Whole Cell Active Inhibitors of Mycobacterial Lipoamide Dehydrogenase Afford Selectivity over the Human Enzyme through Tight Binding Interactions

Tuberculosis remains a leading cause of death from a single bacterial infection worldwide. Efforts to develop new treatment options call for expansion into an unexplored target space to expand the drug pipeline and bypass resistance to current antibiotics. Lipoamide dehydrogenase is a metabolic and antioxidant enzyme critical for mycobacterial growth and survival in mice. Sulfonamide analogs were previously identified as potent and selective inhibitors of mycobacterial lipoamide dehydrogenase in vitro but lacked activity against whole mycobacteria. Here we present the development of analogs with improved permeability, potency, and selectivity, which inhibit the growth of Mycobacterium tuberculosis in axenic culture on carbohydrates and within mouse primary macrophages. They increase intrabacterial pyruvate levels, supporting their on-target activity within mycobacteria. Distinct modalities of binding between the mycobacterial and human enzymes contribute to improved potency and hence selectivity through induced-fit tight binding interactions within the mycobacterial but not human enzyme, as indicated by kinetic analysis and crystallography.

Abstract 1017: Novel inhibitors of AR-v7 nuclear import: new therapeutic opportunities for CRPC

Reactivation of androgen receptor (AR) signaling by active splice variants (AR-Vs) is one of key drivers of castration resistant prostate cancer (CRPC). AR-v7 is the most prevalent AR-V and its expression has been clinically associated with poor overall survival, resistance to the AR inhibitors enzalutamide and abiraterone, as well as taxane resistance. Given that treatment with AR inhibitors and taxanes are the only effective therapeutic modalities in CRPC, development of specific AR-v7 inhibitors is urgently needed. Mechanistically, AR-v7 re-activates AR signaling by being constitutively active in the nucleus. While taxane chemotherapy inhibits the nuclear import of AR which is significantly associated with clinical outcomes in CRPC, it has no effect on AR-v7 nuclear localization and activity. Mechanistically, AR-v7 lacks the microtubule-binding domain and—unlike AR—does not utilize the canonical importin-α/β pathway, or RanGTP for nuclear import. Using wheat germ agglutinin to block active protein nuclear uptake resulted in AR-v7 cytoplasmic sequestration, indicating a requirement for an alternative transport receptor. Further, mutation of AR-v7 dimerization domain (D-box) led to its cytoplasmic sequestration, indicating that the D-box is also required for nuclear import. As inhibition of AR nuclear import is a clinically validated therapeutic strategy, we developed a novel drug discovery platform to identify compounds that specifically inhibit AR-v7 nuclear import. Using cells stably expressing inducible AR-v7 in conjunction with an enzyme complementation assay we tested 166,000 compounds by high throughput screening (HTS). The robust HTS performance (Z>0.8) together with subsequent counter screens including confirmation and compound titration, cell toxicity, a tertiary imaging based screen, led to identification of lead compounds that inhibit AR-v7 nuclear import. The lead compounds share structural features, across two main chemotypes, which are amenable to structure-activity relationship studies to identify the most desirable compound for in vivo studies. Using newly synthesized compounds from each of the two chemotypes, we showed specific dose-dependent inhibition of AR-v7 nuclear import. Currently, we are testing these compounds, on inhibition of AR-v7 transcriptional activity across several cell models including enzalutamide-resistant cells as well as inhibition of tumor growth in AR-v7 xenograft models. In parallel we are testing the lead compound for potential direct binding to the AR-v7 dimerization domain or to candidate alternative nuclear transport receptors. Further development of our lead small molecules will yield novel chemotypes, with desirable pharmacological properties that target the unique AR-v7 nuclear import pathway and can be clinically combined with existing AR therapies.

Note: This abstract was not presented at the meeting.

