-PMPA levels, we next evaluated it in an extended time-course pharmacokinetic study in mice. 4 demonstrated an 80-fold enhancement in exposure versus oral 2-PMPA (AUC_0-t: 52.1 ± 5.9 versus 0.65 ± 0.13 h*nmol/mL) with a calculated absolute oral bioavailability of 50%. In mouse brain, 4 showed similar exposures to that achieved with the IV route (1.2 ± 0.2 versus 1.6 ± 0.2 h*nmol/g). Further, in dogs, relative to orally administered 2-PMPA, 4 delivered a 44-fold enhanced 2-PMPA plasma exposure (AUC_0-t for 4: 62.6 h*nmol/mL versus AUC_0-t for 2-PMPA: 1.44 h*nmol/mL). These results suggest that ODOL promoieties can serve as a promising strategy for enhancing the oral bioavailability of multiply charged compounds, such as 2-PMPA, and enable its clinical translation.

Abstract 3602: JHU395, a nervous tissue penetrant glutamine antagonist, restricts growth of malignant peripheral nerve sheath tumor with inhibition of nucleotide synthesis

Malignant peripheral nerve sheath tumor (MPNST) is a sarcoma that occurs in ~10% of patients with neurofibromatosis type I (NF1). Incomplete surgical resection at diagnosis leads to a 4-year event-free survival rate of &lt;30%. Thus, improved treatments are needed. Recent evidence suggests that perturbing glutamine utilization warrants further exploration as a potential therapeutic strategy for MPNST. Competitive glutamine antagonists (GA) have been studied in several clinical trials for sarcoma previously, but clinical development was hampered by gastrointestinal (GI) toxicity. JHU395 is a broadly active nervous tissue penetrant GA. JHU395 delivers active GA preferentially to nervous tissue which may result in less GI toxicity than was observed in past trials. The primary goals of this study were to evaluate JHU395 in preclinical models of MPNST and to investigate tumor metabolic changes in response to JHU395. We investigated glutamine antagonism on growth of MPNST cells in culture and murine flank MPNST. JHU395 was administered orally for 14 days to mice bearing inoculated tumors derived from the NPcis (NF1+/-;p53+/-) genetically engineered model of MPNST. Tumors were measured every other day and tumor volume was calculated as the primary endpoint. Concurrent evaluations of GI and neurotoxicity were performed as secondary endpoints. GA levels in tumor versus plasma were compared using a previously validated bioanalytical method. In vivo stable isotope labeled glutamine (15N2- or 13C5-labeled) flux analysis and targeted liquid chromatography-mass spectrometry (LC-MS) metabolomics were performed on murine tumors. Compared to immortalized Schwann cells, growth of MPNST was preferentially inhibited by GA (IC50=8 micromolar versus &gt;30 micromolar). JHU395 delivered GA to MPNST cells with &gt;4-fold higher cell-to-plasma ratio compared to native GA and maintained ~2.5-fold higher tumor-to-plasma GA levels in vivo. Mice treated with JHU395 had &gt;40% smaller mean tumor volume compared to controls with no overt toxicity. Quantitiative bioanalysis revealed that JHU395 treated tumors had &gt;60% higher glutamine levels compared to controls 30 minutes after oral dosing. In vivo flux analysis demonstrated that JHU395 preferentially affects tumor glutamine utilization for nucleotide synthesis, while glutamine-derived substrates for the citric acid cycle appear unaffected. In summary, JHU395 inhibits growth of MPNST with inhibition of glutamine utilization in nucleotide synthesis and is well-tolerated. Nervous tissue penetrant glutamine antagonism is a feasible and effective therapeutic approach in preclinical models of MPNST. Future studies will investigate JHU395 in combination with nucleotide synthesis inhibitors in MPNST and investigate JHU395 efficacy in additional sarcoma models including patient-derived samples.

Citation Format: Kathryn M. Lemberg, Liang Zhao, Ying Wu, Jesse Alt, Joanna Marie H. Aguilar, Jenny Lam, Alexandra J. Gadiano, Rana Rais, Pavel Majer, Jaishri Blakeley, Barbara S. Slusher. JHU395, a nervous tissue penetrant glutamine antagonist, restricts growth of malignant peripheral nerve sheath tumor with inhibition of nucleotide synthesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3602.

