South (S)- and North (N)-Methanocarba-7-Deazaadenosine Analogues as Inhibitors of Human Adenosine Kinase
Adenosine kinase (AdK) inhibitors raise endogenous adenosine levels, particularly in disease states, and have potential for treatment of seizures, neurodegeneration, and inflammation. Based on the South (S) ribose conformation and molecular dynamics (MD) analysis of nucleoside inhibitors bound in AdK X-ray crystallographic structures, (S)- and North (N)-methanocarba (bicyclo[3.1.0]hexane) derivatives of known inhibitors were prepared and compared as human (h) AdK inhibitors. 5\xe2\x80\xb2-Hydroxy (34, MRS4202 (S); 55, MRS4380 (N)) and 5\xe2\x80\xb2-deoxy 38a (MRS4203 (S)) analogues, containing 7- and N6-NH phenyl groups in 7-deazaadenine, robustly inhibited AdK activity (IC50 ~100 nM), while the 5\xe2\x80\xb2-hydroxy derivative 30 lacking the phenyl substituents was weak. Docking in the hAdK X-ray structure and MD simulation suggested a mode of binding similar to 5\xe2\x80\xb2-deoxy-5-iodotubercidin and other known inhibitors. Thus, a structure-based design approach for further potency enhancement is possible. The potent AdK inhibitors in this study are ready to be further tested in animal models of epilepsy.
Introduction<!>Chemical synthesis<!>Biochemical evaluation<!>Molecular modeling<!>MD simulation of the X-ray structure of the 1c-AdK complex<!>Docking of selected methanocarba-nucleoside derivatives<!>MD simulations of methanocarba-nucleoside hAdK complexes<!>hAdK conformation during MD simulations<!>Discussion<!>Materials and Methods<!>7-((3aS,3bS,4aS,5R,5aR)-5-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethyltetrahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-4-chloro-7H-pyrrolo[2,3-d]pyrimidine (26)<!>7-((3aS,3bS,4aS,5R,5aR)-5-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethyltetrahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (27)<!>(1R,2S,3R,4R,5S)-1-(4-Chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-4-(hydroxymethyl)bicyclo[3.1.0]hexane-2,3-diol (28)<!>7-((3aS,3bR,4aS,5R,5aR)-5-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethyltetrahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-amine (29)<!>(1R,2S,3R,4R,5S)-1-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-4-(hydroxymethyl)bicyclo[3.1.0]hexane-2,3-diol (30)<!>7-((3aS,3bR,4aS,5R,5aR)-5-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethyltetrahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-5-iodo-N-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine (31a)<!>7-((3aS,3bR,4aS,5R,5aR)-5-(((tert-butyldiphenylsilyl)oxy)methyl)-2,2-dimethyltetrahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-N-(4-fluorophenyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-amine (31b)<!>(1R,2S,3R,4R,5S)-4-(Hydroxymethyl)-1-(5-iodo-4-(phenylamino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)bicyclo[3.1.0]hexane-2,3-diol (32)<!>7-((3aS,3bR,4aS,5R,5aR)-5-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethyltetrahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-N,5-diphenyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine (33a)<!>7-((3aS,3bR,4aS,5R,5aR)-5-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethyltetrahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-N-(4-fluorophenyl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine (33b)<!>7-((3aS,3bR,4aS,5R,5aR)-5-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethyltetrahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-5-(4-fluorophenyl)-N-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine (33c)<!>(1R,2S,3R,4R,5S)-4-(Hydroxymethyl)-1-(5-phenyl-4-(phenylamino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)bicyclo[3.1.0]hexane-2,3-diol (34)<!>((3aS,3bR,4aS,5R,5aR)-2,2-Dimethyl-3b-(5-phenyl-4-(phenylamino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)methanol (35a)<!>((3aS,3bR,4aS,5R,5aR)-3b-(4-((4-Fluorophenyl)amino)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)methanol (35b)<!>((3aS,3bR,4aS,5R,5aR)-3b-(5-(4-Fluorophenyl)-4-(phenylamino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)methanol (35c)<!>N,5-Diphenyl-7-((3aS,3bR,4aS,5S,5aR)-2,2,5-trimethyltetrahydrocyclopropa[3,4]-cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (37a)<!>N-(4-Fluorophenyl)-5-phenyl-7-((3aS,3bR,4aS,5S,5aR)-2,2,5-trimethyltetrahydro-cyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (37b)<!>5-(4-Fluorophenyl)-N-phenyl-7-((3aS,3bR,4aS,5S,5aR)-2,2,5-trimethyltetrahydro-cyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (37c)<!>(1R,2S,3R,4S,5S)-4-Methyl-1-(5-phenyl-4-(phenylamino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)bicyclo[3.1.0]hexane-2,3-diol (38a)<!>(1R,2S,3R,4S,5S)-1-(4-((4-Fluorophenyl)amino)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-4-methylbicyclo[3.1.0]hexane-2,3-diol (38b)<!>(1R,2S,3R,4S,5S)-1-(5-(4-fluorophenyl)-4-(phenylamino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-4-methylbicyclo[3.1.0]hexane-2,3-diol (38c)<!>(3aS,3bR,4aS,5R,5aR)-3b-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)methanol (39)<!>((3aS,3bS,4aS,5R,5aR)-3b-(5-Iodo-4-((triphenyl-l5-phosphanylidene)amino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)methyl diphenyl phosphate (40)<!>N-(7-((3aS,3bS,4aS,5R,5aR)-5-(Azidomethyl)-2,2-dimethyltetrahydrocyclopropa[3,4]-cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1,1,1-triphenyl-l5-phosphanimine (41)<!>7-((3aS,3bS,4aS,5R,5aR)-5-(Azidomethyl)-2,2-dimethyltetrahydrocyclopropa[3,4]-cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-amine (42)<!>(1S,2S,3R,4R,5S)-1-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-4-(azidomethyl)bi-cyclo[3.1.0]hexane-2,3-diol (43)<!>(1S,2S,3R,4R,5S)-1-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-4-(aminomethyl)bicyclo[3.1.0]hexane-2,3-diol acetate (45)<!>(3aS,3bS,4aS,5S,5aR)-3b-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxole-5-carboxylic acid (46)<!>1,3-bis((1S,2S,3R,4S,5S)-5-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-dihydroxybicyclo[3.1.0]hexan-2-yl)urea (47)<!>Benzyl ((3aS,3bS,4aS,5S,5aR)-3b-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)carbamate (48)<!>(1S,2S,3R,4S,5S)-4-Amino-1-(4-amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)bicyclo[3.1.0]hexane-2,3-diol (49)<!>7-((3aR,3bR,4aS,5R,5aS)-3b-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)-4-chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (52)<!>7-((3aR,3bR,4aS,5R,5aS)-3b-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)-5-iodo-N-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine (53)<!>7-((3aR,3bR,4aS,5R,5aS)-3b-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)-N,5-diphenyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine (54)<!>(1R,2R,3S,4R,5S)-1-(Hydroxymethyl)-4-(5-phenyl-4-(phenylamino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)bicyclo[3.1.0]hexane-2,3-diol (55)<!>7-((3aR,3bR,4aS,5R,5aS)-3b-(((tert-Butyldiphenylsilyl)oxy)methyl)-2,2-dimethylhexahydrocyclopropa[3,4]cyclopenta[1,2-d][1,3]dioxol-5-yl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-amine (56)<!>(1R,2R,3S,4R,5S)-4-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-1-(hydroxymethyl)bicyclo[3.1.0]hexane-2,3-diol (57)<!>Quantification of hAdK inhibition<!>Statistical analysis<!>Computational facilities<!>Ligand Preparation<!>Protein Preparation<!>Induced Fit Docking<!>Molecular Dynamics<!>Trajectory Analysis
<p>Endogenous adenosine acts on its G protein-coupled receptors (adenosine receptors, ARs)1 in the central nervous system to suppress seizures2 and pain3 and to blunt the effects of ischemia.4 In addition, adenosine has AR-independent epigenetic effects based on interactions with the transmethylation pathway.5 Extracellular adenosine may originate from intracellular pools or from the action of ectonucleotidases on extracellular ATP.6 There is a dynamic equilibrium between extracellular adenosine levels and its intracellular content that is mediated by either equilibrative (ENTs) or concentrative (CNTs) transporters of nucleosides.7 Within the brain the concentration of adenosine is largely under the control of metabolic clearance through astrocytic adenosine kinase (AdK), which converts adenosine to 5′-AMP.8 AdK exists in two isoforms derived from alternative splicing and alternative promoter use. The short isoform AdK-S resides in the cytoplasm, whereas the long isoform Adk-L is located in the cell nucleus.9 By inhibiting AdK, the adenosine concentration can be exogenously raised. Thus, an indirect means of modulating the concentration of adenosine in the brain, and therefore the basal levels of activation of the ARs, is by administering brain-penetrant human (h) AdK inhibitors. The raised level of adenosine in the brain counteracts seizures by activating the neuroprotective A1AR and attenuates epilepsy progression by decreasing S-adenosyl methionine dependent DNA methylation as an epigenetic mechanism of action.8,10 Increased DNA methylation is a pathological hallmark of chronic epilepsy and associated with disease progression and maintenance of the epileptic state.5,11 Efficient transmethylation reactions, for example in the liver, require the removal of adenosine by AdK,11 and this effect has been demonstrated to occur in the brain, as well.5,8 Unlike adenosine itself, synthetic A1AR agonists, which are also proposed for seizure treatment,10,13 would not inhibit DNA methylation. Overexpression of AdK in the brain is both a result of astroglial activation and a contributing factor to epileptic seizures. Thus, an inhibitor of AdK might have an advantage in seizure control, because it would combine a pharmacological mechanism (increased A1AR activation) with epigenetic mechanisms (decreased DNA methylation) and might preferentially act on pathologically increased AdK as opposed to normal baseline levels of the enzyme. The advantages of 'adenosine augmentation therapies' for epilepsy and its associated comorbidities have already been discussed.14–16</p><p>Several classes of AdK inhibitors have already been introduced and explored for the treatment of seizures and pain (Chart 1, 1–6).17–21 One class consists of nucleosides derived from the known AdK inhibitor 7-iodo-7-deazaadenosine 1a, otherwise known as 5-iodotubercidin (5-IT). N7-[(1′R,2′S,3′R,4′S)-2′,3′-Dihydroxy-4′-aminocyclopentyl]-4-amino-5-iodopyrrolopyrimidine (2, A-134974) acts in the spinal cord to reduce carrageenan-induced inflammatory hyperalgesia.22 Both 1a and its potent analogue, e.g. the AdK inhibitor 4-(N-phenylamino)-5-phenyl-7-(5′-deoxyribofuranosyl)pyrrolo[2,3-d]pyrimidine 4, inhibited maximal electroshock (MES) seizures in rats.2 Compound 4 also reduced the