Marc T. Abrams

Biodistribution of small interfering RNA at the organ and cellular levels after lipid nanoparticle-mediated delivery.

Chemically stabilized small interfering RNA (siRNA) can be delivered systemically by intravenous injection of lipid nanoparticles (LNPs) in rodents and primates. The biodistribution and kinetics of LNP–siRNA delivery in mice at organ and cellular resolution have been studied using immunofluorescence (IF) staining and quantitative polymerase chain reaction (qPCR). At 0.5 and 2 hr post tail vein injection of Cy5-labeled siRNA encapsulated in LNP, the organ rank-order of siRNA levels is liver > spleen > kidney, with only negligible accumulation in duodenum, lung, heart, and brain. Similar conclusions were drawn by using qPCR to measure tissue siRNA levels as a secondary end point. siRNA levels in these tissues decreased by more than 10-fold after 24 hr. Within the liver, LNPs delivered siRNA to hepatocytes, Kupffer cells, and sinusoids in a time-dependent manner, as revealed by IF staining and signal quantitation methods established using OPERA/Columbus software. siRNA first accumulated in liver sinusoids and trafficked to hepatocytes by 2 hr post dose, corresponding to the onset of target mRNA silencing. Fluorescence in situ hybridization methods were used to detect both strands of siRNA in fixed tissues. Collectively, the authors have implemented a platform to evaluate biodistribution of siRNA across cell types and across tissues in vivo, with the objective of elucidating the pharmacokinetic and pharmacodynamic relationship to guide optimization of delivery vehicles.

Quantitative evaluation of siRNA delivery in vivo

Effective small interfering RNA (siRNA)-mediated therapeutics require the siRNA to be delivered into the cellular RNA-induced silencing complex (RISC). Quantitative information of this essential delivery step is currently inferred from the efficacy of gene silencing and siRNA uptake in the tissue. Here we report an approach to directly quantify siRNA in the RISC in rodents and monkey. This is achieved by specific immunoprecipitation of the RISC from tissue lysates and quantification of small RNAs in the immunoprecipitates by stem-loop PCR. The method, expected to be independent of delivery vehicle and target, is label-free, and the throughput is acceptable for preclinical animal studies. We characterized a lipid-formulated siRNA by integrating these approaches and obtained a quantitative perspective on siRNA tissue accumulation, RISC loading, and gene silencing. The described methodologies have utility for the study of silencing mechanism, the development of siRNA therapeutics, and clinical trial design.

Examination of real-time polymerase chain reaction methods for the detection and quantification of modified siRNA.

With the ongoing efforts to develop siRNA-based therapeutics, there is a need for high-throughput detection and quantification of siRNA. Here we report the application of four reverse-transcriptase RT-PCR-based assays for the detection of 2-deoxy-2-fluoro and 2-O-methyl-modified therapeutic siRNA in mouse plasma and tissue. These assays take advantage of the dynamic range, sensitivity, specificity, and high-throughput potential found in PCR assays. Three of these assays require design and optimization of primers and/or probes specific to the siRNA while the fourth utilizes a universal TaqMan probe that is independent of the siRNA sequence, thereby reducing method development time and cost. For the universal assay the range of detection in mouse plasma was 500 to 5e(-5) pg/microl for four of five model Luciferase sequences tested. We found that the universal RT-PCR assay had comparable or better sensitivity and specificity than the other three assays. The universal design provides a rapid, sensitive, and specific assay with minimal method development time that will be well suited for high-throughput analysis of various siRNA sequences.

Anions Modulate the Potency of Geranylgeranyl-Protein Transferase I Inhibitors

We have identified and characterized potent and specific inhibitors of geranylgeranyl-protein transferase type I (GGPTase I), as well as dual inhibitors of GGPTase I and farnesyl-protein transferase. Many of these inhibitors require the presence of phosphate anions for maximum activity against GGPTase Iin vitro. Inhibitors with a strong anion dependence were competitive with geranylgeranyl pyrophosphate (GGPP), rather than with the peptide substrate, which had served as the original template for inhibitor design. One of the most effective anions was ATP, which at low millimolar concentrations increased the potency of GGPTase I inhibitors up to several hundred-fold. In the case of clinical candidate l-778,123, this increase in potency was shown to result from two major interactions: competitive binding of inhibitor and GGPP, and competitive binding of ATP and GGPP. At 5 mm, ATP caused an increase in the apparent K d for the GGPP-GGPTase I interaction from 20 pm to 4 nm, resulting in correspondingly tighter inhibitor binding. A subset of very potent GGPP-competitive inhibitors displayed slow tight binding to GGPTase I with apparent on and off rates on the order of 106 m − 1s− 1 and 10− 3s− 1, respectively. Slow binding and the anion requirement suggest that these inhibitors may act as transition state analogs. After accounting for anion requirement, slow binding, and mechanism of competition, the structure-activity relationship determined in vitro correlated well with the inhibition of processing of GGPTase I substrate Rap1a in vivo.

Aryloxy Substituted N-Arylpiperazinones as Dual Inhibitors of Farnesyltransferase and Geranylgeranyltransferase-I

A series of aryloxy substituted piperazinones with dual farnesyltransferase/geranylgeranyltransferase-I inhibitory activity was prepared. These compounds were found to have potent inhibitory activity in vitro and are promising agents for the inhibition of Ki-Ras signaling.

Expression of Asialoglycoprotein Receptor 1 in Human Hepatocellular Carcinoma

Human hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. Currently, surgical resection is the only effective treatment for HCC if the tumor is resectable. Small molecule, biologics and siRNA anti-cancer drugs have been explored for the treatment of HCC. Selective targeting to tumor tissue rather than normal liver in HCC patients is still a challenge. Galactosamine-mediated targeting delivery of anti-cancer drugs in the liver has been tested because its receptor, asialoglycoprotein receptor 1 (ASGPR1), is expressed in the liver and not in other human tissues. We examined ASGPR1 expression levels by immunohistochemistry in HCC with different grades. Guidance for a targeting delivery strategy for anti-cancer drugs to HCC is suggested in this report.

Diaryl ether inhibitors of farnesyl-protein transferase.

Imidazolemethyl diaryl ethers are potent inhibitors of farnesyl-protein transferase. The SNAr displacement reaction used to prepare these diaryl ethers was amenable to rapid parallel synthesis of FPTase inhibitors. The use of a broad range of commercially available phenols quickly identified compounds which proved active in cells.

The synthesis and biological evaluation of a series of potent dual inhibitors of farnesyl and geranyl-Geranyl protein transferases.

We have prepared a series of potent, dual inhibitors of the prenyl transferases farnesyl protein transferase (FPTase) and geranyl-geranyl protein transferase I (GGPTase). The compounds were shown to possess potent activity against both enzymes in cell culture. Mechanistic analysis has shown that the compounds are CAAX competitive for FPTase inhibition but geranyl-geranyl pyrophosphate (GGPP) competitive for GGPTase inhibiton.

Evaluation of amino acid-based linkers in potent macrocyclic inhibitors of farnesyl-protein transferase

A series of amino acid-based linkers was used to investigate the effects of various substituents upon the potency, pharmacokinetic properties, and conformation of macrocyclic farnesyl-protein transferase inhibitors (FTIs). As a result of the studies described herein, highly potent FTIs with improved pharmacokinetic profiles have been identified.