Citation Format: Seaho Kim, Mohd Azrin Jamalruddin, Eiman Mukhtar, Michael Miller, Leigh Baxt, Stacia Kargman, Andrew Stamford, Peter Meinke, Paraskevi Giannakakou. Novel inhibitors of AR-v7 nuclear import: new therapeutic opportunities for CRPC [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 1017.

Discovery of Novel Tricyclic Heterocycles as Potent and Selective DPP-4 Inhibitors for the Treatment of Type 2 Diabetes

In our efforts to develop second generation DPP-4 inhibitors, we endeavored to identify distinct structures with long-acting (once weekly) potential. Taking advantage of X-ray cocrystal structures of sitagliptin and other DPP-4 inhibitors, such as alogliptin and linagliptin bound to DPP-4, and aided by molecular modeling, we designed several series of heterocyclic compounds as initial targets. During their synthesis, an unexpected chemical transformation provided a novel tricyclic scaffold that was beyond our original design. Capitalizing on this serendipitous discovery, we have elaborated this scaffold into a very potent and selective DPP-4 inhibitor lead series, as highlighted by compound 17c.

2'-Modified Guanosine Analogs for the Treatment of HCV

Novel 2'-modified guanosine nucleosides were synthesized from inexpensive starting materials in 7-10 steps via hydroazidation or hydrocyanation reactions of the corresponding 2'-olefin. The antiviral effectiveness of the guanosine nucleosides was evaluated by converting them to the corresponding 5'-O-triphosphates (compounds 38-44) and testing their biochemical inhibitory activity against the wild-type NS5B polymerase.

Design of Potent and Orally Active GPR119 Agonists for the Treatment of Type II Diabetes

We report herein the design and synthesis of a series of potent and selective GPR119 agonists. Our objective was to develop a GPR119 agonist with properties that were suitable for fixed-dose combination with a DPP4 inhibitor. Starting from a phenoxy analogue (1), medicinal chemistry efforts directed toward reducing half-life and increasing solubility led to the synthesis of a series of benzyloxy analogues. Compound 28 was chosen for further profiling because of its favorable physicochemical properties and excellent GPR119 potency across species. This compound exhibited a clean off-target profile in counterscreens and good in vivo efficacy in mouse oGTT.

Inhibitors of BACE for treating Alzheimer's disease: a fragment-based drug discovery story

Several fragment-based methods have been applied to the discovery of new lead sources for inhibitors of BACE1, an important therapeutic target for Alzheimer's disease. Among the most common fragment hits were various amidine-containing molecules in which the amidine engaged in discrete H-bond donor-acceptor interaction with the BACE1 catalytic dyad. Structure and medicinal chemistry knowledge-based optimization with emphasis on ligand efficiency resulted in identification of a key pharmacophore comprising a non-planar cyclic amidine scaffold directly attached to a phenyl group projecting into S1. This key pharmacophore is a common feature of known clinical candidates and has dominated the recent patent literature. A structural comparison of the non-planar cyclic amidine motif with other BACE1 pharmacophores highlights its uniqueness and distinct advantages.

Identification and characterization of pseudoirreversible nonpeptide antagonists of the neuropeptide Y Y5 receptor and development of a novel Y5-selective radioligand