volumes of infarction in a model of focal cerebral ischemia in rats.23 Another class of nonnucleoside, heterocyclic inhibitors includes the widely used AdK inhibitor 4-amino-5-(3-bromophenyl)-7-(6-morpholino-pyridin-3-yl)pyrido[2,3-d]pyrimidine (3, ABT-702). Potent and selective inhibitors of the AdK of Mycobacterium tuberculosis that do not affect human AdK were found to have antimicrobial activity.24,25 AdK inhibitors were being considered for clinical trials for pain and seizure treatment in the early 2000's, but this effort was discontinued, with one of the inhibitors causing brain hemorrhage in dogs.26 Thus, AdK inhibition holds interest for the control of infectious, as well as neurological diseases. AdK inhibitors also induce anti-inflammatory effects that are adenosine-dependent.27 A potent AdK inhibitor, 4-amino-3-iodo-1-β-D-ribofuranosylpyrazolo[3,4-d]pyrimidine 1b, was also shown to indirectly reduce the expression of inducible nitric oxide synthase and tumor necrosis factor (TNF) in glial cells via activation by adenosine of Gs-coupled ARs.28,29 Recently, the AdK inhibitor 3 was found to promote rodent and porcine islet β-cell replication, which suggests the possible application of such inhibitors to the treatment of diabetes.30 However, other, undesired effects of the inhibitor 1a have been noted; it seems to indirectly inhibit acetyl-CoA carboxylase to promote oxidation of hepatic fatty acids and reduce de novo synthesis of lipids and cholesterol, which raises the AMP/ATP ratio.31 Thus, there might be a need to increase selectivity for AdK within this nucleoside series.</p><p>A common approach in medicinal chemistry to enhance the activity or selectivity of flexible biologically active, small molecules is to introduce a conformational constraint to achieve a desired conformation for interacting with a target biopolymer, i.e. here an enzyme. This lowers the energy barrier of the binding process and can eliminate undesired interactions with other molecular targets that prefer a different conformation of the ligand. One means of sterically constraining the ribose ring of nucleoside derivatives, as already applied to antiviral agents and to receptor ligands, is to incorporate a bicyclic ribose substitute in a conformation that is preferred when the molecule is bound to the protein target.32,33 The methanocarba ([3.1.0]bicyclohexane) ring system is applied to hold the ribose-like ring in either a North (N) or a South (S) conformation. The X-ray structure of human AdK shows a bound nucleoside inhibitor 1c containing a ribose in the (S) conformation, which is similar to the ribose conformation preferred by other nucleoside kinases.34–37 This prompted us to explore the effects of sterically constraining nucleoside inhibitors of human AdK using methanocarba rings.</p><!><p>The intermediate 24 containing the (S)-methanocarba ring with 1′-amino functionalization was required as an intermediate for the target compounds (Scheme 1). We adapted our previously reported synthesis of enantiomerically pure (S)-methanocarba nucleosides via bicyclic intermediate 24,38,39 to a larger scale preparation of this intermediate (Scheme S1, Supporting Information).</p><p>Using the (S)-methanocarba intermediate 24 as a precursor, analogues of known AdK nucleoside inhibitors were prepared. The 7-deazaadenine core was constructed by reacting 24 with symmetrical dichloropyrimidine bearing an acetaldehyde moiety (25),40 which on iodination using NIS followed by the removal of protecting groups in aqueous trifluoroacetic acid resulted in 28. Similarly, the aminolysis of 27 and deprotection rendered 30, the (S)-methanocarba analogue of 1a, in moderate yield.</p><p>Substitution of chlorine on the 6-position of 7-deazapurine using aniline and sodium acetate achieved a complete reaction, but the use of a stronger base i.e. potassium tert-butoxide at lower temperature produced N6-phenyl 7-iodo derivatives 31a and 31b in increased yields. A Suzuki reaction involving arylboronic acids and 31a,b, followed by the removal of a silyl protecting group gave 35a–c, which were subjected to Barton-McCombie deoxygenation41 to yield 5′-deoxy compounds 37a–c. Removal of the protecting groups from 31, 33 and 37a–c gave 32, 34 and 38a–c, respectively, in low to moderate yields.17, 42 Compounds 38b and 38c differ from 38a only in the presence of a fluorine atom in the p-position of either the 4-phenyl-amino or 5-phenyl ring, respectively.</p><p>In an attempt to synthesize 5′-azido compounds (Scheme 2), a Mitsunobu reaction involving dipenylphosphoryl azide (DPPA) and 29 yielded disubstituted 40 exclusively. Surprisingly, this compound was sufficiently stable to be isolated using silica-gel column chromatography. 40 on heating with sodium azide in DMF formed undesired product 41, and attempts to convert this phosphine to 42 or 43 using aqueous TFA were unsuccessful. Alternatively, mesylation of 29 followed by substitution with sodium azide at elevated temperature afforded the desired compound 42 in 96% yield, which under Staudinger reaction conditions gave 44 in good yield.43 The de-protection of the acetonide group from 42 and 44 using aqueous TFA led to 5′-azido and 5′-amino congeners 43 and 45, respectively.</p><p>To arrive at 49 from 39, a Curtius rearrangement strategy was adapted, and to realize this, the 4′-hydroxylmethyl group in 39 was converted to the corresponding carboxylic acid 46 employing a TEMPO-BAIB oxidation44 in aqueous acetonitrile. Initial efforts to prepare the Boc-protected analog of urethane 48 from 46 using DPPA and tert-butanol failed, but instead, after deprotection of the isopropylidine group, resulted in dimer 47. However, a similar reaction with benzyl alcohol formed Cbz-protected compound 48,39 which on deprotection using 33% HBr in acetic acid provided the desired compound 49, as a minor product, and 50 as the major product. Unfortunately, an attempt to convert 50 to the desired compound 49 using NIS in DMF at elevated temperature did not materialize.</p><p>The synthesis of several corresponding (N)-methanocarba analogues was performed as shown in Scheme 3. A protected bicyclic intermediate 51, prepared previously for studies of adenosine receptors,38,39,45 was subjected to a Mitsunobu reaction with 6-chloro-7-iodo-7-deazapurine. The next step provided two divergent pathways leading to target inhibitors: nucleophilic substitution of the 4-chloro group with either ammonia or aniline (followed by a Suzuki coupling at the 5-position). Deprotection of the hydroxyl groups yielded compounds 55 and 57, which are the (N)-methanocarba equivalent of compounds 34 and 30, respectively.</p><!><p>The nucleoside derivatives were tested for inhibitory potential at hAdK using a commercial, nonisotopic assay for the measurement of hAdK activity based on continuous monitoring at 340 nm (appearance of reduced nicotinamide-adenine dinucleotide from a coupled enzymatic reaction). The hAdK-catalyzed phosphorylation of inosine to inosine 5′-monophosphate is coupled to the inosine 5′-monophosphate dehydrogenase-dependent oxidation of the product. Thus, the assay was performed in the presence of dithiothreitol, oxidized nicotinamide-adenine dinucleotide (NAD, 2.5 mM) and ATP (2.75 mM) as cofactors and inosine (2.5 mM) as substrate. hAdK activity was continuously measured via absorption at 340 nm for four hours where measurements were made at five min intervals; however, for graphing and analysis purposes we focused on the first 40 min, which was mostly linear, for determining the slope of initial AdK activity (Figure 1). Percent inhibition of hAdK activity was calculated by determining the change in the slope of the hAdK reaction in the absence or presence of inhibitor during the linear phase of the enzymatic reaction (first 40 min) (Table 1). We included two known AdK inhibitors, compound 1a and 2, as positive controls. Each inhibitor was analyzed at the following concentrations (μM): of 50, 20, 1, 0.50, 0.10, 0.020 and 0.010. Percent residual hAdK activity showed a significant interaction (F78,490=71, p<0.0001) and main effects for both inhibitor (F13,490=626, p<0.0001) and concentration (F6,490=3366, p<0.0001). Post hoc analysis used Bonferroni multiple comparison tests to determine drug differences relative to 2 (most potent known inhibitor used here) at each of the concentrations investigated. At the highest concentration, 28, 30, 45, 49, and 57 significantly varied from 2 with poor inhibition of hAdK. Compound 43 was slightly more potent, varying from 2 at 20 μM. 32 and 55 were moderately potent, beginning to vary from 2 at 1 μM and 500 nM, respectively. Only at a concentration of 100 nM did the inhibition by 34, 38b, and 38c differ from 2, while 38a never significantly varied from 2, indicating that 38a as low as 20 nM was equipotent to 2 in inhibition of hAdK. At lower concentrations 34 and 38a maintained more potent hAdK inhibition; therefore, it was necessary to determine full concentration-response curves to distinguish between the most potent compounds. We performed a detailed concentration-response study of most of the analogues for precise determination of IC50, using the earlier data with the addition of three concentrations (10, 0.20 and 0.050 μM). The IC50 values for potent (S)-methanocarba inhibitors 34 and 38a were 114 and 88 nM, respectively.</p><p>Because the 5′-OH derivative 30 was a poor inhibitor of hAdK, we hypothesized that it might serve as a substrate for hAdK, unlike the corresponding riboside 1a, which is not primarily a substrate.29,43 The Km of adenosine as substrate of hAdK is 700 nM,29 and the nucleoside analogue concentrations that we used in inhibition experiments far exceeded that concentration. By comparison in another kinase system, (S)-methanocarbathymidine, but not (N)-methanocarbathymidine, is a good substrate for herpes simplex virus type 1 thymidine kinase.35 Moreover, (S)-methanocarbathymidine is not a substrate for human cytosolic thymidine kinase isoenzyme 1.35 Thus, it was important to probe the substrate qualities of compound 30, (S)-methanocarbaadenosine derivative, at hAdK. Therefore, we performed three different assays under similar conditions: first, with substrate in the presence of 1 μM 30; second, without substrate in the presence of 1 μM 30; and third as a control, without 30. After 4 h incubation, the resulting mixtures were studied using LC-MS in negative and positive mode (Supporting Information), which could identify and qualitatively measure the levels of nucleosides and their phosphorylated products. In the first and last cases, we detected the final enzymatic product, i.e. xanthosine-5′-phosphate (MW 364+1). However in the first two cases, we found no evidence from the LC-MS analysis that 30 serves as a substrate of hAdK. There was a prominent signal (MW 402+1) from unchanged compound 30, and no detectable or prominent signal of the corresponding 5′-phosphate (MW 482±1).</p><!><p>The selection of novel AdK inhibitors was informed using molecular modeling studies. To date, three X-ray structures of the hAdK in complex with both nucleoside and nonnucleoside inhibitors have been solved, which revealed at least two different enzyme conformations. A closed form was present in the complexes of hAdK with nucleoside 1c36 (PDB ID: 2I6A) and 7-ethynyl-7-deazaadenosine34 (PDB ID: 4O1L), but the enzyme adopted an open conformation in the complex with a bulkier alkynylpyrimidine inhibitor36 (PDB ID: 2I6B). Given the structural similarity of our compounds to 1c, we used the corresponding co-crystallized structure as macromolecular starting point of our analysis.</p><!><p>In a first instance, we subjected the experimentally determined complex (PDB ID: 2I6A) to 30 ns of all atom Molecular Dynamics (MD) simulation, in order to identify the residues mostly involved in the interaction and to explore in detail the conformational space of the inhibitor. In the starting structure,36
