Kinetic and thermodynamic control of g-quadruplex folding

A matter of speed: When allowed to fold in a K(+) /poly(ethylene glycol) solution, the guanine?(G)-rich strand of vertebrate telomere DNA forms a parallel/antiparallel G-quadruplex, which is a (3+1) hybrid, within microseconds before slowly transforming into the parallel one within hours. Thus, the conformation that a G-quadruplex initially adopts under physiological conditions may not be the one it adopts at the equilibrium state.     

Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering “what”, “where”, “how many” and “whose” chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.

An overview of MS-based chemical mapping and profiling, indicating its contributions to the molecular understanding of diseases in precision medicine by answering "what", "where", "how many" and "whose” chemicals underlying clinical phenotypes.     

Hydration of mononucleotides

The sequential addition of water molecules to protonated and deprotonated forms of the four mononucleotides dAMP, dCMP, dGMP, and dTMP was studied experimentally by equilibrium measurements using an electrospray mass spectrometer equipped with a drift cell and theoretically by computational methods including molecular modeling and density functional theory calculations. Experiments were carried out in positive and negative ion mode, and calculations included the protonated and deprotonated forms of the four nucleotides. For deprotonated anionic nucleotides the experimental enthalpies of hydration (DeltaH degrees n) were found to be similar for all four systems and varied between -10.1 and -11.5 kcal mol-1 for the first water molecule (n = 1) and -8.3 and -9.6 kcal mol-1 for additional water molecules (n = 2-4). Theory indicated that the first water molecule binds to the charge-carrying phosphate group. Simulations of deprotonated mononucleotides with four water molecules yielded a large number of structures with similar energies. In some of the structures all four water molecules cluster around the phosphate group, and in other structures the four water molecules each hydrate a different functional group of the nucleotide. These include the phosphate group, the deoxyribose hydroxyl group, and various functional groups on the nucleobases. Experimental DeltaH degrees 1 values for the protonated cationic mononucleotides ranged from -10.5 to -13.5 kcal mol-1 with more negative values (< or =-12 kcal mol-1) for dCMP, dGMP, and dTMP and the least negative value for dAMP. For n = 2-4 DeltaH degrees n values varied from -6.9 to -9.7 kcal/mol and were similar in value to the deprotonated nucleotides except for dAMP. Theory on the protonated nucleotides indicated that the first water molecule binds to the charge-carrying group for dCMP, dGMP, and dTMP. For protonated dAMP, on the other hand, the charge-carrying N3 group is well self-solvated by the phosphate group and not readily available for a hydrogen bond with the water molecule. The insight gained on nucleotide stabilization by individual water molecules is used to discuss the competition between hydration of individual nucleotides and Watson-Crick base pairing.     

Study on the Silylation of Aromatic Hydrocarbons. The Trimethylsilylation of Naphthalene

Direct trimethylsilylation of naphthalene under certain condition has been found to afford substitution as well as addition products: 1-and 2-trimethylsilylnaphtalene (I, II), 1-trimethylsilyl-1,4-dihydronaphthalene (III), trans-1,2-bis(trimethylsilyl)-1,2-dihydronaphthalene (IV-a) and its isomer (IV-b), and 1,2,4-tris(trimethylsilyl)-1,2-dihydronaphthalene (V). The configuration has been determined by nmr spectroscopy, and the possible reaction path was proposed.     

Asymmetric synthesis of hydrobenzofuranones via desymmetrization of cyclohexadienones using the intramolecular Stetter reaction

Dearomatization of phenols followed by oxidation affords cyclohexadienyloxyacetaldehydes, which produce hydrobenzofuranones via asymmetric intramolecular Stetter reaction in good to excellent yield. Quaternary as well as up to three contiguous stereocenters may be formed in good to excellent enantioselectivities and high diastereoselectivities.     

Synthesis and characterization of chitosan-graft-polycaprolactone copolymers

The graft copolymers of chitosan with polycaprolactone (PCL) were prepared through a protection-graft-deprotection route using phthaloylchitosan as intermediate. PCL macromonomers terminated with isocyanate groups reacted with hydroxyl groups of phthaloyl-protected chitosan regioselectively, and then phthaloyl groups were deprotected to give the free amino groups. The graft reaction was carried out in homogeneous system and yielded copolymers with high grafting content due to solubilization. FTIR, NMR and XRD were detected to characterize the resultant chitosan-graft-PCL copolymers.     

Mesoscale organization of CuO nanoribbons: formation of "dandelions"

A two-tiered organizing scheme with multiple-length scales for construction of dandelion-like hollow CuO microspheres has been elucidated: (1) mesoscale formation of rhombic building units from smaller nanoribbons via oriented aggregation and (2) macroscopic organization of these units into the CuO microspheres. This self-assembly concept may also be applicable to other metal oxides by creating geometric constraints for constructional units.     

Synthesis of Cucurbit [ n ] uril-based Rotaxanes

Non-covalent attractive forces are commonly employed in biological systems to drive the assembly of highly orga nized supramolecular entities from relatively simple subunits.     

Intramolecular hydrogen bonding and anion binding of N-benzamido-N'-benzoylthioureas

N-(p-Dimethylamino)benzoyl-N'-phenylthiourea as an N-acylthiourea is known to be unable to bind anions due to a strong intramolecular hydrogen bond (IHB). We show here that by inserting an amido group in the N'-phenyl side the newly designed N-benzamido-N'-benzoylthioureas, despite this IHB too, bind strongly to anions with binding constants on the order of 10(6)-10(7) mol(-1) L. Results suggest that potential anion receptors or organocatalysts could be developed on the basis of this framework with a wide structural diversity.     

Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study

The Escherichia coli peptide deformylase (PDF) and Bacillus thermoproteolyticus thermolysin (TLN) are two representative metal-requiring peptidases having remarkably similar active centers but distinctively different metal preferences. Zinc is a competent catalytic cofactor for TLN but not for PDF. Reaction pathways and the associated energetics for both enzymes were determined using combined semiempirical and ab initio quantum mechanical/molecular mechanical modeling, without presuming reaction coordinates. The results confirmed that both enzymes catalyze via the same chemical steps, and reproduced their different preferences for zinc or iron as competent cofactors. Further analyses indicated that different feasibility of the nucleophilic attack step leads to different metal preferences of the two enzymes. In TLN, the substrate is strongly activated and can serve as the fifth coordination ligand of zinc prior to the chemical steps. In PDF, the substrate carbonyl is activated by the chemical step itself, and becomes the fifth coordination partner of zinc only in a later stage of the nucleophilic attack. These leads to a much more difficult nucleophilic attack in PDF than in TLN. Different from some earlier suggestions, zinc has no difficulty in accepting an activated substrate as the fifth ligand to switch from tetra- to penta-coordination in either PDF or TLN. When iron replaces zinc, its stronger interaction with the hydroxide ligand may lead to higher activation barrier in TLN. In PDF, the stronger interactions of iron with ligands allow iron-substrate coordination to take place either before or at a very early stage of the chemical step, leading to effective catalysis. Our calculations also show combined semiempirical and ab initio quantum mechanical modeling can be efficient approaches to explore complicated reaction pathways in enzyme systems.