Damien Thompson

Randomized Trial of the Combination of Lomeguatrib and Temozolomide Compared With Temozolomide Alone in Chemotherapy Naive Patients With Metastatic Cutaneous Melanoma

PURPOSE To evaluate tumor response, pharmacodynamic effects, and safety of a combination of lomeguatrib (LM), an O6-methylguanine DNA-methyltransferase (MGMT) inactivator, and temozolomide (TMZ), TMZ alone, and LM/TMZ after disease progression on TMZ alone in patients with advanced melanoma. PATIENTS AND METHODS Patients with unresectable stage III or IV cutaneous melanoma who had no prior systemic chemotherapy were randomly assigned to receive either 40 to 80 mg LM and 125 mg/m2 TMZ or 200 mg/m2 TMZ on days 1 through 5 of each 28-day treatment cycle. Drugs were administered orally for up to six cycles of treatment. Patients on TMZ alone were offered LM/TMZ at progression, if fit enough to receive treatment. RESULTS One hundred four patients were enrolled, with 52 in each trial arm. Twenty-seven TMZ-treated patients received LM/TMZ after progression on TMZ. Unexpectedly, analysis of tumor biopsies showed rapid recovery of MGMT after LM/TMZ with 40 mg/d LM. Therefore, doses of LM were escalated to 60 then 80 mg/d. Tumor response rates were 13.5% with LM/TMZ and 17.3% with TMZ alone. No patient responded to LM/TMZ having progressed through TMZ. Median time to disease progression was 65.5 days for LM/TMZ and 68 days for TMZ. All treatments were well tolerated, although hematologic and gastrointestinal adverse events were common. A higher incidence of hematological adverse events was observed in the LM/TMZ combination arm. CONCLUSION The efficacy of LM and TMZ in the current dosing schedule is similar to that of TMZ alone. To maintain MGMT depletion in tumor dosing of LM needs to be continued beyond that of TMZ.

The importance of bleomycin in combination chemotherapy for good-prognosis germ cell carcinoma. Australasian Germ Cell Trial Group.

PURPOSE In an effort to maintain the excellent long-term results achieved with combination chemotherapy for good-prognosis germ cell carcinoma, but to reduce the toxicities encountered, a randomized trial was conducted comparing cisplatin and vinblastine with or without bleomycin. PATIENTS AND METHODS Two hundred eighteen assessable patients with a good prognosis were randomized to receive induction chemotherapy with cisplatin 100 mg/m2 intravenously (IV) day 1 and vinblastine 6 mg/m2 IV days 1 and 2 every 3 weeks (PV) with or without bleomycin 30 mg intramuscularly (IM) weekly (PVB) for a maximum of 12 weeks. Once maximum response was achieved, patients with a complete remission (CR) received two courses of consolidation chemotherapy, while those with residual abnormalities and normal tumor markers underwent surgical resection whenever possible. RESULTS Toxicities encountered in this study were clearly greater for those patients who received bleomycin, with significantly more leukopenia, thrombocytopenia, anemia, alopecia, and renal and pulmonary toxicities. The proportion of patients who achieved CR and had no evidence of disease (resection of all viable malignancy) was 89% for PV and 94% for PVB (P = .29). After a minimum of 4 years of follow-up, relapses have occurred in 7% of patients who received PV and 5% who received PVB. A total of five patients on each therapy arm were successfully treated with further salvage chemotherapy and surgery. Thus, deaths from progressive malignancy have occurred in 15% of patients on PV and 5% on PVB (P = .02), a rate that was partly offset by the higher proportion of toxic deaths with PVB (P = .06). CONCLUSION Despite the toxicities encountered with bleomycin in cisplatin-based combination chemotherapy for these patients, complete deletion of this drug compromises therapeutic efficacy.

Controlling the direction of rectification in a molecular diode

A challenge in molecular electronics is to control the strength of the molecule-electrode coupling to optimize device performance. Here we show that non-covalent contacts between the active molecular component (in this case, ferrocenyl of a ferrocenyl-alkanethiol self-assembled monolayer (SAM)) and the electrodes allow for robust coupling with minimal energy broadening of the molecular level, precisely what is required to maximize the rectification ratio of a molecular diode. In contrast, strong chemisorbed contacts through the ferrocenyl result in large energy broadening, leakage currents and poor device performance. By gradually shifting the ferrocenyl from the top to the bottom of the SAM, we map the shape of the electrostatic potential profile across the molecules and we are able to control the direction of rectification by tuning the ferrocenyl-electrode coupling parameters. Our demonstrated control of the molecule-electrode coupling is important for rational design of materials that rely on charge transport across organic-inorganic interfaces.