1c bound with the glycosidic bond (χ) in the anti conformation (χ = −134.7°) and the sugar moiety in the C1′-exo conformation (P = 125.3°). The analysis of the trajectory (Video S1, left panel) revealed that the anti conformation was retained throughout the simulation, while the sugar ring explored different conformational states (Figure S2). The anti conformation of the glycosidic bond seemed to be compatible with the charge distribution of the residues surrounding the enzyme active site. Indeed, the inhibitor established persistent H-bond interactions with negatively charged residues through the C2′ and C3′ hydroxyl groups and a stable π-π stacking interaction with Phe170 through the purine core. Moreover, the inhibitor was anchored in the active site of the enzyme through a network of H-bond interactions consisting of the N3 atom of the purine core and the C2′ hydroxyl groups associating with the backbone of Ser65 and Gly64, respectively. Concerning the ribose ring conformations of 1c, the starting C1′-exo conformation (Figure S2 i), featuring a bidentate H-bond interaction between the C2′ and C3′ hydroxyl groups and the sidechain of Asp18 (Video S1), was the most favorable in terms of ligand-protein interaction energy (IE) during the simulation (right panel in Video S1 and upper panel in Figure S2). However, after approximately 12 ns of MD simulations, the H-bond network was lost, and the pseudo-sugar ring adopted a C2′-endo (S) conformation (P = 156.7°, Figure S2 ii) with the C2′ and C3′ hydroxyl groups interacting with the Asp18 sidechain and water molecules, respectively (Video S1). At the end of the simulation (Video S1), the ring adopted a less favorable – in terms of IE – C3′-endo (N) conformation (P = 36.4°, Figure S2 iii) that was accompanied by a rotameric switch of the Asp18 sidechain to establish a bidentate H-bond interaction with Arg132 while still interacting with the C3′ hydroxyl group (data not shown). To assess whether this conformation was persistent, we restarted the simulation for another 30 ns in which the inhibitor remained in the (N) conformation (Figure S2). These results prompted us to consider nucleoside inhibitors constrained by the methanocarba ring system in the (N) as well as the (S) conformation. We therefore analyzed from a molecular point of view two isomeric pairs by inspecting in detail the comparison between 30 and 57 and between 34 and 55.</p><!><p>The compounds were docked into the closed form of hAdK by using the Induced Fit Docking (IFD) procedure (see Methods section), because a preliminary attempt to dock bulky diphenyl derivatives 34 and 55 into the rigid enzyme in the closed form failed. In all four IFD poses (Figure 2), the purine core established a π-π stacking interaction with Phe170 and H-bond interactions with the sidechain of Asn14 and the backbone of Ser65, through the N1 and N3 atoms, respectively. Furthermore, the phenyl rings of 34 and 55 (Figures 2C and D) interacted with residues located in the small lid domain (Leu16, Leu40, Leu134, Ala136, Leu138, and Val174) by means of extended hydrophobic contacts. In the derivatives in the (S) conformation (30 and 34, Figure 2A and C, respectively), the methanocarba ring was involved in a tight network of H-bond interactions. The backbone NH of Gly64 and sidechain of Asn68, respectively, served as H-bond donors to the C2′ and C3′ hydroxyl groups. This coordination contributed to placing the same hydroxyl groups in a favorable orientation to act as H-bond donors in a bidentate interaction with the sidechain of Asp18. Moreover, several additional H-bond interactions involving the C5′ hydroxyl group further stabilized this proposed binding mode. However, in the docking poses of the (N) derivatives (57 and 55
Figure 2B and D, respectively), we detected a slightly different interaction pattern to compensate for the loss of the bidentate interaction with Asp18. In particular, the hydroxyl groups at C2′ engaged in H-bond interactions with Gly64 (backbone) and Asn68, while the hydroxyl group at C5′ established a H-bond interaction with the sidechain of Gln38 and with Asn296, in the docking pose of 57 and 55, respectively. As shown below, this different orientation of the (N) isomer was constrained by the closed form of the rigid enzyme, and the bidentate interaction was partially restored by relaxing the protein in a dynamic environment.</p><!><p>The docking poses described above were subjected to 30 ns of all-atom MD simulation. The visualization of the trajectory of the comparison between the 30-hAdK and 57-hAdK complexes (Video S2), revealed that in the 30-hAdK complex (Video S2, left panel) the H-bond interaction network anchoring the C2′ and C3′ hydroxyl groups in a favorable orientation to establish a bidentate interaction with Asp18 sidechain was lost after approximately 14 ns. This conformational change followed the opening of the small lid domain probably triggered by the steric hindrance imposed by the fused three-membered ring. However, in the trajectory of the 57-hAdK complex (Video S2, right panel), the H-bond network was maintained throughout the simulation. A comparison of trajectories of the 34-hAdK and 55-hAdK complexes (Video S3) highlighted the almost immediate opening of the small lid domain for both complexes. This opening established π-π stacking interactions, between Phe170 (purine core) and Phe201 (phenyl-amino group), and van der Waals interactions with the sidechains of Gln38 (phenyl group, data not shown), Leu40 and Leu138 (phenyl-amino group), which persisted throughout the simulation. In the 34-hAdK complex (Video S3, left panel), the C2′ and C3′ hydroxyl groups and the Asp18 sidechain persisted in a reciprocal favorable orientation for almost the entire duration, through the interplay of Asp300, Arg332, and water molecules. The analysis of the trajectory of the 55-hAdK complex (Video S3, right panel), indeed, featured less enduring H-bond networks and more predominant van der Waals interactions that contributed to a net IE profile that was slightly more favorable (Figure S3).</p><!><p>As mentioned above, initial attempts to dock the 34 and 55 in the closed conformation of the enzyme failed. We therefore resorted to an IFD protocol to obtain initial docking poses that we subsequently subjected to MD simulation (30 ns). The analysis of the trajectories revealed that the opening of the small lid domain occurred after a few ns of simulation for the hAK complexes with 34 and 55 (VideoS3, left and right panels), and after approximately 14 ns of simulation for the 30-hAK complex (Video S2, left panel). Superimposition of MD average protein structures with respect to the enzyme starting structure (PDB ID: 2I6A, grey ribbons) is depicted in Figure S4. First, we compared the X-ray structures of the enzyme in the closed conformation (PDB ID: 2I6A, grey ribbons in Figure S4) and the open conformation (PDB ID: 2I6B, green ribbons in Figure S4A). Comparing each MD average structure with the starting conformation highlighted that the enzyme remained in the closed conformation for the hAdK complexes with 1c-(Figure S4B, pink ribbons) and 57 (Figure S4D, green ribbons). However, in the complexes with 30 (Figure S4C yellow ribbons), 34 (Figure S4E, cyan ribbons) and 55 (Figure S4F, orange ribbons) the enzyme approached the open conformation. In particular, in the MD average structures the small lid domain was rotated outward by about 24° with respect to the large domain for both the 34-hAdK and 55-hAdK complexes (comparison with the enzyme starting structure obtained after IFD, C-terminal domain excluded from the analysis), while the rotation angle was approximately 9° for the 1c-hAdK and 30-hAdK complexes. Notably, no dynamic domain was found for the 57-hAdK complex; thus, the enzyme persisted in its closed conformation throughout the simulation. The preference for an open enzyme conformation as well as the rotation angle of the small lid domain during MD simulation of nucleoside inhibitors agreed with modeling studies reported by other authors.46,47</p><p>To further support our hypothesis, we subjected 1a to the same computational protocol (IFD followed by 30 ns of MD simulation run in triplicate, see Table S1). The obtained docking pose (Figure S5A) superimposed well with the experimental binding mode for 1c (RMSD = 0.37 Å), and both the purine core and C2′ and C3′ hydroxyl groups featured the same interaction pattern observed for the methanocarba derivatives. Additional H-bond interactions were detected for the sidechains of Gln38 and Asp300 with the ribose ether oxygen and the C5′ hydroxyl group, respectively. The analysis of the trajectory (Video S4) was consistent with the conformational analysis of the 1c-hAK complex: In particular, 1a persisted for most of the simulation time in the C1′-exo and C2′-endo (S) conformations (65% and 25% of the trajectory, respectively) and maintained a stable network of interactions, such as the bidentate H-bond with the sidechain of Asp18, H-bonds to the backbone of Gly64, Ser65 and the sidechain of Asn14, and the π-π stacking interaction with Phe170. Concerning the enzyme conformation, superimposition of MD average protein structure with the enzyme in the closed conformation (magenta and gray ribbons in Figure S5B, respectively) revealed that the enzyme persisted in the closed conformation. Similarly to what observed for the 57-hAdK complex, no dynamic domain was found for the 1a-hAK complex.