The neuropeptide Y (NPY) Y(5) receptor is believed to be involved in the central regulation of appetite. Thus, antagonists of this receptor have been pursued as potential therapeutic agents for the treatment of obesity. A novel series of potent and selective phenylamide or biaryl urea NPY Y(5) receptor antagonists was identified. Four representative compounds from this series, SCH 208639 (N-[4-[(1,1-dimethylbutyl)thio]phenyl]-2,2-dimethylpropanamide), SCH 430765 (N-[[[3'-fluoro[1,1'-biphenyl]-4-yl]amino]carbonyl]-N-methyl-1-(methylsulfonyl)-4-piperidinamine), SCH 488106 (N-[[[3',5'-difluoro[1,1'-biphenyl]-4-yl]amino]carbonyl]-N-methyl-1-[(5-methyl-3-pyridinyl)carbonyl]-4-piperidinamine) and SCH 500946 (N-[[[5-(3,5-difluorophenyl)-2-pyrazinyl]amino]carbonyl]-N-methyl-1-(methylsulfonyl)-4-piperidinamine), behaved as competitive antagonists in radioligand binding assays, but displayed apparently insurmountable antagonism in a cell-based functional assay. The apparently insurmountable antagonism was due to slow receptor dissociation rates rather than covalent binding, because the antagonists' effects could be reduced by extensive washing of cells after antagonist exposure. A novel radioligand, [(35)S]SCH 500946, was also developed and used to characterize the interaction of these antagonists with the NPY Y(5) receptor. [(35)S]SCH 500946 had high affinity for the NPY Y(5) receptor (K(d)=0.29 nM), and the binding kinetics (k(on) 4.414 x 10(7) M(-)(1) min(-1); k(off) 0.009816 min(-1)) confirmed that the compound slowly dissociates from the receptor. In a competition binding assay, NPY failed to displace [(35)S]SCH 500946 completely, indicating that the binding sites for NPY and [(35)S]SCH 500946 are not identical. These data indicate that the apparent insurmountable antagonism of these NPY Y(5) receptor antagonists is attributable both to slow receptor dissociation rates and to binding at a site distinct from NPY.

Unambiguous structural characterization of hydantoin reaction products using 2D HMBC NMR spectroscopy

Data from two-dimensional (2D) NMR experiments were used to identify the reaction products resulting from the opening of pyroglutamates with isocyanates or thioisocyanates. The reaction has the potential to produce compounds that would have very similar one-dimensional proton ((1)H) or carbon-13 ((13)C) NMR spectra. Careful analysis of (1)H--(1)H COSY, (1)H--(1)H NOESY, and HMBC data, including chemical shifts and coupling constants, were used to distinguish correctly between carbamoyl-2-pyrrolidinone, hydantoin, and perhydro-1,3-diazepine-2,4-dione type structures that could result from this reaction. This work describes their preparation and subsequent identification using 2D NMR spectroscopy, and includes complete (13)C assignments of the reaction products. The 2D NMR techniques and analysis described here can be applied successfully to other synthetic reactions with the potential to produce isomeric products.

Neuropeptide Y receptors as targets for anti-obesity drug development: perspective and current status

Neuropeptide Y is a widely distributed neuropeptide that elicits a plethora of physiological effects via interaction with six different receptors (Y(1)-y(6)). Recent attention has focused on the role of neuropeptide Y in the regulation of energy homeostasis. Neuropeptide Y stimulates food intake, inhibits energy expenditure, increases body weight and increases anabolic hormone levels by activating the neuropeptide Y Y(1) and Y(5) receptors in the hypothalamus. Based on these findings, several neuropeptide Y Y(1) and Y(5) receptor antagonists have been developed recently as potential anti-obesity agents. In addition, mice lacking neuropeptide Y, the neuropeptide Y Y(1) receptor or the neuropeptide Y Y(5) receptor have been generated. The data obtained to date with these newly developed tools suggests that neuropeptide Y receptor antagonists, particularly neuropeptide Y Y(1) receptor antagonists, may be useful anti-obesity agents. However, the redundancy of the neurochemical systems regulating energy homeostasis may limit the effect of ablating a single pathway. In addition, patients in whom the starvation response is activated, such as formerly obese patients who have lost weight or patients with complete or partial leptin deficiency, may be the best candidates for treatment with a neuropeptide Y receptor antagonist.