Abstract 3620: Tumor targeted delivery of glutamine antagonist: Use of CES1-/- mice

6-diazo-5-oxo-L-norleucine (DON), a potent glutamine antagonist, broadly blocks glutamine utilizing reactions critical for the synthesis of nucleic acids, amino acids, proteins and the generation of alpha-ketoglutarate for energy metabolism. DON has shown robust efficacy in multiple preclinical cancer models and exploratory clinical studies. Although promising, development of DON was halted due to its dose-limiting gastrointestinal (GI)-toxicities, as the GI system is highly dependent on glutamine utilization. Given DON’s promising efficacy, we developed novel tumor cell-targeted glutamine antagonists intended to circulate intact as inert prodrug/s in plasma and be preferentially biotransformed to DON in tumor cells. Our prodrug strategy of utilizing elevated protease activities in cancer tissues (e.g. Histone deacetylase, Cathepsin-L) led to the discovery of a highly innovative prodrug pharmacophore. Using a well-defined screening paradigm, we discovered compound 6, (isopropyl 2-(6-acetamido-2-(adamantane-1-carboxamido) hexanamido)-6-diazo-5-oxohexanoate), that showed stability in plasma, liver and intestinal homogenates, yet was readily cleaved to DON in P493B human tumor cells. When directly compared to DON, compound 6, exhibited a 55-fold enhanced P493B cell-to-plasma ratio. In a time-dependent study, compound 6 showed sustained DON delivery to P493B cells while maintaining minimal release in human plasma. Moreover, in a cell proliferation assay, compound 6 showed dose-dependent inhibition of P493B cell growth. One challenging aspect of prodrug development is the selection of appropriate animal model, as it can be confounded by interspecies variation in metabolism, specifically in the varying levels of the carboxylesterase enzyme, CES1, which is highly abundant in rodent plasma but not present in human plasma. We hypothesized that CES1-/- mice would recapitulate human metabolism and serve as a suitable model for our prodrug containing ester promoiety on its carboxylate. Using plasma from CES1-/- mice, wild-type mice and human, we confirmed that compound 6 exhibited similar stability in CES1-/- mice and human plasma but not in wild-type mice plasma. We then performed pharmacokinetic evaluation in C57BL/6 CES1-/- mice bearing flank murine EL4 tumors. Following subcutaneous dosing (1mg/kg DON equivalent), compound 6 exhibited excellent pharmacokinetics with a ~5-fold higher DON tumor exposures (AUC= 5.1 nmol/g*h) versus plasma (1.1 nmol/ml*h) and a 11-fold higher tumor exposures versus GI-tissues (toxicity site; AUC = 0.45 nmol/ml*h). These studies describe discovery of a tumor targeted glutamine antagonist. In addition, we introduce a murine model, that recapitulates human metabolism and can be broadly utilized in prodrug development. Future studies will investigate the dose dependent efficacy and safety of compound 6 in tumor bearing C57BL/6 CES1-/- mice.

Citation Format: Rana Rais, Jesse Alt, Ranjeet Dash, Lukáš Tenora, Pavel Majer, Barbara S. Slusher. Tumor targeted delivery of glutamine antagonist: Use of CES1-/- mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3620.

Correction: JHU-083 selectively blocks glutaminase activity in brain CD11b+ cells and prevents depression-associated behaviors induced by chronic social defeat stress

During this process, we found that we need add the following sentence in the manuscript within the Acknowledgement section.

Tumor-Targeted Delivery of 6-Diazo-5-oxo-l-norleucine (DON) Using Substituted Acetylated Lysine Prodrugs

6-Diazo-5-oxo-l-norleucine (DON) is a glutamine antagonist with robust anticancer efficacy; however, its therapeutic potential was hampered by its biodistribution and toxicity to normal tissues, specifically gastrointestinal (GI) tissues. To circumvent DON's toxicity, we synthesized a series of tumor-targeted DON prodrugs designed to circulate inert in plasma and preferentially activate over DON in tumor. Our best prodrug 6 (isopropyl 2-(6-acetamido-2-(adamantane-1-carboxamido)hexanamido)-6-diazo-5-oxohexanoate) showed stability in plasma, liver, and intestinal homogenates yet was readily cleaved to DON in P493B lymphoma cells, exhibiting a 55-fold enhanced tumor cell-to-plasma ratio versus that of DON and resulting in a dose-dependent inhibition of cell proliferation. Using carboxylesterase 1 knockout mice that were shown to mimic human prodrug metabolism, systemic administration of 6 delivered 11-fold higher DON exposure to tumor (target tissue; AUC_{0- t} = 5.1 nmol h/g) versus GI tissues (toxicity tissue; AUC_{0- t} = 0.45 nmol h/g). In summary, these studies describe the discovery of a glutamine antagonist prodrug that provides selective tumor exposure.

