Low nanogram detection of nucleotides using fast atom bombardment-mass spectrometry

The effect of trimethylsilyl (TMS) derivatization on detection limits of mononucleotides in fast atom bombardment-mass spectrometry (FAB-MS) was examined. FAB-MS methods were developed to optimize sensitivity using adenosine 5'-monophosphate as a model compound and then applied to reference standards of two clinically important nucleotides: tricyclic nucleoside-5'-monophosphate (TCNMP) and 5-fluoro-2'-deoxyuridine-5'-monophosphate (FdUMP). The detection limit for the TMS derivative of TCNMP was 2.5-5 ng/microliters and less than 2.5 ng/microliters for FdUMP as its TMS derivative. This is greater than two orders of magnitude more sensitive than the FAB-MS analysis of the corresponding free compounds. These low detection limits for the TMS derivatives were obtained using a narrow scan range, signal averaging, detection in the negative ion mode, and 3-nitrobenzyl alcohol as the matrix. Hydrolysis of one or more of the labile TMS groups did occur, with the extent of hydrolysis being greatest in the more protic matrices.     

Synthesis and biological activation of an ethylene glycol-linked amino acid conjugate of cyclic cidofovir

Cidofovir (HPMPC) is a broad-spectrum anti-viral agent whose potential, particularly in biodefense scenarios, is limited by its low oral bioavailability. Two prodrugs (3 and 4) created by conjugating ethylene glycol-linked amino acids (L-Val, L-Phe) with the cyclic form of cidofovir (cHPMPC) via a P-O ester bond were synthesized and their pH-dependent stability (3 and 4), potential for in vivo reconversion to drug (3), and oral bioavailability (3) were evaluated. The prodrugs were stable in buffer between pH 3 and 5, but underwent rapid hydrolysis in liver (t(1/2) = 3.7 min), intestinal (t(1/2) = 12.5 min), and Caco-2 cell homogenates (t(1/2) = 20.2 min). In vivo (rat), prodrug 3 was >90% reconverted to cHPMPC. The prodrug was 4x more active than ganciclovir (IC50 value, 0.68 microM vs 3.0 microM) in a HCMV plaque reduction assay. However, its oral bioavailability in a rat model was similar to the parent drug. The contrast between the promising activation properties and unenhanced transport of the prodrug is briefly discussed.     

Acyclic sugar analogs of triciribine: lack of antiviral and antiproliferative activity correlate with low intracellular phosphorylation

Triciribine and triciribine monophosphate have antiviral and antiproliferative activity at low or submicromolar concentrations. In an effort to improve and better understand this activity, we have synthesized a series of acyclic analogs and evaluated them for activity against select viruses and cancer cell lines. We conclude that the rigid ribosyl ring system of triciribine must be intact in order to be phosphorylated and to obtain significant antiviral and antiproliferative activity.     

Kinetic analysis of the influence of inverse effectors (inhibitors and activators) on enzymatic (transport) activity of proteins

The method is proposed for calculation of the most important parameters of the two-stage enzymatic or transport process--modification factors alpha and beta (which characterize the effector action mechanism) as well as the inhibition constant K(i) or activation constant K(a) (characterize the effector affinity for protein). The method was derived as based on the analysis of kinetic regularities of the action of reversible effectors (inhibitors and activators) on the catalytic (transport) activity of proteins. The method is based on the titration of enzymatic (transport) protein by the substrate with the absence and with presence of the effector taken in one of concentrations as well as determination (under the fixed substrate concentration) of the inhibition coefficient i(0.5) (in case of the inhibitor action) or the activation coefficient a(0.5) (in case of the activator action). Practical use of the method has been demonstrated on the example of reversible inhibition to eosine Y (2', 4', 5', 7' - tetrabromofluorescein) ofthe reaction of enzymatic hydrolysis of ATP catalyzed by highly purified transport Ca2+, Mg(2+)-ATPase isolated from the smooth-muscle sarcolemma. In this case the inhibitory effect is characterized by the following parameters: alpha = 6-8 > 1; beta = 0.50-0.53 < 1; inhibition constant K(i) = 10(-9) - 10(-8) M. Consequently, judging from the values of alpha and beta, the eosine Y effect on the analyzed Ca2+, Mg(2+)-dependent ATP-hydrolase enzymatic reaction is based on the mechanism of the mixed inhibition (one can observe the inhibition of the both stages of enzymatic transformation--the substrate binding with the enzyme and decomposition of "Michaelis complex" in the direction of formation of the reaction products). The inhibitor itself, in correspondence with K(ij) values is characterized by rather high affinity for Ca2+, Mg(2+)-ATPase. It is supposed that the proposed approach can be useful when identifying the type of the reversible effector action on the enzymatic (transport) activity of proteins, estimation of real affinity of the inhibitors and activators for the latter.     