</p><!><p>The application of AdK inhibitors to CNS disorders such as epilepsy and chronic pain experienced a hiatus during the past decade, due to possible side effects of the known inhibitors. Critical gaps to be addressed are isoform selectivity (cytoplasmic versus nuclear AdK), cell-type selectivity (neuron versus astrocyte), and trans-membrane transport. Thus, there is a need for a new class of inhibitors with enhanced selectivities, such as nucleosides that have a major distinction from the known riboside inhibitors, such as 1a and 2.</p><p>We have utilized an alternative ribose-like ring system, e.g. two isomeric methanocarba pseudoribose substitutions, in nucleoside derivatives to demonstrate that inhibition of AdK is compatible with these major structural changes. By virtue of the bridged bicycloaliphatic ring, a rigid (S) 3′-exo or (N) 2′-exo envelope conformation is permanently locked in these nucleoside analogues. The most potent inhibitors, (S)-methanocarba derivatives 34, 38a, 38b and 38c and (N)-methanocarba derivative 55 were approximately two-fold less potent than the reference compound 2. The apparent discrepancy for the IC50 of 2 in our study of 48 nM, compared to its previously reported sub-nM IC50,22 is because of the use of a different assay system. The previous assay used was based on a radioactive assay using adenosine as a substrate,17 and ours is a commercial spectrophotometric assay based on inosine as substrate.</p><p>The presence of a p-F substitution in either the 5-phenyl 38b or 4-phenylamino 38c ring in the (S)-methanocarba series maintained the inhibitory potency of analogue 38a. We synthesized and compared potencies of two pairs of corresponding (S) and (N)-methanocarba 4′-CH2OH derivatives. We conclude that both conformations maintain potency at hAdK and can provide a path to novel nucleoside inhibitors. 5-Iodo analogues 32 (S) and 57 (N) displayed comparable potency, and the pair of more potent 4-phenylamino-5-phenyl analogues 34 (S) and 55 (N) also displayed similar IC50 values. This conclusion was consistent with X-ray structures of known inhibitors bound to hAdK36,37 and with molecular docking and MD analyses of several of the present derivatives.</p><p>A similar attempt to constrain analogues of 2′-deoxynucleoside inhibitors of adenosine deaminase (ADA) using the [3.1.0]bicyclohexane ring system failed.48 Although the enzyme preferred the (N) methanocarba nucleoside over the (S), the relative rate of deamination was ~100-fold lower than adenosine, which suggested a possible role of the 4′-oxygen atom of native ribose in an anomeric effect to assist hydrolysis by ADA. In (S)-methanocarba nucleosides, the syn-conformation of the pseudoglycosidic bond is thought to be more stable than the anti-conformation, but in the X-ray structure of hAdK complexes, the nucleoside anti-conformation is present. The analysis of MD simulation starting from the X-ray complex suggests that the anti conformation best suits the electrostatic potential distribution of the enzyme active site, featuring a highly hydrophobic cavity that hosts the purine core next to a region full of charged residues that anchors the ribose ring.</p><p>As far as the conformational preference of the enzyme is concerned, the active site of AdK appears to be highly flexible, as both (S)-methanocarba (C3′-exo, P=198°) compound 34 and its (N)-methanocarba (C2′-exo, P=342°) analogue 55 are equipotent inhibitors. It has to be noted that the synthesized locked conformers deviate by ±18° from the ideal (N) and (S) conformations of ribose. Interestingly, the near equipotency of (N) and (S) methanocarba isomers did not apply to conformationally locked analogues of 1a lacking the phenyl moieties. (S)-Conformers 30 and 49 were weak inhibitors of hAdK, while the inhibitory potencies of 1a and its (N)-methanocarba counterpart 57 were comparable. A possible explanation is provided by the modeling results: the bulky N6,C7-diphenyl substituents do not fit into the hAdK closed form and, as emerged from MD simulations, induced the opening of the small lid domain. The enzyme open conformation is expected to exhibit a higher plasticity with respect to closed conformation to which smaller 1a mimics are predicted to bind. As a consequence, this enzyme conformation could accommodate the pseudo-sugar ring locked in either the (S) or (N) conformation. Thus, hAdK might indeed prefer the (N)-conformer as inhibitor in the closed/catalytic-phase of the enzyme.</p><p>When comparing pairs of methanocarba isomers, a distinction needs to be made between those having or lacking bulky phenyl groups, which largely determine the enzyme conformational preference. Indeed, when phenyl groups are attached to the purine core, the opening of the small lid domain occurs to host them. Those groups establish additional van der Waals interactions and hydrophobic contacts with the lid, which compensate for any geometrical factors in the ribose region. However, for the small nucleoside inhibitors, the conformation of the pseudoribose ring predominates. In compound 30, the interactions with the backbone NH groups of Gly64 and Ser65 appear to be missing, because of steric hindrance of the cyclopropyl ring of the (S) isomer. Those interactions impose a specific conformation of adenosine analogues and might help maintain the enzyme in the closed conformation by allowing the C2′ and C3′ hydroxyl groups of the inhibitors to H-bond with Asp18 of the lid. A mutagenesis study of AdK from Leishmania donovani reported the indispensable role of Asp16 (the equivalent of Asp18 in the hAdK) for the catalytic activity and suggested its involvement in a bidentate interaction with the hydroxyl group in C2′ and C3′ position of adenosine.80</p><p>Thus, we have discovered novel high potency inhibitors of hAdK, which can now be evaluated in vivo, for example in effects on DNA methylation, in comparison to riboside inhibitors such as 1a.5 The brain penetration by these analogues remains undetermined, which could be a complicating factor because nucleosides often have low entry into the CNS.49 Nevertheless, the slightly greater hydrophobicity of the (S)-methanocarba derivatives (cLog P of 49 is −0.11; tPSA is 120 Å) compared to ribosides (cLog P of the tetrahydrofuryl equivalent of 49 is −1.15; tPSA is 130 Å) might be beneficial for crossing the blood brain barrier. Furthermore, there remains the possibility that the specificity for AdK is enhanced in these (S)-methanocarba derivatives, which is crucial for avoiding possible side effects already noted for known AdK inhibitors. Although we have shown the feasibility of using this ribose conformational constraint in AdK inhibitors, there remains room for structural optimization to improve the inhibitory potency, considering that some of the known inhibitors achieve sub-nM affinity.</p><p>The interaction of these (S)-methanocarba analogues with nucleoside transporters that are relevant to adenosine derivatives, such as ENT1 and CNT2,50 remains to be characterized. The ability to serve as substrate or inhibitor of nucleoside transporters could affect the biodistribution or availability of the compounds in vivo.49,51 An analogue of the potent ENT1 inhibitor S-(4-nitrobenzyl)-thioinosine containing the opposite ring twist conformation ((N) methanocarba) was shown to inhibit ENT1, and other fixed conformations of 2′-deoxynucleosides were evaluated.52,53 (S)-Methanocarba 2′-deoxyadenosine inhibited both ENTs and CNTs, although less potently than 2′-deoxyadenosine.</p><p>The bioavailability and the in vivo activity of these inhibitors remain to be determined. Other nucleoside derivatives were protective in seizure models when administered peripherally.17 For example, the Br analogue of carbocyclic nucleoside 2 was found to be orally active in vivo in models of pain and inflammation.21 5′-Deoxynucleoside analogues of 1a were noted to be more potent in vivo than 5′-amino analogues, possibly because of enhanced passage across the blood-brain barrier by virtue of being less polar.17 Among the new (S)-methanocarba AdK inhibitors, 5′-deoxy analogue 38a and especially the fluoro analogues 38b and 38c appear to be the least polar, based on their tendency to dissolve in organic solvents.</p><p>It is possible that transient treatment with AdK inhibitors would have long-lasting therapeutic benefits for treatment of CNS disorders, not only by raising the basal level of AR activation but also through epigenetic reprogramming. A high level of adenosine in the brain drives the enzymatic equilibrium in the presence of S-adenosylhomocysteine (SAH) hydrolase in the direction of increased SAH formation. SAH in turn inhibits DNA methyltransferases through product inhibition.39,54 Because the epigenetic effects related to changes in the DNA methylation status would persist, it might be possible to reduce the duration of drug administration, thus avoiding toxicities associated with prolonged, chronic dosing. A transient dosing regimen might also avoid possible side effects, such as liver toxicity.12 Compounds 38a and 55 were submitted to the Psychoactive Drug Screening Program (PDSP) for screening at 45 receptors, channels and transporters (Supporting Information).55
