Palladium-catalyzed C-N cross-coupling reactions toward the synthesis of drug-like molecules

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Chemistry; and, (S.B.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. ).The development of methodologies for C-N bond formation reactions is an important scientific challenge because of many academic and industrial applications. This work will focus particularly on palladium-catalyzed cross-couplings of amine-containing compounds with aryl halides. The scope of the BrettPhos precatalyst for the cross-coupling of ortho-substituted aryl iodides with amides is studied using substrates with a variety of functional groups. Due to potential metal-chelating issues with some of the substrates used in this study, a proposed ligand synthesis is discussed in which one of the methoxy groups of BrettPhos is replaced with a morpholine capable of occupying palladium's open coordination site during its catalytic cycle. A final C-N bond formation study focuses on the cross-coupling of aryl halides with amidine salts. For this cross-coupling, a methodology has been developed that can be applied to various electron-rich, electron-poor, and electron-neutral substrates. Furthermore, the products of this cross-coupling can be used for a subsequent electrocyclization through a reaction with aldehyde, demonstrating that a relatively simple two-pot methodology can be used to make relatively complex substrates with pharmaceutical applications. Both amides and amidines are common moieties in drug-like molecules because of the various biological activities of these functional groups. Potential medicinal applications of the developed cross-coupling of amidine salts with aryl halides methodology are described. Thus, methodologies for various palladium-catalyzed, C-N cross-couplings as well as a potential ligand synthesis to be used for palladium catalysis are herein discussed.by Camille Z. McAvoy.S.B

Conformational dynamics of a membrane protein chaperone enables spatially regulated substrate capture and release

Membrane protein biogenesis poses enormous challenges to cellular protein homeostasis and requires effective molecular chaperones. Compared with chaperones that promote soluble protein folding, membrane protein chaperones require tight spatiotemporal coordination of their substrate binding and release cycles. Here we define the chaperone cycle for cpSRP43, which protects the largest family of membrane proteins, the light harvesting chlorophyll a/b-binding proteins (LHCPs), during their delivery. Biochemical and NMR analyses demonstrate that cpSRP43 samples three distinct conformations. The stromal factor cpSRP54 drives cpSRP43 to the active state, allowing it to tightly bind substrate in the aqueous compartment. Bidentate interactions with the Alb3 translocase drive cpSRP43 to a partially inactive state, triggering selective release of LHCP’s transmembrane domains in a productive unloading complex at the membrane. Our work demonstrates how the intrinsic conformational dynamics of a chaperone enables spatially coordinated substrate capture and release, which may be general to other ATP-independent chaperone systems

A Disorder-to-Order Transition Activates an ATP-Independent Membrane Protein Chaperone

The 43 kDa subunit of the chloroplast signal recognition particle, cpSRP43, is an ATP-independent chaperone essential for the biogenesis of the light harvesting chlorophyll-binding proteins (LHCP), the most abundant membrane protein family on earth. cpSRP43 is activated by a stromal factor, cpSRP54, to more effectively capture and solubilize LHCPs. The molecular mechanism underlying this chaperone activation is unclear. Here, a combination of hydrogen–deuterium exchange, electron paramagnetic resonance, and NMR spectroscopy experiments reveal that a disorder-to-order transition of the ankyrin repeat motifs in the substrate binding domain of cpSRP43 drives its activation. An analogous coil-to-helix transition in the bridging helix, which connects the ankyrin repeat motifs to the cpSRP54 binding site in the second chromodomain, mediates long-range allosteric communication of cpSRP43 with its activating binding partner. Our results provide a molecular model to explain how the conformational dynamics of cpSRP43 enables regulation of its chaperone activity and suggest a general mechanism by which ATP-independent chaperones with cooperatively folding domains can be regulated

Palladium-Catalyzed N-Monoarylation of Amidines and a One-Pot Synthesis of Quinazoline Derivatives

A method for the Pd-catalyzed N-arylation of both aryl and alkyl amidines with a wide range of aryl bromides, chlorides, and triflates is described. The reactions proceed in short reaction times and with excellent selectivity for monoarylation. A one-pot synthesis of quinazoline derivatives, via addition of an aldehyde to the crude reaction mixture following Pd-catalyzed N-arylation, is also demonstrated.National Institutes of Health (U.S.) (Grant GM58160)National Institutes of Health (U.S.) (Postdoctoral Fellowship F32GM097771

Palladium-Catalyzed N-Monoarylation of Amidines and a One-Pot Synthesis of Quinazoline Derivatives

A method for the Pd-catalyzed N-arylation of both aryl and alkyl amidines with a wide range of aryl bromides, chlorides, and triflates is described. The reactions proceed in short reaction times and with excellent selectivity for monoarylation. A one-pot synthesis of quinazoline derivatives, via addition of an aldehyde to the crude reaction mixture following Pd-catalyzed N-arylation, is also demonstrated

Palladium-Catalyzed N-Monoarylation of Amidines and a One-Pot Synthesis of Quinazoline Derivatives

[Image: see text] A method for the Pd-catalyzed N-arylation of both aryl and alkyl amidines with a wide range of aryl bromides, chlorides, and triflates is described. The reactions proceed in short reaction times and with excellent selectivity for monoarylation. A one-pot synthesis of quinazoline derivatives, via addition of an aldehyde to the crude reaction mixture following Pd-catalyzed N-arylation, is also demonstrated