Screening of benzenesulfonamide in combination with chemically diverse fragments against carbonic anhydrase by differential scanning fluorimetry

Abstract

The differential scanning fluorimetry (DSF) screening of 5.692 fragments in combination with benzenesulfonamide (BSA) against bovine carbonic anhydrase (bCA) delivered >100 hits that either caused, on their own, a significant thermal shift (ΔT_m , °C) in the protein melting temperature or significantly influenced the thermal shift observed for BSA alone. Three hits based on 1,2,3-triazole moiety represent the periphery of the recently reported potent inhibitors of hCA II, IX and XII which were efficacious in vivo. Such a re-discovery of suitable BSA periphery essentially validates the new fragment-based approach to the discovery of future CAIs. Structures of other validated fragment hits are reported.     

Synthesis, transport and antiviral activity of Ala-Ser and Val-Ser prodrugs of cidofovir

We report the synthesis and biological evaluation of Ala-(Val-)l-Ser-CO₂R prodrugs of 1, where a dipeptide promoiety is conjugated to the P(OH)₂ group of cidofovir (1) via esterification by the Ser side chain hydroxyl group and an ethyl group (4 and 5) or alone (6 and 7). In a murine model, oral administration of 4 or 5 did not significantly increase total cidofovir species in the plasma compared to 1 or 2, but 7 resulted in a 15-fold increase in a rat model and had an in vitro EC₅₀ value against human cytomegalovirus comparable to 1. Neither 6 nor 7 exhibited toxicity up to 100 μM in KB or HFF cells.     

Further validation of strecker-type α-aminonitriles as a new class of potent human carbonic anhydrase II inhibitors: hit expansion within the public domain using differential scanning fluorimetry leads to chemotype refinement

Abstract

Testing of an expanded, 800-compound set of analogues of the earlier described Strecker-type α-aminonitriles (selected from publicly available Enamine Ltd. Screening Collection) in thermal shift assay against bovine carbonic anhydrase (bCA) led to further validation of this new class of inhibitors and identification a new, refined chemotype represented by inhibitors with 10-improved potency.      

Egg capsules and larval development of Nassarius burchardi (Philippi, 1849) and Nassarius jonasii Dunker, 1846 and comparisons with other Nassariidae (Caenogastropoda)

Adult Nassarius burchardi and N. jonasii were maintained in a laboratory, allowed to spawn and their early life stages described. N. burchardi veligers hatched from bulliform, oval capsules and N. jonasii veligers hatched from circular capsules with axial ridges. The capsules are compared with those described for other Nassariidae. All eggs developed within the capsules and hatching occurred within six to eight days in the laboratory. The planktotrophic veligers developed in four to five weeks before settling and metamorphosing. The veligers of both species were of comparable size and morphology and spent similar times developing as other Nassarius species from temperate waters. The two species differ in protoconch microsculpture.     

Synthesis and antiviral activity of 2-substituted analogs of triciribine

Triciribine (TCN) and triciribine monophosphate (TCN-P) have antiviral and antineoplastic activity at low or submicromolar concentrations. In an effort to improve and better understand this activity, we have conducted a structure-activity relationship study to explore the effect of substitutions at the 2-position of triciribine. 2-Methyl- (2-Me-TCN), 2-ethyl- (2-Et-TCN), 2-phenyl- (2-Ph-TCN), 2-chloro- (2-Cl-TCN), and 2-aminotriciribine (2-NH2-TCN) were designed and synthesized to determine the effects of substitutions at the 2-position which change the steric, electronic, and hydrophobic properties of TCN, while maintaining the integrity of the tricyclic ring system. These compounds were evaluated for activity against human immunodeficiency virus (HIV-1), herpes simplex virus type 1 (HSV-1), and human cytomegalovirus (HCMV) and were found to be either less active than TCN and TCN-P or inactive at the highest concentrations tested, 100 microM. We conclude that substitutions at the 2-position of triciribine adversely affect the antiviral activity most likely because these analogs are not phosphorylated to active metabolites.     

Straightforward hit identification approach in fragment-based discovery of bromodomain-containing protein 4 (BRD4) inhibitors

A combination approach of a fragment screening and “SAR by catalog” was used for the discovery of bromodomain-containing protein 4 (BRD4) inhibitors. Initial screening of 3695-fragment library against bromodomain 1 of BRD4 using thermal shift assay (TSA), followed by initial hit validation, resulted in 73 fragment hits, which were used to construct a follow-up library selected from available screening collection. Additionally, analogs of inactive fragments, as well as a set of randomly selected compounds were also prepared (3?×?3200 compounds in total). Screening of the resulting sets using TSA, followed by re-testing at several concentrations, counter-screen, and TR-FRET assay resulted in 18 confirmed hits. Compounds derived from the initial fragment set showed better hit rate as compared to the other two sets. Finally, building dose-response curves revealed three compounds with IC₅₀?=?1.9–7.4?μM. For these compounds, binding sites and conformations in the BRD4 (4UYD) have been determined by docking.