Characterization of human, dog and rabbit corpus cavernosum type 5 phosphodiesterases

Human, dog and rabbit corpus cavernosum type 5 phosphodiesterases (PDE5) were isolated and their characteristics were compared. The three enzymes showed Km values of 0.8, 2.1 and 2.3 uM, respectively. They exhibited similar pH-dependence with optimal pH being 7.5. They required Mg++ for activity and the activity was suppressed by high concentrations of Zn++ (0.1-1 mM). Sildenafil potently inhibited the three enzymes with IC50 values of 3.6, 1.7 and 3.0 nM, respectively. Dipyridamole and IBMX (3-isobutyl-1-methylxanthine) each also inhibited the three enzymes with similar, albeit lower, potencies (IC50 about 1.1 and 5.7 uM, respectively). However, zaprinast exhibited a significantly higher potency against the rabbit enzyme (IC50 53 nM) than against the human and dog PDE5s (IC5s 332 and 217 nM, respectively). Thus, the corpus cavernosum PDE5s are very similar among the various species with the only significant difference being their sensitivity to zaprinast. Human platelet PDE5 was also characterized by comparison with the corpus cavernosum enzyme. The platelet enzyme exhibited a Km, pH-, Mg++- and Zn++-dependence, and sensitivity to sildenafil and zaprinast very similar to those of the corpus cavernosum PDE5. However, compared with corpus cavernosum PDE5, the platelet enzyme exhibited higher sensitivity to dipyridamole and IBMX (IC50 0.46 and 1.8 uM, respectively). This study shows that despite similar kinetics and enzymatic properties, corpus cavernosum PDE5s from different species, and corpus cavernosum and platelet PDE5s, can have differential sensitivity to pharmacological inhibitors.

Inhibition of cellular action of thrombin by N3-cyclopropyl-7-[[4-(1-methylethyl)phenyl]methyl]-7H-pyrrolo[3, 2-f]quinazoline-1,3-diamine (SCH 79797), a nonpeptide thrombin receptor antagonist

A growing body of evidence suggests an important contribution of the cellular actions of thrombin to thrombosis and restenosis following angioplasty. Recently we reported on SCH 79797 (N3-cyclopropyl-7-¿[4-(1-methylethyl)phenyl]methyl¿-7H-pyrrolo[3, 2-f]quinazoline-1,3-diamine) and its analogs as new potent, nonpeptide thrombin receptor antagonists. This study further characterizes the biochemical and pharmacological actions of pyrroloquinazoline inhibitors of protease activated receptor-1 (PAR-1) in human platelets and coronary artery smooth muscle cells (hCASMC). SCH 79797 and its N-methyl analog (SCH 203099) inhibited binding of a high-affinity thrombin receptor-activating peptide ([(3)H]haTRAP, Ala-Phe(p-F)-Arg-ChA-HArg-[(3)H]Tyr-NH(2)) to PAR-1 with IC(50) values of 70 and 45 nM, respectively. SCH 79797 inhibited [(3)H]haTRAP binding in a competitive manner. SCH 79797 and SCH 203099 inhibited alpha-thrombin- and haTRAP-induced aggregation of human platelets, but did not inhibit human platelet aggregation induced by the tethered ligand agonist for protease-activated receptor-4 (PAR-4), gamma-thrombin, ADP, or collagen. SCH 203099 inhibited surface expression of P-selectin induced by haTRAP and thrombin, and it did not increase P-selectin expression or prevent thrombin cleavage of the receptor. Thrombin and TFLLRNPNDK-NH(2) (TK), a PAR-1-selective agonist, produced transient increases in cytosolic free Ca(2+) concentration ([Ca(2+)](i)) in hCASMC. This increase in [Ca(2+)](i) was inhibited effectively by SCH 79797. However, the Ca(2+) transients induced by SLIGKV-NH(2,) a PAR-2-selective agonist, were not inhibited by SCH 79797. Thrombin- and TK-stimulated [(3)H]thymidine incorporation also was inhibited completely by SCH 79797. The results of this study demonstrate that SCH 79797 and SCH 203099 are potent, selective antagonists of PAR-1 in human platelets and hCASMC. These data also suggest that the thrombin stimulation of Ca(2+) transients and mitogenesis in hCASMC is mediated primarily through activation of PAR-1.