JHU-083 selectively blocks glutaminase activity in brain CD11b+ cells and prevents depression-associated behaviors induced by chronic social defeat stress

There are a number of clinically effective treatments for stress-associated psychiatric diseases, including major depressive disorder (MDD). Nonetheless, many patients exhibit resistance to first-line interventions calling for novel interventions based on pathological mechanisms. Accumulating evidence implicates altered glutamate signaling in MDD pathophysiology, suggesting that modulation of glutamate signaling cascades may offer novel therapeutic potential. Here we report that JHU-083, our recently developed prodrug of the glutaminase inhibitor 6-diazo-5-oxo-L-norleucine (DON) ameliorates social avoidance and anhedonia-like behaviors in mice subjected to chronic social defeat stress (CSDS). JHU-083 normalized CSDS-induced increases in glutaminase activity specifically in microglia-enriched CD11b⁺ cells isolated from the prefrontal cortex and hippocampus. JHU-083 treatment also reverses the CSDS-induced inflammatory activation of CD11b⁺ cells. These results support the importance of altered glutamate signaling in the behavioral abnormalities observed in the CSDS model, and identify glutaminase in microglia-enriched CD11b⁺ cells as a pharmacotherapeutic target implicated in the pathophysiology of stress-associated psychiatric conditions such as MDD.

The unraveling of substrate specificity of histone deacetylase 6 domains using acetylome peptide microarrays and peptide libraries

Histone deacetylase 6 (HDAC6) is a multidomain cytosolic hydrolase acting mostly on nonhistone protein substrates. Investigations of the substrate specificity of HDAC6 are confounded by the presence of 2 catalytically active deacetylase domains (DD1 and DD2). In this study, acetylome peptide microarrays and peptide libraries were used to map the substrate specificity of DD1 and DD2 of human HDAC6. The results show that DD1 is solely responsible for the deacetylation of substrates harboring the acetyllysine at their C terminus, whereas DD2 exclusively deacetylates peptides with an internal acetyllysine residue. Also, statistical analysis of the deacetylation data revealed amino acid preferences at individual positions flanking the acetyllysine, where glycine and arginine residues are favored at positions N-terminal to the central acetyllysine; negatively charged glutamate is strongly disfavored throughout the sequence. Finally, the deacylation activity of HDAC6 was profiled by using a panel of acyl derivatives of the optimized peptide substrate and showed that HDAC6 acts as a proficient deformylase. Our data thus offer a detailed insight into the substrate preferences of the individual HDAC6 domains at the peptide level, and these findings can in turn help in elucidating the biologic roles of the enzyme and facilitate the development of new domain-specific inhibitors as research tools or therapeutic agents.-Kutil, Z., Skultetyova, L., Rauh, D., Meleshin, M., Snajdr, I., Novakova, Z., Mikesova, J., Pavlicek, J., Hadzima, M., Baranova, P., Havlinova, B., Majer, P., Schutkowski, M., Barinka, C. The unraveling of substrate specificity of histone deacetylase 6 domains using acetylome peptide microarrays and peptide libraries.

Identification and Enantiodivergent Synthesis of (5 Z,9 S)-Tetradec-5-en-9-olide, a Queen-Specific Volatile of the Termite Silvestritermes minutus

The queens of social insects differ from sterile colony members in many aspects of their physiology. Besides adaptations linked with their specialization for reproduction and extended lifespan, the queens also invest in the maintenance of their reproductive dominance by producing exocrine chemicals signaling their presence to the nestmates. The knowledge of the chemistry of queen-specific cues in termites is scarce. In addition to the contact recognition based on cuticular hydrocarbons, long-range signals mediated by volatiles are expected to participate in queen signaling, especially in populous colonies of higher termites (Termitidae). In queens of the higher termite Silvestritermes minutus (Syntermitinae), we have detected a previously undescribed volatile. It is present in important quantities on the body surface and in the headspace, ovaries, and body cavity. MS and GC-FTIR data analyses led us to propose the structure of the compound to be a macrolide 10-pentyl-3,4,5,8,9,10-hexahydro-2 H-oxecin-2-one. We performed enantiodivergent syntheses of two possible enantiomers starting from enantiopure ( S)-glycidyl tosylate. The synthetic sequence involved macrolide-closing metathesis quenched with a ruthenium scavenging agent. The absolute and relative configuration of the compound was assigned to be (5 Z,9 S)-tetradec-5-en-9-olide. Identification and preparation of the compound allow for investigation of its biological significance.