38a was found to inhibit radioligand binding at the human 5HT7 (serotonin) receptor with a Ki value of 0.71 μM and did not substantially inhibit binding at any of the other off-target sites examined (<50% inhibition at 10 μM). 55 was found to inhibit radioligand binding at the human 5HT2B receptor with a Ki value of 51 nM and did not substantially inhibit binding at any of the other off-target sites examined. Also, 38a was found to be inactive (10 μM) as agonist or antagonist at human P2Y1, P2Y2, P2Y4, and P2Y11Rs (calcium transients) expressed in 1321N1 astrocytoma cells and protease-activated receptor (PAR)1 expressed in mouse KOLF cells. Nevertheless, the off-target interactions of the present set of compounds would have to be examined more extensively.</p><p>In conclusion, the development of novel AdK inhibitors, by virtue of their ability to raise the level of endogenous adenosine, particularly in disease states, remains of interest for the potential treatment of seizures and neurodegenerative and inflammatory conditions. We demonstrated that the class of constrained bicyclic ribonucleoside analogues retain inhibitory activity at this enzyme and are amenable to structural modification to enhance the potency. The SAR for ring-constrained analogues deviates from the SAR determined previously for ribosides; analogues with aryl groups at the 7-deaza and N6 positions of adenine are greatly favored, with (S) ≈ (N). We determined that the (S) conformation permits a range of substitutions, but amino derivatives 45 and 49 were much less potent than expected from the ribose equivalents. However, a difference between the (N)- and (S)-methanocarba series is that the methanocarba equivalent of reference riboside 1a is more potent in the (N) than in the (S) series (55 and 30, respectively).</p><p>We have identified compounds 34, 38a, 38b, 38c and 55 as hAdK inhibitors with IC50 values of ~100 nM. The successful docking and MD simulation of selected members of this series in the enzyme structure suggests that a structure-based design approach for further enhancement is possible. Although we have not yet explored all of the potential off-target effects and adenosine-receptor related side effects of this structural class, it is possible that the novel non-ribose ring system will provide a cleaner pharmacological profile. The potent AdK inhibitors in this study are now ready for further tests in animal models of epilepsy and its development.</p><!><p>All chemicals and anhydrous solvents were obtained directly from commercial sources. All reactions were carried out under nitrogen atmosphere using anhydrous solvents, unless specified otherwise. Room temperature or rt refers to 25 ± 5 °C. Silica-gel pre-coated with F254 on aluminum plates were used for TLC. The spots were examined under ultraviolet light at 254 nm and further visualized by anisaldehyde or Cerium ammonium molybdate stain solution. Column chromatography was performed on silica gel (40–63 μm, 60 Å). NMR spectra were recorded on a Bruker 400 MHz spectrometer. Chemical shifts are given in ppm (δ), calibrated to the residual solvent signals or TMS. High resolution mass (HRMS) measurements were performed on a proteomics optimized Q-TOF-2 (Micromass-Waters). The RP-HPLC was performed using Phenomenex Luna 5μm C18(2)100A, AXIA, 21.2×250 mm column. Purity was determined using Agilent ZORBAX SB-Aq, 5μm, 4.6×150 mm column attached to Agilent 1100 HPLC system, and a linear gradient of acetonitrile/water as mobile phase with a flow rate of 1.0 mL/min (acetonitrile/5 mM tetrabutylammonium dihydrogen phosphate in the case of 45 and 49). The purity of all screened compounds is >95% as determined by HPLC with detection at 254 nm. tPSA and cLog P were calculated using ChemDraw Professional V. 15.0 (PerkinElmer, Boston, MA). All chemical reagents were obtained from Sigma-Aldrich (St. Louis, MO), except 2-(4,6-dichloropyrimidine-5-yl)acetaldehyde 25 (Small Molecules, Inc., Hoboken, NJ).</p><!><p>The amine 24 (200 mg, 0.46 mmol) was dissolved in ethanol (4 mL). To this was added 4,6-dichloropyrimidin-5-acetaldehyde 25 (88 mg, 0.46 mmol) and triethylamine (TEA, 128 μL, 0.92 mmol). The reaction mixture was heated to 90 °C under reflux condenser overnight, volatiles evaporated under reduced pressure, residue purified by silica-gel flash column chromatography to afford compound 26 as a white foam (200 mg, 76%, Rf = 0.45, TLC eluent = 20% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.40 (s, 1H), 7.79 – 7.65 (m, 4H), 7.49 – 7.34 (m, 6H), 7.28 (d, J = 3.6 Hz, 1H), 6.51 (d, J = 3.6 Hz, 1H), 4.98 (dd, J = 1.6, 7.1 Hz, 1H), 4.60 (dd, J = 0.8, 7.1 Hz, 1H), 4.12 (d, J = 7.9 Hz, 2H), 2.58 (t, J = 7.9 Hz, 1H), 2.11 (ddd, J = 1.4, 5.5, 9.9 Hz, 1H), 1.62 (t, J = 5.6 Hz, 1H), 1.58 (s, 3H), 1.44 (ddd, J = 1.8, 5.8, 9.8 Hz, 1H), 1.22 (s, 3H), 1.08 (s, 9H). 13C NMR (101 MHz, CDCl3) δ 151.72, 151.64, 150.44, 135.63, 135.61, 133.56, 133.50, 130.37, 129.81, 129.79, 127.75, 118.19, 111.51, 99.44, 84.57, 83.24, 65.03, 49.68, 47.51, 31.32, 26.90, 26.36, 24.06, 19.34, 16.63. HRMS m/z [M+H]+ for C32H36ClN3O3Si calculated 574.2293, found 574.2290.</p><!><p>To a dried mixture of compound 26 (200 mg, 0.35 mmol) and N-iodosuccinimide (NIS, 135 mg, 0.42 mmol) was added anhydrous DMF (5 mL) under nitrogen atmosphere. The solution was heated to 65 °C with stirring for 6 h. The volatiles were evaporated under vacuum, and the residue was purified by silica-gel flash column chromatography to afford 27 as a white foam (225 mg, 92%, Rf = 0.50, TLC eluent = 20% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.36 (s, 1H), 7.80 – 7.68 (m, 4H), 7.53 – 7.34 (m, 7H), 4.94 (d, J = 7.0 Hz, 1H), 4.59 (d, J = 7.0 Hz, 1H), 4.08 (d, J = 7.9 Hz, 2H), 2.57 (t, J = 7.8 Hz, 1H), 2.10 (dd, J = 5.5, 9.9 Hz, 1H), 1.61 (t, J = 5.6 Hz, 1H), 1.57 (s, 3H), 1.42 (dd, J = 5.8, 10.0 Hz, 1H), 1.21 (s, 3H), 1.08 (s, 9H). 13C NMR (101 MHz, CDCl3) δ 152.47, 151.39, 150.77, 135.62, 135.60, 135.58, 134.79, 133.47, 133.44, 129.84, 129.82, 129.64, 127.77, 127.77, 127.71, 117.52, 111.61, 84.40, 83.14, 64.92, 49.87, 47.43, 31.38, 26.89, 26.56, 26.34, 24.04, 19.33, 16.64. HRMS m/z [M+H]+ for C32H35ClIN3O3Si calculated 700.1259, found 700.1253.</p><!><p>To compound 27 (20 mg, 0.029 mmol) was added 70% aqueous trifluoroacetic acid (TFA, 1.5 mL) and the mixture stirred at room temperature for 1.5 h. The volatiles were evaporated under vacuum and the residual TFA was chased first with water (2 × 2 mL), and then neutralized with a mixture of water (2 mL) and a few drops of triethylamine. The residue after evaporation was purified by silica-gel flash column chromatography to afford 28 as a white solid (10 mg, 83%, Rf = 0.50, TLC eluent = 10% methanol in dichloromethane). 1H NMR (400 MHz, CD3OD) δ 8.63 (s, 1H), 7.86 (s, 1H), 4.69 (dd, J = 2.0, 6.5 Hz, 1H), 4.14 – 4.02 (m, 2H), 3.93 (dd, J = 4.9, 11.3 Hz, 1H), 2.34 (t, J = 4.6 Hz, 1H), 2.01 – 1.92 (m, 2H), 1.31 (ddd, J = 2.0, 4.3, 8.2 Hz, 1H). 13C NMR (101 MHz, CD3OD) δ 153.63, 152.31, 151.19, 139.06, 119.11, 77.64, 73.84, 65.49, 51.54, 51.31, 50.55, 26.50, 15.48. HRMS m/z [M+H]+ for C13H13ClIN3O3 calculated 421.9768, found 421.9771.</p><!><p>Compound 27 (75 mg, 0.11 mmol) was placed in a glass pressure tube with stir bar and treated with ethanol (5 mL) followed by 7 N ammonia in methanol (5 mL). The tube was capped tightly and heated to 120 °C for 18 h with stirring. The solvents were evaporated and the residue purified by silica-gel flash column chromatography to afford 29 as a white solid (65 mg, 89%, Rf = 0.45, TLC eluent = 5% methanol in dichloromethane). 1H NMR (400 MHz, CDCl3) δ 7.82 (s, 1H), 7.75 – 7.65 (m, 3H), 7.51 – 7.44 (m, 2H), 7.43 – 7.36 (m, 5H), 7.31 (s, 1H), 4.90 (dd, J = 1.6, 7.1 Hz, 1H), 4.58 (dd, J = 1.3, 7.2 Hz, 1H), 4.00 (d, J = 7.6 Hz, 1H), 2.56 (t, J = 7.5 Hz, 1H), 2.12 (ddd, J = 1.4, 5.4, 9.9 Hz, 1H), 1.62 (t, J = 5.7 Hz, 1H), 1.57 (s, 3H), 1.40 (ddd, J = 1.8, 5.9, 10.0 Hz, 1H), 1.22 (s, 4H), 1.08 (s, 9H). 13C NMR (101 MHz, CDCl3) δ 152.60, 148.78, 141.90, 135.61, 135.55, 133.35, 133.24, 132.89, 130.02, 129.94, 127.84, 127.80, 111.83, 103.11, 84.65, 83.15, 64.89, 50.27, 47.28, 31.53, 26.91, 26.86, 26.32, 24.04, 19.33, 16.72. HRMS m/z [M+H]+ for C32H37IN4O3Si calculated 681.1758, found 681.1749.</p><!><p>Following the procedure described to synthesize 28, compound 29 (13 mg, 0.019 mmol) afforded 30 as a white solid which was further purified by RP-HPLC (3.6 mg, 47%, Rf = 0.25, TLC eluent = 10% methanol in dichloromethane; RP-HPLC (C18) Rt = 18.9 min, water/acetonitrile 75/25 → 25/75 in 40 min at 5mL/min). 1H NMR (400 MHz, CD3OD) δ 8.08 (s, 1H), 7.35 (s, 1H), 4.57 (dd, J = 2.0, 6.6 Hz, 1H), 4.05 – 3.97 (m, 2H), 3.79 (dd, J = 3.6, 11.5 Hz, 1H), 2.25 (t, J = 2.9 Hz, 1H), 1.84 – 1.76 (m, 2H), 1.18 – 1.09 (m, 1H). 13C NMR (101 MHz, CD3CN) δ 158.58, 152.56, 150.84, 132.31, 105.11, 77.55, 74.12, 65.56, 51.15, 50.56, 49.18, 26.79, 14.94. HRMS m/z [M+H]+ for C13H15IN4O3 calculated 403.0267, found 403.0269.</p><!><p>To a solution of pre-dried compound 27 (75 mg, 0.11 mmol) and aniline (12 μL, 0.13 mmol) in anhydrous THF (1 mL) at −20 °C under nitrogen atmosphere was added potassium t-butoxide solution (1M in THF, 160 μL, 0.16 mmol) drop wise and stirred at this temperature for 1 h. The reaction was quenched by adding sat. NH4Cl (1 mL) and the products extracted into ethyl acetate (3×2 mL). The separated organic layers were combined, washed with brine, dried over anhydrous Na2SO4 and evaporated, and the residue was purified by silica-gel flash column chromatography to afford 31a as a white foam (65 mg, 80%, Rf = 0.30, TLC eluent = 10% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.27 (s, 1H), 8.23 (brs, 1H), 7.78 – 7.64 (m, 8H), 7.50 – 7.34 (m, 7H), 7.21 (s, 1H), 4.99 (dd, J = 1.6, 7.1 Hz, 1H), 4.59 (dd, J = 1.1, 7.0 Hz, 1H), 4.11 (d, J = 7.8 Hz, 2H), 2.55 (t, J = 7.8 Hz, 1H), 2.08 (ddd, J = 1.3, 5.4, 9.8 Hz, 1H), 1.63 – 1.54 (m, 4H), 1.46 – 1.38 (m, 1H), 1.22 (s, 3H), 1.09 (s, 9H). HRMS m/z [M+H]+ for C38H41IN4O3Si calculated 757.2071, found 757.2067.</p><!><p>Following the procedure described for the synthesis of 31a, compound 27 (60 mg, 0.086 mmol) gave 31b as a white foam (47 mg, 70%, Rf = 0.2, TLC eluent = 10% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.23 (s, 1H), 7.89 (s, 1H), 7.77 – 7.64 (m, 6H), 7.48 – 7.35 (m, 6H), 7.17 (s, 1H), 7.09 (dd, J = 8.3, 9.0 Hz, 2H), 5.01 (dd, J = 1.6, 7.1 Hz, 1H), 4.62 – 4.56 (m, 1H), 4.13 (d, J = 8.0 Hz, 2H), 2.54 (t, J = 8.0 Hz, 1H), 2.07 (ddd, J = 1.3, 5.4, 9.8 Hz, 1H), 1.57 (s, 3H), 1.55 (m, 1H), 1.41 (ddd, J = 1.7, 5.6, 9.8 Hz, 1H), 1.21 (s, 3H), 1.08 (s, 9H). 19F NMR (376 MHz, CDCl3) δ −119.03. HRMS m/z [M+H]+ for C38H40FIN4O3Si calculated 775.1977, found 775.1971.</p><!><p>Following the reaction procedure described for the synthesis of 28, compound 31a (20 mg, 0.035 mmol) gave 32 as a white solid which was further purified by RP-HPLC (3.35 mg, 27%, Rf = 0.45, TLC eluent = 10% methanol in dichloromethane; RP-HPLC (C18) Rt = 25.6 min, water/acetonitrile 50/50 → 10/90 in 40 min at 5 mL/min). 1H NMR (400 MHz, CD3OD) δ 8.27 (s, 1H), 7.74 (dd, J = 1.1, 8.7 Hz, 1H), 7.45 (s, 1H), 7.41 – 7.33 (m, 2H), 7.17 – 7.09 (m, 1H), 4.60 (dd, J = 2.0, 6.6 Hz, 1H), 4.08 – 3.99 (m, 2H), 3.81 (dd, J = 3.7, 11.5 Hz, 1H), 2.29 – 2.25 (m, 1H), 1.87 – 1.79 (m, 2H), 1.17 (ddp, J = 2.1, 3.6, 5.7 Hz, 1H). HRMS m/z [M+H]+ for C19H19IN4O3 calculated 479.0580, found 479.0589.</p><!