Background DNA aptamers represent a novel strategy in anti-cancer medicine. These compounds are short sequences of DNA that have protein binding effects via shape specific recognition of a target protein in an interaction which is analogous to antibody-antigen binding. AS1411, a DNA aptamer that targets nucleolin (a protein which is overexpressed in many tumor types), was evaluated in patients with metastatic, predominantly clear-cell, renal cell carcinoma (RCC) who had failed treatment with ≥1 previous tyrosine kinase inhibitor. We present the first manuscript reporting the use of this novel anti-cancer agent in humans. Methods In this phase II, single-arm study, AS1411 was administered at 40 mg/kg/day by continuous intravenous infusion on days 1–4 of a 28-day cycle, for two cycles. Primary endpoint was overall response rate; progression-free survival (PFS) and safety were secondary endpoints. Results 35 patients were enrolled and treated; 33 completed two treatment cycles. Median number of prior therapies was 2 (range 1–7). One patient (2.9%) had a response to treatment. The response was dramatic (84% reduction in the sum of longest diameters of selected target tumor lesions) and durable (the patient remains free of progression 2 years after completing therapy). No responses were seen in the other patients. Median PFS was 4 months. Only 34% of patients had an AS1411-related adverse event, all of which were mild or moderate. Conclusions AS1411 appears to have limited activity in unselected patients with metastatic RCC. However, rare, dramatic and durable responses can be observed and toxicity is low. Further studies with nucleolin targeted compounds may benefit from efforts to discover predictive biomarkers of response. Currently, promising pre-clinical studies are ongoing using AS1411 conjugated to traditional cytotoxic agents to selectively deliver these treatments to tumor cells. DNA aptamers represent a novel way to target cancer cells at a molecular level and continue to be developed with a view to improving treatment and imaging in cancer medicine.

Plane-wave density functional theory calculations have been carried out to explore possible pathways in methanol steam reforming (MSR) on Cu(111). We focus on reactions involving the adsorbed formaldehyde intermediate (CH(2)O) produced by methanol decomposition and the surface hydroxyl (OH) species generated by dissociative adsorption of H(2)O. Several possible pathways leading to the H(2) + CO(2) products have been identified. The two most likely pathways involve the formate (CHOO), rather than the carboxyl (COOH), intermediate, and they possess barriers lower than that of the rate-limiting step of MSR, namely the dehydrogenation of adsorbed methoxyl (CH(3)O) species.

Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensible role in cellular signaling, and their malfunctioning is implicated in many diseases. A better understanding of the catalytic mechanism will help design novel and effective mechanism-based inhibitors of these enzymes. In this work, ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg2+ ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. Implications of our results in this and other protein kinases are discussed.

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The effect of Zn on the CO adsorption and oxidation reaction is examined experimentally and theoretically on two PdZn catalysts with different compositions, namely the intermetallic 1:1 β-PdZn and α-PdZn as a solid solution of 9 at% Zn in Pd. These bimetallic catalysts, made using an aerosol derived method, are homogeneous in phase and composition so that the measured reactivity excludes support effects. Both specific reactivities for CO oxidation on these two PdZn catalysts were measured. It was found that the initial rates are high and different between these catalysts, presumably due to the weakening of the CO adsorption and easier binding of oxygen to Pd sites modified by Zn. However, the rates decrease with time and become comparable to that on Pd at the steady state. With the help of density functional theory, it was suggested that the transient kinetics are due to the oxidation of Zn during the catalysis, which yields pure Pd where the reaction takes place.