Abstract 4963: Targeting glutamine metabolism as a means of enhancing antitumor T-cell responses

Tumors possess specialized metabolic programming that facilitates their rapid growth. We have developed a novel glutamine antagonist (JHU-083) that not only demonstrates single-agent efficacy in a variety of mouse tumor models but also synergizes with anti-PD-1, adoptive cellular therapy (ACT) and A2aR antagonism to overcome resistance to immunotherapy and promote durable cures. Interestingly, we have observed that JHU-083 markedly enhances endogenous antitumor T-cell responses even in the absence of additional immunotherapy. Flow cytometry analyses of tumor-infiltrating lymphocyte (TIL) reveal markedly increased infiltration of CD8+ T cells with increased proliferative index (Ki67) and the generation of robust memory phenotypes in JHU-083 treated mice. Interestingly, Gene Set Enrichment Analyses (GSEA) using RNA-sequencing data revealed that CD8+ TIL from vehicle treated mice showed significantly enhanced expression of apoptotic transcriptional programs compared with TIL from mice treated with JHU-083. Consistent with flow cytometry data, GSEA showed CD8+ TILs from mice treated with glutamine antagonism expressed transcriptional programs characteristic of long-lived memory cells. To this end, vaccination experiments in mice treated with JHU-083 demonstrate that many of the phenotypic changes observed in TIL can be generated outside the TME and are due to direct effects of glutamine blockade on effector T cells. Our studies show that these transcriptional changes are associated with profound remodeling of the histone epigenetic code and correlate with decreased intracellular levels of α-ketoglutarate in response to glutamine antagonism. Supplementation with dimethyl α-ketoglutarate, a cell-permeable form of α-ketoglutarate, partially reverses phenotypic and epigenetic changes in CD8 T cells undergoing activation in the setting of glutamine antagonism. These findings are consistent with inhibition of a family of enzymes known as α-ketoglutarate dependent dioxygenases, which are responsible for a broad range of demethylation reactions, including histone and DNA demethylation. Overall, our work demonstrates that glutamine antagonism can directly inhibit tumor growth and survival while also reprogramming maladaptive antitumor T-cell responses to enhance endogenous antitumor immunity. Such observations support the development of our novel glutamine antagonists as both monotherapy and in combination with immunotherapy.

Citation Format: Robert Leone, Judson Englert, Im-Meng Sun, Min-Hee Oh, Jesse Alt, Im-Hong Sun, Ada J. Tam, Pavel Majer, Rana Rais, Barbara Slusher, Jonathan Powell. Targeting glutamine metabolism as a means of enhancing antitumor T-cell responses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4963.

Abstract 3524: Novel prodrugs of the glutamine antagonist 6-diazo-5-oxo-norleucine (DON) as treatment for malignant peripheral nerve sheath tumor

Neurofibromatosis Type I (NF1) is a heritable tumor predisposition syndrome in which up to 10% of patients develop malignant peripheral nerve sheath tumor (MPNST), an aggressive sarcoma. For MPNST that is incompletely resected at diagnosis, traditional cytotoxic chemotherapeutic strategies offer a 5 year event-free survival of less than 40%; thus new therapeutic strategies are desperately needed. Reprogramming of energy metabolism, whereby tumor cells take up more glutamine than healthy cells and direct this substrate to replenish metabolites for proliferation, is a hallmark of several cancers that has not been effectively leveraged for treatment of MPNST. Our group has recently described JHU 395, a nervous system targeted prodrug of the glutamine antagonist 6-diazo-5-oxo-norleucine (DON) which delivers DON preferentially to the brain resulting in less gastrointestinal toxicity, which was the main toxicity of DON in past clinical trials. The primary goals of this study were to evaluate glutamine antagonism and JHU 395 activity in MPNST. Using multiple Schwann and MPNST cell lines we investigated cell proliferation in culture under glutamine deprivation and antagonism. Mass spectrometry (MS)-based metabolomic profiling was used to characterize differences between MPNST cells treated with vehicle versus DON. MS-based bioanalytical methods were also used to investigate DON delivery to tumor cells by JHU 395. We found that growth of MPNST cells in culture is preferentially inhibited by glutamine deprivation and DON treatment when compared to immortalized Schwann cells derived from non-tumored nerve (IC50 of 8-9 micromolar versus &gt;30 micromolar). Targeted metabolomics analyses of DON treated human MPNST cells demonstrated multiple differences in downstream glutamine-dependent metabolites including intermediates in purine synthesis and amino acid synthesis, suggesting that DON acts broadly within the tumor cell to inhibit growth. While DON showed limited partitioning into MPNST cells versus plasma, JHU 395 preferentially delivered DON into MPNST with over 5-fold higher cell-to-plasma ratio. Prodrug pharmacokinetic studies in mouse demonstrated that oral administration of the prodrug safely delivered DON at micromolar concentrations to peripheral nerve. In conclusion, compared to healthy Schwann cells, MPNST cells have unique vulnerability to antagonizing glutamine utilization. The nervous system directed prodrug JHU 395 enhances DON delivery to MPNST and represents a novel potential therapeutic approach for these aggressive tumors. Based on these results we have initiated efficacy studies of JHU 395 in the murine NPcis (NF1+/-;p53+/-) model of MPNST.