><p>A mixture of DME (1.7 mL) and ethanol (0.3 mL) was heated to 90 °C for 10 min and cooled to room temperature. This solution was added to a vacuum dried mixture of 31a (75 mg, 0.13 mmol), phenylboronic acid (19 mg, 0.16 mmol) and Pd(PPh3)4 (7.5 mg, 0.007 mmol). A sonicated aqueous saturated Na2CO3 solution was added to this mixture, and the flask immersed in to a pre-heated oil bath at 90 °C and stirred for 7 h. The solvents were evaporated under vacuum, and the residue was partitioned between water and dichloromethane (3 × 10 mL), organic layer separated, dried over anhydrous Na2SO4, and then evaporated. The residue was purified by silica-gel flash column chromatography to afford pure product 33a as a white foam (60 mg, 86%, Rf = 0.25, TLC eluent = 10% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.32 (s, 1H), 7.80 – 7.66 (m, 6H), 7.52 – 7.33 (m, 11H), 7.31 – 7.26 (m, 2H), 7.07 (s, 1H), 7.05 – 6.99 (m, 1H), 5.13 (dd, J = 1.5, 7.1 Hz, 1H), 4.64 (d, J = 7.0 Hz, 1H), 4.18 (d, J = 7.9 Hz, 2H), 2.58 (t, J = 7.9 Hz, 1H), 2.14 (ddd, J = 1.3, 5.5, 9.8 Hz, 1H), 1.64 – 1.56 (m, 4H), 1.49 (ddd, J = 1.7, 5.7, 9.8 Hz, 1H), 1.24 (s, 3H), 1.10 (s, 9H). HRMS m/z [M+H]+ for C44H46N4O3Si calculated 707.3417, found 707.3405.</p><!><p>Following the procedure described for the synthesis of 33a, compound 31b (50 mg, 0.0645 mmol) gave 33b as a white foam (35 mg, 75%, Rf = 0.15, TLC eluent = 10% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.25 (s, 1H), 7.73 (ddt, J = 1.7, 4.0, 8.1 Hz, 5H), 7.56 – 7.29 (m, 13H), 7.07 (s, 1H), 7.03 – 6.81 (m, 2H), 5.11 (dd, J = 1.6, 7.1 Hz, 1H), 4.69 – 4.57 (m, 1H), 4.16 (d, J = 7.9 Hz, 2H), 2.58 (t, J = 7.8 Hz, 1H), 2.14 (ddd, J = 1.3, 5.4, 9.9 Hz, 1H), 1.61 (t, J = 6.0 Hz, 1H), 1.58 (s, 3H), 1.49 (ddd, J = 1.8, 5.8, 9.8 Hz, 1H), 1.24 (s, 3H), 1.09 (s, 9H). 19F NMR (376 MHz, CDCl3) δ −119.7. HRMS m/z [M+H]+ for C44H45FN4O3Si calculated 725.3323, found 725.3322.</p><!><p>Following the procedure described for the synthesis of 33a, compound 31a (50 mg, 0.0645 mmol) gave 33c as a white foam (40 mg, 75%, Rf = 0.15, TLC eluent = 10% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.31 (s, 1H), 7.78 – 7.70 (m, 4H), 7.42 (dddd, J = 2.0, 6.0, 8.3, 14.5 Hz, 10H), 7.28 (t, J = 7.8 Hz, 3H), 7.15 (d, J = 8.4 Hz, 2H), 7.07 – 7.00 (m, 2H), 5.12 (dd, J = 1.5, 7.1 Hz, 1H), 4.64 (dd, J = 1.3, 7.2 Hz, 1H), 4.19 (d, J = 7.9 Hz, 2H), 2.58 (t, J = 7.8 Hz, 1H), 2.14 (ddd, J = 1.3, 5.4, 9.8 Hz, 1H), 1.61 (t, J = 3.8 Hz, 1H), 1.59 (s, 3H), 1.49 (ddd, J = 1.7, 5.7, 9.8 Hz, 1H), 1.24 (s, 3H), 1.10 (s, 9H). 19F NMR (376 MHz, CDCl3) δ −114.31 (q, J = 3.7, 4.4 Hz). HRMS m/z [M+H]+ for C44H45FN4O3Si calculated 725.3323, found 725.3317.</p><!><p>Following the reaction procedure described for the synthesis of 28, compound 33a (17 mg, 0.024 mmol) gave 34 as a white solid which was further purified by RP-HPLC (4.7 mg, 46%, Rf = 0.25, TLC eluent = 5% methanol in dichloromethane; RP-HPLC (C18) Rt = 29.8 min, water/acetonitrile 50/50 → 10/90 in 40 min at 5 mL/min). 1H NMR (400 MHz, CD3OD) δ 8.32 (s, 1H), 7.65 – 7.51 (m, 4H), 7.51 – 7.42 (m, 3H), 7.33 (s, 1H), 7.30 – 7.22 (m, 2H), 7.03 (ddt, J = 1.1, 7.1, 7.7 Hz, 1H), 4.70 (dd, J = 2.0, 6.6 Hz, 1H), 4.14 – 4.01 (m, 2H), 3.84 (dd, J = 3.6, 11.5 Hz, 1H), 2.33 – 2.27 (m, 1H), 1.93 – 1.81 (m, 2H), 1.24 (ddd, J = 2.1, 5.1, 8.9 Hz, 1H). HRMS m/z [M+H]+ for C25H24N4O3 calculated 429.1927, found 429.1935.</p><!><p>Compound 33a (60 mg, 0.089 mmol) was dissolved in anhydrous THF (2 mL), treated with tetrabutylammonium fluoride (1 M in THF, 93 μL, 0.093 mmol) at 0 °C and stirred overnight at room temperature. The solvent was evaporated and the residue purified by silica-gel flash column chromatography to afford 35a as a white foamy solid (38 mg, 96%, Rf = 0.15, TLC eluent = 30% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.44 (s, 1H), 7.59 – 7.47 (m, 6H), 7.47 – 7.40 (m, 1H), 7.36 – 7.26 (m, 2H), 7.13 (s, 1H), 7.11 – 7.00 (m, 2H), 5.07 (dd, J = 1.8, 6.9 Hz, 1H), 4.90 (dd, J = 1.6, 6.9 Hz, 1H), 4.12 (d, J = 11.5 Hz, 1H), 3.89 (dt, J = 3.14, 12.1 Hz, 1H), 2.50 (dd, J = 1.2, 3.2 Hz, 1H), 2.10 (ddd, J = 1.5, 5.2, 9.7 Hz, 1H), 1.64 – 1.55 (m, 4H), 1.40 – 1.21 (m, 4H). HRMS m/z [M+H]+ for C28H28N4O3 calculated 469.2240, found 469.2241.</p><!><p>Following the procedure described for the synthesis of 35a, compound 33b (35 mg, 0.048 mmol) gave 35b as a white foam (20 mg, 85%, Rf = 0.35, TLC eluent = 50% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.53 (s, 1H), 7.51 (d, J = 4.4 Hz, 4H), 7.44 (ddd, J = 2.5, 4.6, 9.0 Hz, 3H), 7.14 (s, 1H), 6.99 (t, J = 8.6 Hz, 2H), 5.06 (dd, J = 1.7, 6.9 Hz, 1H), 4.89 (dd, J = 1.5, 6.9 Hz, 1H), 4.13 (dd, J = 1.4, 11.4 Hz, 1H), 3.93 (dd, J = 3.1, 11.4 Hz, 1H), 2.51 (dd, J = 1.3, 3.0 Hz, 1H), 2.10 (ddd, J = 1.5, 5.2, 9.7 Hz, 1H), 1.64 – 1.60 (m, 1H), 1.58 (s, 3H), 1.37 – 1.31 (m, 1H), 1.29 (s, 3H). 13C NMR (101 MHz, CDCl3) δ 160.33, 157.92, 154.57, 151.42, 150.10, 134.83, 134.80, 134.31, 129.39, 129.27, 128.04, 124.57, 122.33, 122.25, 116.28, 115.85, 115.63, 111.32, 102.48, 85.80, 84.72, 65.72, 50.36, 46.90, 32.12, 26.59, 24.41, 16.44. 19F NMR (376 MHz, CDCl3) δ −118.65. HRMS m/z [M+H]+ for C28H27FN4O3 calculated 487.2145, found 487.2148.</p><!><p>Following the procedure described for the synthesis of 35a, compound 33c (40 mg, 0.055 mmol) gave 35c as a white foam (25 mg, 93%, Rf = 0.15, TLC eluent = 30% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.51 (s, 1H), 7.49 (ddd, J = 2.1, 3.2, 8.7 Hz, 4H), 7.35 – 7.28 (m, 2H), 7.24 – 7.17 (m, 2H), 7.12 (s, 1H), 7.07 (tt, J = 1.1, 7.1 Hz, 1H), 5.05 (dd, J = 1.7, 6.9 Hz, 1H), 4.89 (dd, J = 1.4, 6.9 Hz, 1H), 4.12 (dd, J = 1.4, 11.4 Hz, 1H), 3.91 (dd, J = 3.0, 11.4 Hz, 1H), 2.10 (ddd, J = 1.5, 5.1, 9.8 Hz, 1H), 1.61 (t, J = 5.3 Hz, 1H), 1.58 (s, 3H), 1.35 – 1.30 (m, 1H), 1.29 (s, 3H). 13C NMR (101 MHz, CDCl3) δ 163.88, 161.41, 154.55, 151.55, 150.10, 138.73, 131.07, 130.99, 130.31, 130.27, 129.18, 124.65, 123.71, 120.41, 116.45, 116.24, 115.12, 111.33, 102.65, 85.79, 84.72, 65.71, 50.35, 46.90, 32.11, 26.59, 24.41, 16.44. 19F NMR (376 MHz, CDCl3) δ −113.56. HRMS m/z [M+H]+ for C28H27FN4O3 calculated 487.2145, found 487.2146.</p><!><p>To a solution of compound 35a (10 mg, 0.022 mmol) and DMAP (8 mg, 0.065 mmol) in anhydrous acetonitrile (0.5 mL) was added O-p-tolylchlorothionoformate (36, 8 μL, 0.052 mmol) drop wise at room temperature. The mixture was stirred for 4 h, and then the volatile organics were evaporated under reduced pressure. The residue was suspended in ethyl acetate (5 mL) and washed with water and brine. The organic layer was dried over anhydrous sodium sulfate, and the solvent evaporated to dryness. The residue obtained was dried under high vacuum for 2h and then, suspended in anhydrous toluene (1.5 mL). Tributyltin hydride (17 μL, 0.065 mmol) and azoisobutyronitrile (AIBN, 10 mg, 0.065 mmol) was added, and the flask was immersed in to an oil bath at 120 °C for 2h. Volatile materials were evaporated, and the residue was purified by silica-gel flash column chromatography to afford compound 37a as a white foam (5 mg, 52%, Rf = 0.60, TLC eluent = 30% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.49 (s, 1H), 7.58 – 7.46 (m, 6H), 7.46 – 7.38 (m, 1H), 7.33 – 7.26 (m, 2H), 7.05 (s, 1H), 7.04 – 6.99 (m, 1H), 6.94 (s, 1H), 5.31 (dd, J = 1.7, 7.0 Hz, 1H), 4.50 (dd, J = 1.4, 7.0 Hz, 1H), 2.40 (q, J = 7.5 Hz, 1H), 1.92 (ddd, J = 1.4, 5.4, 9.7 Hz, 1H), 1.56 (d, J = 7.3 Hz, 3H), 1.55 (s, 3H), 1.41 (ddd, J = 1.8, 5.6, 9.7 Hz, 1H), 1.27 (s, 3H). HRMS m/z [M+H]+ for C28H28N4O2 calculated 453.2291, found 453.2285.</p><!><p>Following the procedure described for the synthesis of 37a, compound 35b (20 mg, 0.041 mmol) gave 37b as a white foam (5 mg, 57% based on 11 mg starting material recovered, Rf = 0.75, TLC eluent = 30% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.45 (s, 1H), 7.58 – 7.29 (m, 8H), 7.08 (s, 1H), 6.99 – 6.86 (m, 2H), 5.28 (dd, J = 1.6, 7.0 Hz, 1H), 4.54 – 4.46 (m, 1H), 2.41 (q, J = 7.5 Hz, 1H), 1.93 (ddd, J = 1.4, 5.4, 9.7 Hz, 1H), 1.59 – 1.52 (m, 7H), 1.41 (ddd, J = 1.9, 5.8, 9.8 Hz, 1H), 1.27 – 1.26 (m, 3H). 19F NMR (376 MHz, CDCl3) δ −119.6. HRMS m/z [M+H]+ for C28H27FN4O2 calculated 471.2196, found 471.2188.</p><!><p>Following the procedure described for the synthesis of 37a, compound 35c (25 mg, 0.051 mmol) gave 37c as a white foam (7 mg, 90% based on 12 mg starting material recovered, Rf = 0.75, TLC eluent = 30% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.47 (s, 1H), 7.39 (brs, 4H), 7.31 – 7.20 (m, 3H), 7.11 (t, J = 7.8 Hz, 2H), 7.05 (s, 1H), 7.05 – 7.00 (m, 1H), 5.28 (dd, J = 1.7, 7.0 Hz, 1H), 4.50 (dd, J = 1.4, 7.1 Hz, 1H), 2.41 (q, J = 7.4 Hz, 1H), 1.94 (ddd, J = 1.5, 5.4, 9.7 Hz, 1H), 1.59 – 1.52 (m, 7H), 1.43 – 1.37 (m, 1H), 1.27 (s, 3H). 19F NMR (376 MHz, CDCl3) δ −114.30. HRMS m/z [M+H]+ for C28H27FN4O2 calculated 471.2196, found 471.2204.</p><!><p>Following the reaction procedure described for the synthesis of 28, compound 37 (5 mg, 0.011 mmol) gave 38a as a white solid which was further purified by RP-HPLC (3 mg, 66%, Rf = 0.30, TLC eluent = 5% methanol in dichloromethane; RP-HPLC (C18) Rt = 43.8 min, water/acetonitrile 50/50 → 10/90 in 40 min at 5 mL/min). 1H NMR (400 MHz, CD3OD) δ 8.34 (s, 1H), 7.62 – 7.49 (m, 4H), 7.46 (dq, J = 1.0, 7.0 Hz, 3H), 7.32 – 7.21 (m, 3H), 7.07 – 6.97 (m, 1H), 3.80 (dt, J = 1.3, 6.3 Hz, 1H), 2.19 (q, J = 7.2 Hz, 1H), 1.92 (t, J = 5.2 Hz, 1H), 1.81 (ddd, J = 1.4, 4.8, 9.1 Hz, 1H), 1.43 (d, J = 7.4 Hz, 2H), 1.21 (ddd, J = 1.8, 5.4, 9.0 Hz, 1H). 13C NMR (101 MHz, CD3OD) δ 155.44, 152.66, 152.18, 140.38, 136.00, 130.36, 130.28, 129.90, 128.75, 126.02, 124.25, 121.26, 116.76, 103.85, 77.89, 77.12, 43.13, 30.78, 30.35, 19.94, 16.73. HRMS m/z [M+H]+ for C25H24N4O2 calculated 413.1978, found 413.1977.</p><!><p>Following the procedure described for the synthesis of 28, compound 37b (5 mg, 0.011 mmol) gave 38b as a white solid which was purified further by RP-HPLC (2.4 mg, 53%, Rf = 0.3, TLC eluent = 5% methanol in dichloromethane; RP-HPLC (C18) Rt = 42.7 min, water/acetonitrile 50/50 → 10/90 in 40 min @ 5 mL/min). 1H NMR (400 MHz, CD3OD) δ 8.32 (s, 1H), 7.61 – 7.50 (m, 4H), 7.50 – 7.40 (m, 3H), 7.24 (s, 1H), 7.05 – 6.97 (m, 2H), 4.85 – 4.82 (m, 1H), 3.80 (dt, J = 1.3, 6.3 Hz, 1H), 2.23 – 2.15 (m, 1H), 1.95 – 1.89 (m, 1H), 1.81 (ddd, J = 1.4, 4.7, 9.3 Hz, 1H), 1.43 (d, J = 7.4 Hz, 3H), 1.21 (ddd, J = 1.9, 5.4, 9.1 Hz, 1H). 19F NMR (376 MHz, CD3OD) δ −121.81 (tt, J = 4.8, 8.4 Hz). HRMS m/z [M+H]+ for C25H23FN4O2 calculated 431.1883, found 431.1881.</p><!><p>Following the procedure described for the synthesis of 28, compound 37c (7 mg, 0.015 mmol) gave 38c as a white solid which was purified further by RP-HPLC (4 mg, 63%, Rf = 0.3, TLC eluent = 5% methanol in dichloromethane; RP-HPLC (C18) Rt = 41.9 min, water/acetonitrile 50/50 → 10/90 in 40 min @ 5 mL/min). 38c was soluble in chloroform, but not methanol. 1H NMR (400 MHz, DMSO-d6) δ 8.37 (s, 1H), 7.63 – 7.48 (m, 5H), 7.37 – 7.23 (m, 5H), 6.98 (tt, J = 1.2, 7.4 Hz, 1H), 4.78 – 4.73 (m, 1H), 3.63 (d, J = 6.1 Hz, 1H), 2.10 – 2.02 (m, 1H), 1.72 (t, J = 5.0 Hz, 1H), 1.67 – 1.62 (m, 1H), 1.37 (d, J = 7.4 Hz, 3H), 1.24 – 1.16 (m, 1H). 19F NMR (376 MHz, DMSO-d6) δ −115.78 (tt, J = 5.5, 9.1 Hz). HRMS m/z [M+H]+ for C25H23FN4O2 calculated 431.1883, found 431.1887.