Gradient-driven motion of multivalent ligand molecules along a surface functionalized with multiple receptors

The kinetics of multivalent (multisite) interactions at interfaces is poorly understood, despite its fundamental importance for molecular or biomolecular motion and molecular recognition events at biological interfaces. Here, we use fluorescence microscopy to monitor the spreading of mono-, di- and trivalent ligand molecules on a receptor-functionalized surface, and perform multiscale computer simulations to understand the surface diffusion mechanisms. Analogous to chemotaxis, we found that the spreading is directional (along a developing gradient of vacant receptor sites) and is strongly dependent on ligand valency and concentration of a competing monovalent receptor in solution. We identify multiple surface diffusion mechanisms, which we call walking, hopping and flying. The study shows that the interfacial behaviour of multivalent systems is much more complex than that of monovalent ones.

Alchemical free energy simulations for biological complexes: powerful but temperamental …

Free energy simulations compare multiple ligand:receptor complexes by “alchemically” transforming one into another, yielding binding free energy differences. Since their introduction in the 1980s, many technical and theoretical obstacles were surmounted, and the method (“MDFE,” since molecular dynamics are often used) has matured into a powerful tool. We describe its current status, its effectiveness, and the challenges it faces. MDFE has provided chemical accuracy for many systems but remains expensive, with significant human overhead costs. The bottlenecks have shifted, partly due to increased computer power. To study diverse sets of ligands, force field availability and accuracy can be a major difficulty. Another difficulty is the frequent need to consider multiple states, related to sidechain protonation or buried waters, for example. Sophisticated, automated methods to sample these states are maturing, such as constant pH simulations. Meanwhile, combinations of MDFE and simpler approaches, like continuum dielectric models, can be very effective. As illustrations, we show how, with careful force field parameterization, MDFE accurately predicts binding specificities between complex tetracycline ligands and their targets. We describe substrate binding to the aspartyl‐tRNA synthetase enzyme, where many distinct electrostatic states play a role, and a histidine and a Mg2+ ion act as coupled switches that help enforce a strict preference for the aspartate substrate, relative to several analogs. Overall, MDFE has achieved a predictive status, where novel ligands can be studied and molecular recognition elucidated in depth. It should play an increasing role in the analysis of complex cellular processes and biomolecular engineering. Copyright

On the Remarkable Role of Surface Topography of the Bottom Electrodes in Blocking Leakage Currents in Molecular Diodes

It was proposed in 1974 that molecules could rectify, but molecular diodes with simultaneously high rectification ratios, yields of working junctions, and reproducibility are rare, despite a huge body of experimental work. Although every type of molecular junction contains a certain distribution of defects induced by the topography of the surface, the roles of these defects in the device performance are rarely studied. We show that control over the topography of the bottom electrode in self-assembled monolayer (SAM)-based junctions in terms of the number of grains, the width of the grain boundaries, and the roughness improves the yield of working junctions from 60% to near 100%, increases reproducibility by a factor of 3, and boosts the rectification ratio of a molecular diode (from nearly unity to ~1.0 × 10(2)) by minimizing the leakage currents. We found that commonly used metal surfaces fabricated by direct deposition methods are inferior to template-stripped surfaces, which are flat and contain only small areas of exposed grain boundaries, at which SAMs cannot pack well. Thus, for molecular diodes to perform well, it is crucial to minimize leakage currents by limiting the amount of exposed grain boundaries.

Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions.