Citation Format: Kathryn Lemberg, Ying Wu, Jesse Alt, Liang Zhao, Alexandra J. Gadiano, Chabely Rodriguez, Rana Rais, Pavel Majer, Jaishri Blakeley, Barbara Slusher. Novel prodrugs of the glutamine antagonist 6-diazo-5-oxo-norleucine (DON) as treatment for malignant peripheral nerve sheath tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3524.

Abstract 4730: Targeting glutamine metabolism enhances tumor specific immunity by inhibiting the generation and function of suppressive myeloid cells

In order to sustain their inexorable growth, tumors have specialized reprogrammed metabolism. This metabolism creates an acidic, hypoxic and nutrient-depleted tumor microenvironment (TME). Such an environment inhibits antitumor effector cells while promoting the differentiation and function of inhibitory cells such as T regulatory cells, myeloid-derived suppressor cells (MDSC) and tumor-associated macrophages (TAM). We hypothesized that by targeting tumor metabolism we could alter the TME and “condition” tumors to be more susceptible to immunotherapy. To this end, along with the Johns Hopkins Drug Discovery Program we developed a novel prodrug of 6-diazo-5-oxo-l-norleucine, inhibitor of glutamine metabolism (JHU-083). Recently, it has been shown that M2 macrophages require glutamine metabolism for differentiation and function. In light of the similarities between M2 macrophages and suppressive myeloid cells, we hypothesized that JHU-083 might inhibit the generation and function of MDSCs and TAMs. We tested this hypothesis in the 4T1 breast cancer model and 3LL lung carcinoma model. These tumors are relatively resistant to immunotherapy and are characterized by increased generation of MDSCs and distant spontaneous metastasis. JHU-083 treated mice suppressed tumor growth compared to the vehicle treated group. Immunologically, we observed markedly reduced numbers of MDSCs in circulating blood within 3 days of drug treatment compared to vehicle group, leading to favorable CD8 to MDSCs ratios. Consistently, JHU083-treated group displayed significantly decreased percentages and numbers of MDSCs in the tumor, and increased tumor infiltrating CD8 cells. Interestingly, JHU-083 treatment induced TAM reprogramming. While the TAM from the vehicle treated group displayed increased M2 markers and arginase; the JHU-083 treated tumor-infiltrating cells showed increased TNF-a producing M1-like macrophage phenotypes compared to vehicle group. These TNF-a producing cells were negatively correlated with tumor sizes. Notably, JHU083 treatment not only controlled primary tumor growth but also drastically reduced spontaneous lung metastasis. The decrease of MDSCs infiltration in the lung were also observed in JHU083-treated group. Mechanistically, our data suggest that JHU-083 inhibits CSF2/CSF3 production and survival of the tumor itself as well as directly affects macrophage metabolism and signaling. Also, LC-MS based metabolites analysis from JHU-083 treated tumors revealed reduced kynurenine:tryptophan ratios compared to the control group, indicating the metabolic modulation of the tumor microenvironment. Overall, our data support a novel role for glutamine inhibitor, JHU-083, in enhancing tumor-specific Immunity by targeting suppressive myeloid cells.

Citation Format: Min-Hee Oh, Im-Hong Sun, Liang Zhao, Im-Meng Sun, Wei Xu, Chirag Patel, Robert Leone, Ada J. Tam, Judd Englert, Pavel Majer, Rana Rais, Barbara Slusher, Maureen R. Horton, Jonathan D. Powell. Targeting glutamine metabolism enhances tumor specific immunity by inhibiting the generation and function of suppressive myeloid cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4730.

N-Substituted Prodrugs of Mebendazole Provide Improved Aqueous Solubility and Oral Bioavailability in Mice and Dogs

Mebendazole (MBZ) was developed as a broad-spectrum anthelmintic but has recently shown efficacy as an anticancer agent. The use of MBZ for cancer, however, is challenging due to its poor solubility leading to poor bioavailability. Herein, we developed a prodrug approach with various N-linked promoieties including acyloxymethyl, aminoacyloxymethyl, and substituted phosphonooxymethyl in attempt to improve these characteristics. Compound 12, containing an (((((isopropoxycarbonyl)oxy)methoxy)phosphoryl)oxy)methyl promoiety, showed a >10 000-fold improvement in aqueous solubility. When evaluated in mice, 12 displayed a 2.2-fold higher plasma AUC_{0- t} and a 1.7-fold improvement in brain AUC_{0- t} with a calculated oral bioavailability of 52%, as compared to 24% for MBZ-polymorph C (MBZ-C), the most bioavailable polymorph. In dogs, 12 showed a 3.8-fold higher plasma AUC_{0- t} with oral bioavailability of 41% compared to 11% for MBZ-C. In summary, we have identified a prodrug of MBZ with better physicochemical properties and enhanced bioavailability in both mice and dog.

Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes

Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by including quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function by using a challenging set of 10 inhibitors binding to carbonic anhydrase II through Zn²⁺ in the active site. This new dataset consists of the high-resolution (1.1-1.4 Å) crystal structures and experimentally determined inhibitory constant (K_i ) values. It allows for evaluation of the common approximations, such as representing the solvent implicitly or by using a single target conformation combined with a set of ligand docking poses. SQM/COSMO attained a good correlation of R² of 0.56-0.77 with the experimental inhibitory activities, benefiting from careful handling of both noncovalent interactions (e.g. charge transfer) and solvation. This proof-of-concept study of SQM/COSMO ranking for metalloprotein-ligand systems demonstrates its potential for hit-to-lead applications.

General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases

Rhomboid-family intramembrane proteases regulate important biological processes and have been associated with malaria, cancer, and Parkinson's disease. However, due to the lack of potent, selective, and pharmacologically compliant inhibitors, the wide therapeutic potential of rhomboids is currently untapped. Here, we bridge this gap by discovering that peptidyl α-ketoamides substituted at the ketoamide nitrogen by hydrophobic groups are potent rhomboid inhibitors active in the nanomolar range, surpassing the currently used rhomboid inhibitors by up to three orders of magnitude. Such peptidyl ketoamides show selectivity for rhomboids, leaving most human serine hydrolases unaffected. Crystal structures show that these compounds bind the active site of rhomboid covalently and in a substrate-like manner, and kinetic analysis reveals their reversible, slow-binding, non-competitive mechanism. Since ketoamides are clinically used pharmacophores, our findings uncover a straightforward modular way for the design of specific inhibitors of rhomboid proteases, which can be widely applicable in cell biology and drug discovery.

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N-substituted peptidyl α-ketoamides are nanomolar inhibitors of rhomboid proteases

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Peptidyl ketoamides inhibit rhomboids covalently, reversibly, and non-competitively

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The peptide and ketoamide substituent independently modulate potency and selectivity

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Peptidyl ketoamides are selective for rhomboids, sparing most human serine proteases

Discovery of a para-Acetoxy-benzyl Ester Prodrug of a Hydroxamate-Based Glutamate Carboxypeptidase II Inhibitor as Oral Therapy for Neuropathic Pain

4-Carboxy-α-[3-(hydroxyamino)-3-oxopropyl]-benzenepropanoic acid 1 is a potent hydroxamate-based inhibitor of glutamate carboxypeptidase II. In an attempt to improve its poor oral pharmacokinetics, we synthesized a series of prodrugs by masking its hydrophilic hydroxamate group. Prodrugs were evaluated for oral availability in mice and showed varying degree of plasma exposure to 1. Of these, para-acetoxybenzyl-based, 4-(5-(((4-acetoxybenzyl)oxy)amino)-2-carboxy-5-oxopentyl)benzoic acid, 12, provided 5-fold higher plasma levels of 1 compared to oral administration of 1 itself. Subsequently, para-acetoxybenzyl-based prodrugs with additional ester promoiety(ies) on carboxylate(s) were examined for their ability to deliver 1 to plasma. Isopropyloxycarbonyloxymethyl (POC) ester 30 was the only prodrug that achieved substantial plasma levels of 1. In vitro metabolite identification studies confirmed stability of the ethyl ester of benzoate while the POC group was rapidly hydrolyzed. At oral daily dose-equivalent of 3 mg/kg, 12 exhibited analgesic efficacy comparable to dose of 10 mg/kg of 1 in the rat chronic constrictive injury model of neuropathic pain.