</p><!><p>Following the reaction procedure described for the synthesis of 35, compound 29 (65 mg, 0.095 mmol) gave 39 as a white solid (45 mg, quantitative yield, Rf = 0.20, TLC eluent = 5% methanol in dichloromethane). 1H NMR (400 MHz, CDCl3) δ 8.23 (s, 1H), 7.19 (s, 1H), 6.81 (dd, J = 1.8, 12.5 Hz, 1H), 5.70 (s, 3H), 4.94 (dd, J = 1.8, 6.9 Hz, 1H), 4.83 (dd, J = 1.5, 6.9 Hz, 1H), 4.05 (dt, J = 1.5, 11.5 Hz, 1H), 3.91 – 3.78 (m, 1H), 2.51 – 2.42 (m, 1H), 2.01 (ddd, J = 1.5, 5.2, 9.7 Hz, 1H), 1.58 – 1.53 (m, 4H), 1.27 (s, 3H), 1.23 (ddd, J = 1.9, 5.5, 9.7 Hz, 1H). HRMS m/z [M+H]+ for C16H19IN4O3 calculated 443.0580, found 443.0585.</p><!><p>To an ice cold solution of 39 (20 mg, 0.045 mmol) and triphenylphosphine (17 mg, 0.063 mmol) in anhydrous THF (1 mL) was added diisopropyl azodicarboxylate (DIAD, 13 μL, 0.063 mmol) dropwise. After 5 min diphenylphosphorylazide (DPPA, 14 μL, 0.063 mmol) was added and stirred at 0 °C for 30 min and then at room temperature overnight. The reaction mixture was heated to 60 °C for 4h. Solvents evaporated to dryness, residue suspended in ethyl acetate, washed with water and brine, dried over anhydrous Na2SO4. Solvent was evaporated and the residue purified by silica-gel flash column chromatography to afford the product 40 as a white solid (Rf = 0.80, TLC eluent = 5% methanol in dichloromethane). 1H NMR (400 MHz, CD3OD) δ 7.98 – 7.88 (m, 4H), 7.86 (s, 1H), 7.63 (s, 1H), 7.55 (ddd, J = 1.6, 5.2, 7.3 Hz, 2H), 7.47 (ddd, J = 3.3, 6.8, 8.7 Hz, 5H), 7.36 – 7.08 (m, 12H), 7.07 – 6.98 (m, 2H), 4.89 (dd, J = 1.6, 7.2 Hz, 1H), 4.69 – 4.63 (m, 2H), 4.54 – 4.48 (m, 1H), 2.55 (t, J = 6.9 Hz, 1H), 1.83 – 1.75 (m, 1H), 1.57 – 1.40 (m, 5H), 1.14 (s, 3H). HRMS m/z [M+H]+ for C46H42IN4O6P2 calculated 935.1624, found 935.1628.</p><!><p>The intermediate compound 40 was dissolved in anhydrous DMF and treated with excess of NaN3. The mixture was heated to 65 °C overnight. Solvent evaporated, the residue purified by silica-gel flash column chromatography to afford the title compound 41 as a white solid (Rf = 0.30, TLC eluent = 20% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.02 – 7.91 (m, 7H), 7.55 – 7.49 (m, 3H), 7.48 – 7.40 (m, 6H), 7.05 (s, 1H), 5.07 (dd, J = 1.6, 7.1 Hz, 1H), 4.54 (dd, J = 1.4, 7.1 Hz, 1H), 3.85 (qd, J = 8.1, 12.1 Hz, 2H), 2.41 (t, J = 8.1 Hz, 1H), 1.86 (ddd, J = 1.4, 5.4, 9.7 Hz, 1H), 1.55 (s, 3H), 1.49 (t, J = 5.6 Hz, 1H), 1.41 (ddd, J = 1.7, 5.8, 9.7 Hz, 1H), 1.22 (s, 3H). HRMS m/z [M+H]+ for C34H32IN7O2P calculated 728.1400, found 728.1406.</p><!><p>To a solution of compound 41 (15 mg, 0.034 mmol) in anhydrous pyridine (0.5 mL) under a nitrogen atmosphere was added methanesulfonyl chloride (MsCl, 6 μL, 0.068 mmol) at 0 °C. After stirring the reaction mixture for 4 h, volatiles were evaporated under vacuum and the residue partitioned between water and ethyl acetate (3 × 5 mL). The organic layer was separated, combined, dried over anhydrous Na2SO4 and solvent evaporated. The residue was dissolved in anhydrous DMF (0.5 mL) and sodium azide (22 mg, 0.34 mmol) was added, the mixture was heated to 60 °C for 4 h. The solvent was evaporated under high vacuum, and the residue was suspended in ethyl acetate, washed with water and brine, and dried over anhydrous Na2SO4. The residue after evaporation was purified by silica-gel flash column chromatography to afford title compound 42 as a white foamy solid (15 mg, 95%, Rf = 0.45, TLC eluent = 5% methanol in dichloromethane). 1H NMR (400 MHz, CDCl3) δ 8.24 (s, 1H), 7.12 (s, 1H), 5.63 (s, 2H), 5.08 (dd, J = 1.7, 7.1 Hz, 1H), 4.57 (dd, J = 1.4, 7.1 Hz, 1H), 3.92 (dd, J = 7.9, 12.1 Hz, 1H), 3.83 (dd, J = 8.3, 12.1 Hz, 1H), 2.46 (t, J = 8.1 Hz, 1H), 1.95 (ddd, J = 1.4, 5.4, 9.8 Hz, 1H), 1.59 – 1.52 (m, 4H), 1.41 (ddd, J = 1.7, 5.9, 9.8 Hz, 1H), 1.25 (s, 3H). HRMS m/z [M+H]+ for C16H18IN7O2 calculated 468.0645,found 468.0647.</p><!><p>Following the reaction procedure described for the synthesis of 28, compound 42 (8 mg, 0.017 mmol) gave 43 as a white solid which was further purified by RP-HPLC (3.1 mg, 42%, Rf = 0.25, TLC eluent = 5% methanol in dichloromethane; RP-HPLC (C18) Rt = 28.5 min, water/acetonitrile 75/25 → 25/75 in 40 min at 5 mL/min). 1H NMR (400 MHz, CD3OD) δ 8.11 (s, 1H), 7.31 (s, 1H), 4.66 (dd, J = 1.9, 6.5 Hz, 1H), 3.94 – 3.84 (m, 2H), 3.73 (dd, J = 7.4, 12.2 Hz, 1H), 2.30 – 2.22 (m, 1H), 1.91 – 1.81 (m, 2H), 1.23 – 1.17 (m, 1H). HRMS m/z [M+H]+ for C13H14IN7O2 calculated 428.0332, found 428.0336.</p><p>7-((3aS,3bS,4aS,5R,5aR)-5-(Aminomethyl)-2,2-dimethyltetrahydrocyclopropa[3,4]-cyclopenta[1,2-d][1,3]dioxol-3b(3aH)-yl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-amine (44): compound 42 (8 mg, 0.017 mmol) was dissolved in anhydrous THF (0.5 mL), to this was added triphenylphosphine (9 mg, 0.034 mmol) and stirred at room temperature overnight. Ammonium hydroxide (25%, 30 μL) was added and heated to 65 °C under reflux condenser for 4h. Solvent was evaporated and the residue was purified by silica-gel flash column chromatography to afford 44 (6 mg, 80%, Rf = 0.10, TLC eluent = 10% methanol and 1% triethylamine in dichloromethane). HRMS m/z [M+H]+ for C16H20IN5O2 calculated 442.0740, found 442.0736.</p><!><p>Following the reaction procedure described for the synthesis of 28, compound 44 (6 mg, 0.0136 mmol) after purification by RP-HPLC gave 45 as a white solid (1.91 mg, 35% ; RP-HPLC (C18) Rt = 29.6 min, 10 mM triethylammonium acetate in water/acetonitrile 90/10 → 65/35 in 40 min at 5 mL/min). 1H NMR (400 MHz, CD3OD) δ 8.11 (s, 1H), 7.34 (s, 1H), 4.56 (d, J = 6.8 Hz, 1H), 4.00 (d, J = 6.6 Hz, 1H), 3.38 (t, J = 5.9 Hz, 2H), 2.43 (t, J = 5.0 Hz, 1H), 1.95 - 1.70 (m, 5H), 1.27 (t, J = 7.2 Hz, 1H). HRMS m/z [M+H]+ for C13H16IN5O2 calculated 402.0427, found 402.0421.</p><!><p>To a solution of compound 39 (40 mg, 0.09 mmol) in acetonitrile-water (4:1, 2.0 mL) was added bis(acetoxy)iodobenzene (BAIB, 64 mg, 0.20 mmol) and 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO, 12 mg, 0.077 mmol) at room temperature. After stirring for 18 h at room temperature, the volatiles were evaporated under high vacuum. The residue was purified by silica-gel column chromatography to afford 46 as a light yellow solid (20 mg, 49%, Rf = 0.20, TLC eluent = 5% methanol in dichloromethane). 1H NMR (400 MHz, CDCl3) δ 8.23 (s, 1H), 7.21 (s, 1H), 6.10 (s, 2H), 5.02 (dd, J = 1.7, 7.1 Hz, 1H), 4.94 (dt, J = 1.2, 6.8 Hz, 1H), 3.30 (s, 1H), 2.31 (ddd, J = 1.5, 5.3, 10.0 Hz, 1H), 1.67 (t, J = 5.7 Hz, 1H), 1.57 (s, 3H), 1.48 (ddd, J = 1.8, 6.0, 9.9 Hz, 1H), 1.25 (s, 4H). HRMS m/z [M+H]+ for C16H17IN4O4 calculated 457.0373, found 457.0381.</p><!><p>1H NMR (400 MHz, CD3OD) δ 8.21 (s, 1H), 7.35 (s, 1H), 4.74 (dd, J = 2.1, 6.3 Hz, 1H), 4.19 (s, 1H), 3.92 – 3.86 (m, 1H), 2.91 – 2.77 (m, 6H), 2.04 (t, J = 5.4 Hz, 1H), 1.88 (s, 4H), 1.28 (td, J = 3.6, 6.3, 7.2 Hz, 2H), 1.16 (t, J = 7.3 Hz, 9H). HRMS m/z [M+H]+ for C25H26I2N10O5 calculated 801.0255, found 801.0250.</p><!><p>To a solution of compound 46 (20 mg, 0.0437 mmol) in anhydrous THF (0.5 mL) was added triethylamine (12 μL, 0.0875 mmol) and diphenylphosphoryl azide (DPPA, 15 μL, 0.065 mmol) at room temperature. After stirring overnight at room temperature, the solvent was evaporated under reduced pressure and the residue was dissolved in anhydrous toluene (1.0 mL). To this mixture was added benzyl alcohol (50 μL, 0.48 mmol) and heated to 120 °C for 5 h. The volatile compounds were evaporated under reduced pressure and the residue purified by silica-gel column chromatography to afford 48 as a light yellow solid (4.0 mg, 17%, Rf = 0.65, TLC eluent = 5% methanol in dichloromethane). 1H NMR (400 MHz, CDCl3) δ 8.22 (s, 1H), 7.56 (d, J = 8.8 Hz, 2H), 7.49 – 7.29 (m, 4H), 7.15 (s, 1H), 5.78 (s, 2H), 5.25 – 5.12 (m, 2H), 4.96 (dd, J = 1.9, 6.7 Hz, 1H), 4.59 (dd, J = 1.9, 6.6 Hz, 1H), 4.36 (d, J = 8.7 Hz, 1H), 1.97 (ddd, J = 1.9, 5.8, 10.3 Hz, 1H), 1.66 (t, J = 6.0 Hz, 1H), 1.55 (s, 3H), 1.41 (ddd, J = 1.9, 6.3, 10.3 Hz, 1H), 1.22 (s, 3H). HRMS m/z [M+H]+ for C23H24IN5O4 calculated 562.0951, found 562.0955.</p><!><p>To a solution of compound 48 (3.0 mg, 5.34 μmol) in anhydrous dichloromethane (0.1 mL) was added 33% HBr in acetic acid (5 μL, 27.5 μmol) at 0 °C and stirred at room temperature for 0.5 h. The volatiles were evaporated under vacuum and the residual acid was chased by evaporating repeatedly with dichloromethane (HRMS indicated 2′,3′-isopropylidene deprotected compound). The above procedure was repeated and stirred for 1.5 h [Note: a straight 2 h reaction degraded the starting material]. The volatiles were evaporated under vacuum and the residual acid was removed by evaporating repeatedly with dichloromethane. The product mixture was dissolved in methanol and subjected to RP-HPLC (C18) purification to afford 49 and 50 as a white solid. Compound 49 acetate salt (0.35 mg, 17%; RP-HPLC (C18) Rt = 29.4 min, 10 mM triethylammonium acetate in water/acetonitrile 90/10 → 65/35 in 40 min at 5 mL/min). 1H NMR (400 MHz, CD3OD) δ 8.13 (s, 1H), 7.33 (s, 1H), 4.81 (dd, J = 2.2, 6.4 Hz, 1H), 3.90 (dd, J = 1.9, 6.4 Hz, 1H), 1.95 (t, J = 5.5 Hz, 1H), 1.88 – 1.81 (m, 1H), 1.35 – 1.25 (m, 2H). HRMS m/z [M+H]+ for C12H14IN5O2 calculated 388.0270, found 388.0268. (1R,2S,3R,4S,5S)-4-amino-1-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)bicyclo[3.1.0]hexane-2,3-diol (50): RP-HPLC (C18) Rt = 15.8 min, 10 mM triethylammonium acetate in water/acetonitrile 90/10 → 65/35 in 40 min at 5 mL/min). 1H NMR (400 MHz, CD3OD) δ 8.10 (s, 1H), 7.13 (d, J = 3.6 Hz, 1H), 6.51 (d, J = 3.6 Hz, 1H), 4.86 – 4.83 (m, 1H), 3.96 – 3.88 (m, 1H), 1.95 (dd, J = 5.0, 5.8 Hz, 1H), 1.83 (ddd, J = 1.9, 5.0, 9.5 Hz, 1H), 1.30 (ddd, J = 2.0, 5.7, 9.3 Hz, 1H). HRMS m/z [M+H]+ for C12H15N5O2 calculated 262.1299, found 262.1303.</p><!><p>Compound 51 (46 mg, 0.105 mmol) was dried by evaporating with anhydrous toluene (2×1 mL). To the dried compound was added anhydrous THF (1 mL), triphenylphosphine (83 mg, 0.315 mmol) and 6-chloro-7-iodo-7-deazapurine (88 mg, 0.315 mmol). The mixture was cooled to 0 °C and added diisopropylazodicarboxylate (62 μL, 0.315 mmol) dropwise. After 30 minutes, the reaction mixture was brought to room temperature and stirred overnight (18h). The volatiles were evaporated under reduced pressure and the residue purified by silica-gel chromatography to afford 52 as light yellow foam (65 mg, 88%, Rf = 0.55, TLC eluent = 20% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.61 (s, 1H), 7.74 (s, 1H), 7.71 – 7.63 (m, 4H), 7.47 – 7.34 (m, 6H), 5.35 (s, 1H), 5.31 (dd, J = 1.4, 7.3 Hz, 1H), 4.51 – 4.45 (m, 1H), 4.29 (dd, J = 0.7, 11.0 Hz, 1H), 3.42 (d, J = 11.0 Hz, 1H), 1.60 (ddd, J = 1.5, 4.4, 9.3 Hz, 1H), 1.53 (s, 3H), 1.23 (s, 3H), 1.12 – 1.15 (m, 1H), 1.16 (s, 9H), 0.92 – 0.84 (m, 1H). HRMS m/z [M+H]+ for C32H35ClIN3O3Si calculated 700.1259, found 700.1266.