Molecular recognition between the aminoacyl-tRNA synthetase enzymes and their cognate amino acid ligands is essential for the faithful translation of the genetic code. In aspartyl-tRNA synthetase (AspRS), the co-substrate ATP binds preferentially with three associated Mg2+ cations in an unusual, bent geometry. The Mg2+ cations play a structural role and are thought to also participate catalytically in the enzyme reaction. Co-binding of the ATP·\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{Mg}_{3}^{2+}\) \end{document} complex was shown recently to increase the Asp/Asn binding free energy difference, indicating that amino acid discrimination is substrate-assisted. Here, we used molecular dynamics free energy simulations and continuum electrostatic calculations to resolve two related questions. First, we showed that if one of the Mg2+ cations is removed, the Asp/Asn binding specificity is strongly reduced. Second, we computed the relative stabilities of the three-cation complex and the 2-cation complexes. We found that the 3-cation complex is overwhelmingly favored at ordinary magnesium concentrations, so that the protein is protected against the 2-cation state. In the homologous LysRS, the 3-cation complex was also strongly favored, but the third cation did not affect Lys binding. In tRNAbound AspRS, the single remaining Mg2+ cation strongly favored the Asp-adenylate substrate relative to Asn-adenylate. Thus, in addition to their structural and catalytic roles, the Mg2+ cations contribute to specificity in AspRS through long range electrostatic interactions with the Asp side chain in both the pre- and post-adenylation states.

Free-Energy Simulations and Experiments Reveal Long-Range Electrostatic Interactions and Substrate-Assisted Specificity in an Aminoacyl-tRNA Synthetase

Specific recognition of their cognate amino acid substrates by the aminoacyl‐tRNA synthetase enzymes is essential for the correct translation of the genetic code. For aspartyl‐tRNA synthetase (AspRS), electrostatic interactions are expected to play an important role, since its three substrates (aspartate, ATP, tRNA) are all electrically charged. We used molecular‐dynamics free‐energy simulations and experiments to compare the binding of the substrate Asp and its electrically neutral analogue Asn to AspRS. The preference for Asp is found to be very strong, with good agreement between simulations and experiment. The simulations reveal long‐range interactions that electrostatically couple the amino acid ligand, ATP, and its associated Mg2+ cations, a histidine side chain (His448) next to the amino acid ligand and a flexible loop that closes over the active site in response to amino acid binding. Closing this loop brings a negatively charged glutamate into the active site; this causes His448 to recruit a labile proton, which interacts favorably with Asp and accounts for most of the Asp/Asn discrimination. Cobinding of the second substrate, ATP, increases specificity for Asp further and makes the system robust towards removal of His448, which is mutated to a neutral amino acid in many organisms. Thus, AspRS specificity is assisted by a labile proton and a cosubstrate, and ATP acts as a mobile discriminator for specific Asp binding to AspRS. In asparaginyl‐tRNA synthetase, a close homologue of AspRS, a few binding‐pocket differences modify the charge balance so that asparagine binding predominates.

Gold nanoparticles stabilized by thioether dendrimers

Ligand-stabilized gold nanoparticles (Au NPs) are promising materials for nanotechnology with applications in electronics, catalysis, and sensors. These applications depend on the ability to synthesize stable and monodisperse NPs. Herein, the design and synthesis of two series of dendritic thioether ligands and their ability to stabilize Au NPs is presented. The dendrimers have 1,3,5-trisubstituted benzene branching units bridged by either meta-xylene or ethylene moieties. A comparison between the two ligands shows how both size control and the stability of the NPs are influenced by the nature of the ligand-NP wrapping interaction. The meta-xylene-bridged ligands provided NPs with a narrow size distribution centered around a diameter of 1.2 nm, whereas the NPs formed with ethylene-bridged dendrimers lack long-term stability with NP aggregation detected by UV/Vis spectroscopy and transmission electron microscopy. The bulkier tert-butyl-functionalized meta-xylene bridges form larger ligand shells that inhibit further growth of the NPs and thus provide a simple route to stable and monodisperse Au NPs that may find use as functional components in nanoelectronic devices.

Monofunctionalized Gold Nanoparticles Stabilized by a Single Dendrimer Form Dumbbell Structures upon Homocoupling

The assembly of dumbbell structures as organic-inorganic hybrid materials is presented. Gold nanoparticles (NPs) with a mean diameter of 1.3 nm were synthesized in very good yields using a stabilizing dendrimer based on benzylic thioether subunits. The extended dendritic ligand covers the NP surface and contains a peripheral protected acetylene, providing coated and monofunctionalized NPs. These NPs themselves can be considered as large molecules, and thus, applying a wet-chemical deprotection/oxidative acetylene coupling protocol exclusively provides dimers of NPs interlinked by a diethynyl bridge. The concept not only enables access to novel organic/inorganic hybrid architectures but also promises new approaches in labeling technology.