Enhanced Brain Delivery of 2-(Phosphonomethyl)pentanedioic Acid Following Intranasal Administration of Its γ-Substituted Ester Prodrugs

2-(Phosphonomethyl)pentanedioic acid (2-PMPA) is a potent and selective inhibitor of glutamate carboxypeptidase-II (GCPII) with efficacy in multiple neurological and psychiatric disease models, but its clinical utility is hampered by low brain penetration due to the inclusion of multiple acidic functionalities. We recently reported an improvement in the brain-to-plasma ratio of 2-PMPA after intranasal (IN) dosing in both rodents and primates. Herein, we describe the synthesis of several 2-PMPA prodrugs with further improved brain delivery of 2-PMPA after IN administration by masking of the γ-carboxylate. When compared to IN 2-PMPA in rats at 1 h post dose, γ-(4-acetoxybenzyl)-2-PMPA (compound 1) resulted in significantly higher 2-PMPA delivery to both plasma (4.1-fold) and brain (11-fold). Subsequent time-dependent evaluation of 1 also showed high brain as well as plasma 2-PMPA exposures with brain-to-plasma ratios of 2.2, 0.48, and 0.26 for olfactory bulb, cortex, and cerebellum, respectively, as well as an improved sciatic nerve to plasma ratio of 0.84. In contrast, IV administration of compound 1 resulted in similar plasma exposure of 2-PMPA versus the IN route (AUC_IV: 76 ± 9 h·nmol/mL versus AUC_IN: 99 ± 24 h·nmol/mL); but significantly lower nerve and brain tissue exposures with tissue-to-plasma ratios of 0.21, 0.03, 0.04, and 0.04 in nerve, olfactory bulb, cortex, and cerebellum, respectively. In primates, IN administration of 1 more than doubled 2-PMPA concentrations in the cerebrospinal fluid relative to previously reported levels following IN 2-PMPA. The results of these experiments provide a promising strategy for testing GCPII inhibition in neurological and psychiatric disorders.

N-(Pivaloyloxy)alkoxy-carbonyl Prodrugs of the Glutamine Antagonist 6-Diazo-5-oxo-l-norleucine (DON) as a Potential Treatment for HIV Associated Neurocognitive Disorders

Aberrant excitatory neurotransmission associated with overproduction of glutamate has been implicated in the development of HIV-associated neurocognitive disorders (HAND). The glutamine antagonist 6-diazo-5-oxo-l-norleucine (DON, 14) attenuates glutamate synthesis in HIV-infected microglia/macrophages, offering therapeutic potential for HAND. We show that 14 prevents manifestation of spatial memory deficits in chimeric EcoHIV-infected mice, a model of HAND. 14 is not clinically available, however, because its development was hampered by peripheral toxicities. We describe the synthesis of several substituted N-(pivaloyloxy)alkoxy-carbonyl prodrugs of 14 designed to circulate inert in plasma and be taken up and biotransformed to 14 in the brain. The lead prodrug, isopropyl 6-diazo-5-oxo-2-(((phenyl(pivaloyloxy)methoxy)carbonyl)amino)hexanoate (13d), was stable in swine and human plasma but liberated 14 in swine brain homogenate. When dosed systemically in swine, 13d provided a 15-fold enhanced CSF-to-plasma ratio and a 9-fold enhanced brain-to-plasma ratio relative to 14, opening a possible clinical path for the treatment of HAND.

Co-option of the sphingolipid metabolism for the production of nitroalkene defensive chemicals in termite soldiers

The aliphatic nitroalkene (E)-1-nitropentadec-1-ene (NPD), reported in early seventies in soldiers of the termite genus Prorhinotermes, was the first documented nitro compound produced by insects. Yet, its biosynthetic origin has long remained unknown. Here, we investigated in detail the biosynthesis of NPD in P. simplex soldiers. First, we track the dynamics in major metabolic pathways during soldier ontogeny, with emphasis on likely NPD precursors and intermediates. Second, we propose a hypothesis of NPD formation and verify its individual steps using in vivo incubations of putative precursors and intermediates. Third, we use a de novo assembled RNA-Seq profiles of workers and soldiers to identify putative enzymes underlying NPD formation. And fourth, we describe the caste- and age-specific expression dynamics of candidate initial genes of the proposed biosynthetic pathway. Our observations provide a strong support to the following biosynthetic scenario of NPD formation, representing an analogy of the sphingolipid pathway starting with the condensation of tetradecanoic acid with l-serine and leading to the formation of a C₁₆ sphinganine. The C₁₆ sphinganine is then oxidized at the terminal carbon to give rise to 2-amino-3-hydroxyhexadecanoic acid, further oxidized to 2-amino-3-oxohexadecanoic acid. Subsequent decarboxylation yields 1-aminopentadecan-2-one, which then proceeds through six-electron oxidation of the amino moiety to give rise to 1-nitropentadecan-2-one. Keto group reduction and hydroxyl moiety elimination lead to NPD. The proposed biosynthetic sequence has been constructed from age-related quantitative dynamics of individual intermediates and confirmed by the detection of labeled products downstream of the administered labeled intermediates. Comparative RNA-Seq analyses followed by qRT-PCR validation identified orthologs of serine palmitoyltransferase and 3-ketodihydrosphingosine reductase genes as highly expressed in the NPD production site, i.e. the frontal gland of soldiers. A dramatic onset of expression of the two genes in the first days of soldier's life coincides with the start of NPD biosynthesis, giving further support to the proposed biosynthetic hypothesis.