</p><!><p>Following the procedure described for the synthesis of 31a, compound 52 (125 mg, 0.178 mmol) gave 53 as a white foam (85 mg, 63%, Rf = 0.3, TLC eluent = 10% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.47 (s, 1H), 8.19 (s, 1H), 7.79 – 7.64 (m, 6H), 7.53 (s, 1H), 7.48 – 7.34 (m, 8H), 7.20 – 7.13 (m, 1H), 5.36 (s, 1H), 5.33 (dd, J = 1.4, 7.2 Hz, 1H), 4.49 (dd, J = 1.5, 7.2 Hz, 1H), 4.32 (d, J = 11.2 Hz, 1H), 3.36 (d, J = 11.1 Hz, 1H), 1.62 (ddd, J = 1.5, 4.4, 9.3 Hz, 1H), 1.52 (s, 3H), 1.24 (s, 3H), 1.17 (s, 8H), 1.16 – 1.13 (m, 1H), 0.83 (ddd, J = 1.5, 5.6, 9.3 Hz, 1H). HRMS m/z [M+H]+ for C38H41IN4O3Si calculated 757.2071, found 757.2072.</p><!><p>Following the procedure described for the synthesis of 33a, compound 53 (85 mg, 0.112 mmol) gave 54 as a white foam (65 mg, 82%, Rf = 0.25, TLC eluent = 10% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.53 (s, 1H), 7.66 – 7.56 (m, 4H), 7.50 (d, J = 8.0 Hz, 3H), 7.45 – 7.34 (m, 7H), 7.34 – 7.24 (m, 6H), 7.07 – 7.00 (m, 1H), 5.45 (s, 1H), 5.36 (dd, J = 1.4, 7.2 Hz, 1H), 4.62 (dd, J = 1.5, 7.3 Hz, 1H), 4.29 (d, J = 11.0 Hz, 1H), 3.41 (d, J = 11.0 Hz, 1H), 1.76 (ddd, J = 1.5, 4.4, 9.3 Hz, 1H), 1.55 (s, 3H), 1.27 (s, 3H), 1.18 (dd, J = 4.4, 5.6 Hz, 1H), 0.94 (s, 9H), 0.92 – 0.83 (m, 1H). HRMS m/z [M+H]+ for C44H46N4O3Si calculated 707.3417, found 707.3414.</p><!><p>Following the procedure described for the synthesis of 28, compound 54 (15 mg, 0.021 mmol) afforded 55 as a white solid which was further purified by RP-HPLC (7 mg, 77%, Rf = 0.15, TLC eluent = 5% methanol in dichloromethane; RP-HPLC (C18) Rt = 24.9 min, water/acetonitrile 50/50 → 10/90 in 40 min @ 5 mL/min). 1H NMR (400 MHz, 9:1 CD3OD-CDCl3) δ 8.34 (s, 1H), 7.75 (d, J = 1.8 Hz, 1H), 7.63 – 7.40 (m, 7H), 7.28 (t, J = 7.7 Hz, 2H), 7.03 (td, J = 1.1, 7.4 Hz, 1H), 5.11 (s, 1H), 4.80 (dd, J = 1.5, 6.8 Hz, 1H), 4.28 (d, J = 11.7 Hz, 1H), 3.87 (dd, J = 1.3, 6.8 Hz, 1H), 3.28 (d, J = 6.9 Hz, 1H), 1.63 (dd, J = 3.8, 8.9 Hz, 1H), 1.54 (t, J = 4.6 Hz, 1H), 0.77 – 0.69 (m, 1H). 13C NMR (101 MHz, 9:1 CD3OD-CDCl3) δ 155.20, 151.61, 150.10, 139.46, 135.42, 129.94, 129.93, 129.63, 128.42, 124.27, 122.91, 121.24, 116.99, 103.22, 77.84, 72.04, 64.34, 63.18, 37.74, 24.46, 11.96. HRMS m/z [M+H]+ for C25H24N4O3 calculated 429.1927, found 429.1924.</p><!><p>Following the procedure described for the synthesis of 29, compound 52 (20 mg, 0.028 mmol) gave 56 as a white foam (16 mg, 82%, Rf = 0.45, TLC eluent = 50% ethyl acetate in hexanes). 1H NMR (400 MHz, CDCl3) δ 8.25 (s, 1H), 7.76 – 7.60 (m, 4H), 7.49 (s, 1H), 7.47 – 7.33 (m, 6H), 6.20 (s, 2H), 5.37 – 5.26 (m, 2H), 4.53 – 4.40 (m, 1H), 4.30 (d, J = 11.0 Hz, 1H), 3.36 (d, J = 11.0 Hz, 1H), 1.59 (ddd, J = 1.5, 4.4, 9.3 Hz, 1H), 1.51 (s, 3H), 1.25 – 1.21 (m, 3H), 1.16 (s, 9H), 1.13 (dd, J = 4.5, 5.7 Hz, 1H), 0.82 (ddd, J = 1.5, 5.6, 9.3 Hz, 1H). HRMS m/z [M+H]+ for C32H37IN4O3Si calculated 681.1758, found 681.1769.</p><!><p>Following the procedure described for the synthesis of 28, compound 56 (16 mg, 0.019 mmol) afforded 57 as a white solid (7.5 mg, 79%, Rf = 0.25, TLC eluent = 10% methanol in dichloromethane). 1H NMR (400 MHz, CD3OD) δ 8.11 (s, 1H), 7.79 (s, 1H), 4.99 (s, 1H), 4.72 (dd, J = 1.6, 6.7 Hz, 1H), 4.26 (dd, J = 1.0, 11.7 Hz, 1H), 3.74 (dt, J = 1.2, 6.7 Hz, 1H), 3.33 (d, J = 15.5 Hz, 1H), 3.27 (d, J = 11.7 Hz, 1H), 1.57 – 1.43 (m, 2H), 0.70 (ddd, J = 1.8, 4.5, 8.0 Hz, 1H). 13C NMR (101 MHz, CD3OD) δ 158.81, 152.52, 150.32, 129.15, 105.15, 78.26, 72.29, 64.43, 63.50, 50.37, 37.97, 24.66, 12.12. HRMS m/z [M+H]+ for C13H15IN4O3 calculated 403.0267, found 403.0271.</p><!><p>The nucleoside derivatives were tested for inhibitory activity at hAdK using a commercial kit for the measurement of hAdK activity (ADK Phosphorylation Assay Kit, Ref. #K0507-02, NovoCib, Lyon, France). For use in the assay compounds 28, 30, 32, 43, 45 and 49 were dissolved in 60% DMSO in purified water, 34 was prepared in 80% DMSO solution, and 38a was in 88% DMSO solution, while 38b, 38c, 55, and 57 were prepared in 100% DMSO. Reactions were performed at 37°C in a total volume of 200 μL containing 100 mM Tris/HCl, 250 mM KCl, 10 mM MgCl2, 2.5 mM NAD, 2.75 mM ATP, 20 mU/mL IMPDH, 2.2 mU hAdK. All assays were run in triplicate and then replicated on a different plate. hAdK activity was assayed by measuring specific absorption at 340 nm at 5 min time intervals using a Spectromax Plate Reader (Molecular Devices, CA, USA). All reactions were started by the addition of 2.5 mM inosine (t0) and maintained for a total of 4 h. Baseline absorption prior to the addition of inosine was subtracted from all measurements. Percent inhibition of hAdK activity was calculated based on the slope during the linear phase of the progression of the enzymatic reaction (quantified between 0 and 40 min after inosine addition) and normalized to the slope of the enzymatic reaction in the presence of the vehicle DMSO (1% v/v final concentration of reaction mix).</p><!><p>Two-way ANOVA was used to determine significances between compound and concentration with percent residual hAdK activity based on slope as the primary dependent measure. Slopes were calculated for the first 40 min of activity for each compound and concentration combination. Post hoc analyses were used to determine specific between group differences relative to 2 using Bonferroni multiple corrections test.</p><!><p>Ligand geometry optimization and molecular docking simulations were carried out using a 8 Intel® Xeon® X5482 CPU workstation. Membrane MD simulations were run on four NVIDIA® Tesla® K20X by exploiting the computational resources of the NIH HPC Biowulf cluster (http://biowulf.nih.gov).</p><!><p>The compounds were built using Maestro56 and subjected to gas phase geometry optimization with the Jaguar 8.9 quantum chemistry package57 using density functional theory (DFT) with the B3LYP hybrid functional and the 6-31G** (34 and 55) or LACVP** (1c, 1a, 30, and 57) basis set. Frequency calculations were performed to ensure the structures represented minima on the potential energy surfaces.</p><!><p>The structure of hAdK in complex with 1c was retrieved from the RCSB PDB database58 (http://www.rcsb.org, PDB ID: 2I6A) and prepared as follows: after manual removal of co-crystallized ligand and water molecules, ionization states of protein sidechains and hydrogen positions were assigned with the Protein Preparazion Wizard tool.59</p><!><p>The ligands were docked by means of the IFD procedure based on Glide search algorithm60 using the Standard Protocol and OPLS3 force field.61 The centroid of the co-crystallized 5I5 ligand residue was selected as center of the Glide grid (inner box side = 10 Å; outer box side = auto). Ligands were initially docked rigidly into the receptor by applying a scaling factor of 0.5 to both ligand and protein van der Waals radii. Up to 20 poses per ligand were collected and the sidechains of residues within 5 Å of the ligand were refined with Prime.62 Ligands were re-docked into the newly generated receptor conformations with Glide60 by generating up to 10 poses using the SP scoring function and reverting the vdW radii scaling factors to their default values.</p><!><p>MD simulations were carried out with the ACEMD program63 using periodic boundaries conditions and the AMBER14SB64/General Amber Force Filed (GAFF)65 force fields for the protein and ligand atoms, respectively. To derive force field parameters, ligands were subjected to energy minimization with Gaussian 0966 at the HF/6-31G* level of theory. After geometry optimization, ligand parameters and RESP partial charges were derived with antechamber and parmchk tools as implemented in ambertools2014.64 Protein-ligand complexes were solvated by a cubic water box with cell borders placed at least 12 Å away from any protein atom using TIP3P as water model.67 The systems were neutralized with Na+/Cl− counter-ions to a final salt concentration of 0.150 M. After 2000 steps of energy minimization (conjugate-gradient method), the systems were equilibrated with 50000 steps (100 ps) of NVE followed by 1 ns of NPT simulations by applying harmonic positional constraints on protein and ligand atoms, that were gradually reduced (scaling factor = 0.1). During the equilibration, the temperature was maintained at 310 K using a Langevin thermostat68 with a low damping constant of 1 ps−1, and the pressure was maintained at 1 atm using a Berendensen barostat.69 Bond lengths involving hydrogen atoms were constrained using the M-SHAKE70 algorithm with an integration timestep of 2 fs. The equilibrated systems were then subjected to 30 ns of unrestrained MD simulations in a NVT ensemble. Long-range Coulomb interactions were handled using the particle mesh Ewald summation method (PME)71 with mesh spacing set to 1.0 Å. A non-bonded cutoff distance of 9 Å with a switching distance of 7.5 Å was used. Each simulation was run in triplicate.</p><!><p>Selection of representative trajectories was based upon the total ligand-protein interaction energy (IEtot). In particular, for each ligand-protein system, the IEtot expressed as the sum of van der Waals (IEvdW) and electrostatic (IEele) contribution was computed at frames extracted every 50 ps with the mdenergy function implemented in VMD72 exploiting NAMD 2.10.73 From the IEtot values so obtained, we derived a modified version of the Dynamic Scoring Function74 (herein defined as wDSFtot) by computing the cumulative sum of ligand-protein IEtot and dividing the value for the ligand RMSD with respect to the starting conformation as follows: 
wDSFtot=∑i=1nIEtotRMSD</p><p>wDSFtot slope values were derived as previously reported74 and for each ligand-protein system the replica that returned the highest absolute slope value (Table S1) was selected. IE vs simulation time graphs were generated with Gnuplot.75</p><p>Sugar pseudorotation phase angle76 (P) during MD simulations was computed with a in house tcl script with the endocyclic torsions υ0-υ4 angles defined as reported in Figure S6 by using the following equation: 
P=tan-1(υ4+υ1)-(υ3+υ0)2υ2(sin36°+sin72°)</p><p>Ligand root mean square deviation and fluctuation (RMSD and RMSF, respectively) and protein alpha carbon atoms RMSD with respect to the starting docking pose were computed with the RMSD trajectory tool (RSMDTT) implemented in VMD. MD average protein structures were derived with the g_covar function implemented in GROMACS77,78 and rigid body rotation angles were computed through the DYNDOM web server.79</p>