Structure of 18'-epivinblastine

Methyl (3aR-[3a alpha,4 beta,5 beta,5a beta,9(3R*,5S*,7R*,9R*), 10bR,13a alpha])-4-(acetyloxy)-3a-ethyl-9-[5-ethyl-1,4,5,6,7,8,9, 10-octahydro-5-hydroxy-9-(methoxycarbonyl)-2H-3,7- methanoazacycloundecino[5,4-b]indol-9-yl]-3a,4,5,5a,6,11,12, 13a-octahydro-5-hydroxy-8-methoxy-6-methyl-1H-indolizino-[8,1-c,d] carbazole- 5-carboxylate methanol solvate, C46H58N4O9. 2CH3OH (1), Mr = 875.07, monoclinic, P2(1), a = 10.2759 (12), b = 22.353 (3), c = 10.4051 (12) A, beta = 106.502 (9) degrees, V = 2291.6 (5) A3, Z = 2, Dx = 1.27 g cm-3, Mo K alpha radiation, lambda = 0.7107 A, mu = 0.8397 cm-1, F(000) = 940, T = 198 K, R = 0.0470 for 2751 reflections, Fo greater than or equal to 4 sigma(Fo). The C ring of the vindoline moiety is in the boat conformation with the hydroxy group and the tertiary N in the bowsprit positions resulting in a fairly short intramolecular hydrogen-bonding interaction. The relevant parameters for O3--H3...N9 are O...N 2.651 (6), H...N 1.94 (5) A and O--H...N 147 (5) degrees. The D and E rings are in the sofa and envelope conformations, respectively. The piperidine ring of the catharanthine portion of the molecule assumes the chair conformation while the conformation of the azacyclononene ring is a boat-chair. An intramolecular hydrogen bond between the indolino NH of the catharanthine moiety and methoxy O (O25) of the vindoline moiety is also observed. The relevant parameters for N16'--H16'...O25 are N...O 2.827 (6), H...N2.14 (6) A and O--H...N 136 (5) degrees.

Structure of a novel bisindole derivative

(3aR-[3a alpha,4 beta,5a beta,9[1R,3R(2S),5R,7aS,-12aS],10bR,13a alpha])-Methyl-4-(acetyloxy)-3a-ethyl-3a,4,5,5a,6,11,12,13a-oct ahy dro-9- [1,2,3,4,6,7,7a,- 12-octahydro-3-(2-hydroxy-2-hydroxymethylbutyl)- 1-(methoxycarbonyl)indolizino[1,2-b]indol-7a-yl]-5- hydroxy-8-methoxy-6-methyl-1H-indolizino[8,1-c,d]- carbazole-5-carboxylate methanol hydrate solvate, C46H60N4O10.CH3OH.H2O, Mr = 879 x 06, monoclinic, P2(1), a = 8 x 2878 (8), b = 31 x 018 (4), c = 9 x 2267 (7) A, beta = 105 x 211 (7) degrees, V = 2288 x 8 (4) A3, Z = 2, Dx = 1 x 28 g cm-3, mu = 0 x 8580 cm-1, Mo K alpha radiation, lambda = 0 x 7107 A, F(000) = 944, T = 198 K, R = 0 x 0382 for 2931 reflections [Fo greater than or equal to 4 sigma(Fo)]. A very short intramolecular hydrogen-bonding interaction is observed between the hydroxyl group and N9 of the vindoline portion of the molecule. The relevant parameters are: O3--H3O...N9, O...N 2 x 598 (4), H...N 1 x 68 (5) A, O--H...N 164 (5) degrees. Molecules related by the 2(1) screw operation are hydrogen bonded into columns parallel to b.(ABSTRACT TRUNCATED AT 250 WORDS)