ALK5 kinase inhibitory activity and synthesis of 2,3,4-substituted 5,5-dimethyl-5,6-dihydro-4H-pyrrolo[1,2-b]pyrazoles

A series of 2,3,4-substituted 5,5-dimethyl-5,6-dihydro-4H-pyrrolo[1,2-b]pyrazoles (DPPs) was synthesized and evaluated for their ALK5 inhibition activity. The most potent compounds displayed submicromolar IC₅₀ values for ALK5. Preliminary profiling of one of the most active compounds in a panel of 50 protein kinases revealed its selectivity for ALK5. In cells, the compounds caused dose-dependent dephosphorylation of SMAD2, a well-established substrate of ALK5. In addition, the compounds blocked translocation of SMAD2/3 to nuclei of cells stimulated with TGFβ and the protein remained predominantly in cytoplasm, further confirming their molecular target. Therefore, novel DPP derivatives proved to be active as ALK5 inhibitors.

Sensitive Versatile Fluorogenic Transmembrane Peptide Substrates for Rhomboid Intramembrane Proteases

Rhomboid proteases are increasingly being explored as potential drug targets, but their potent and specific inhibitors are not available, and strategies for inhibitor development are hampered by the lack of widely usable and easily modifiable in vitro activity assays. Here we address this bottleneck and report on the development of new fluorogenic transmembrane peptide substrates, which are cleaved by several unrelated rhomboid proteases, can be used both in detergent micelles and in liposomes, and contain red-shifted fluorophores that are suitable for high-throughput screening of compound libraries. We show that nearly the entire transmembrane domain of the substrate is important for efficient cleavage, implying that it extensively interacts with the enzyme. Importantly, we demonstrate that in the detergent micelle system, commonly used for the enzymatic analyses of intramembrane proteolysis, the cleavage rate strongly depends on detergent concentration, because the reaction proceeds only in the micelles. Furthermore, we show that the catalytic efficiency and selectivity toward a rhomboid substrate can be dramatically improved by targeted modification of the sequence of its P5 to P1 region. The fluorogenic substrates that we describe and their sequence variants should find wide use in the detection of activity and development of inhibitors of rhomboid proteases.

DNA-linked Inhibitor Antibody Assay (DIANA) for sensitive and selective enzyme detection and inhibitor screening

Human diseases are often diagnosed by determining levels of relevant enzymes and treated by enzyme inhibitors. We describe an assay suitable for both ultrasensitive enzyme quantification and quantitative inhibitor screening with unpurified enzymes. In the DNA-linked Inhibitor ANtibody Assay (DIANA), the target enzyme is captured by an immobilized antibody, probed with a small-molecule inhibitor attached to a reporter DNA and detected by quantitative PCR. We validate the approach using the putative cancer markers prostate-specific membrane antigen and carbonic anhydrase IX. We show that DIANA has a linear range of up to six logs and it selectively detects zeptomoles of targets in complex biological samples. DIANA's wide dynamic range permits determination of target enzyme inhibition constants using a single inhibitor concentration. DIANA also enables quantitative screening of small-molecule enzyme inhibitors using microliters of human blood serum containing picograms of target enzyme. DIANA's performance characteristics make it a superior tool for disease detection and drug discovery.

Discovery of 6-Diazo-5-oxo-l-norleucine (DON) Prodrugs with Enhanced CSF Delivery in Monkeys: A Potential Treatment for Glioblastoma

The glutamine antagonist 6-diazo-5-oxo-l-norleucine (DON, 1) has shown robust anticancer efficacy in preclinical and clinical studies, but its development was halted due to marked systemic toxicities. Herein we demonstrate that DON inhibits glutamine metabolism and provides antitumor efficacy in a murine model of glioblastoma, although toxicity was observed. To enhance DON's therapeutic index, we utilized a prodrug strategy to increase its brain delivery and limit systemic exposure. Unexpectedly, simple alkyl ester-based prodrugs were ineffective due to chemical instability cyclizing to form a unique diazo-imine. However, masking both DON's amine and carboxylate functionalities imparted sufficient chemical stability for biological testing. While these dual moiety prodrugs exhibited rapid metabolism in mouse plasma, several provided excellent stability in monkey and human plasma. The most stable compound (5c, methyl-POM-DON-isopropyl-ester) was evaluated in monkeys, where it achieved 10-fold enhanced cerebrospinal fluid to plasma ratio versus DON. This strategy may provide a path to DON utilization in glioblastoma multiforme patients.