Single-triggered AB6 self-immolative dendritic amplifiers

Self-immolative dendrimers are a unique class of molecules that are able to disassemble upon undergoing a specific triggering reaction through domino-like fragmentations. We have designed and synthesized a novel AB(6) self-immolative dendritic adaptor that amplifies a single cleavage event into the release of six reporter units. The disassembly mechanism is based on a specifically triggered cleavage event followed by elimination of a cyclic urea derivative and six consecutive quinone methide eliminations. The system was disassembled under both organic and aqueous conditions by either chemical or enzymatic triggering. Various reporter molecules and triggering groups were introduced onto the dendritic adaptor to obtaining sensor molecules with enhanced properties for diagnostics and imaging.     

Self‐immolative dendrimers as novel drug delivery platforms

Self‐immolative dendrimers were recently developed and introduced as a potential platform for a single‐triggered multi‐prodrug. These unique structural dendrimers can release all of their tail units through domino‐like chain fragmentation, which is initiated by a single cleavage at the dendrimer core. The incorporation of drug molecules as the tail units and an enzyme substrate as the trigger generates a multi‐prodrug unit that is activated with a single enzymatic cleavage. We have demonstrated several examples of self‐immolative dendritic prodrug systems and have shown significant advantages with respect to the appropriate monomeric prodrug. We anticipate that single‐triggered, dendritic prodrugs will be exploited to further improve selective chemotherapeutic approaches in cancer therapy. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1569–1578, 2006     

Fuel‐Responsive Allosteric DNA‐Based Aptamers for the Transient Release of ATP and Cocaine

We show herein that allostery offers a key strategy for the design of out‐of‐equilibrium systems by engineering allosteric DNA‐based nanodevices for the transient loading and release of small organic molecules. To demonstrate the generality of our approach, we used two model DNA‐based aptamers that bind ATP and cocaine through a target‐induced conformational change. We re‐engineered these aptamers so that their affinity towards their specific target is controlled by a DNA sequence acting as an allosteric inhibitor. The use of an enzyme that specifically cleaves the inhibitor only when it is bound to the aptamer generates a transient allosteric control that leads to the release of ATP or cocaine from the aptamers. Our approach confirms that the programmability and predictability of nucleic acids make synthetic DNA/RNA the perfect candidate material to re‐engineer synthetic receptors that can undergo chemical fuel‐triggered release of small‐molecule cargoes and to rationally design non‐equilibrium systems.     

Conformational studies of resin-bound vancomycin and the complex of vancomycin and Ac2-L-Lys-D-Ala-D-Ala

The molecular target of vancomycin, a commonly used glycopeptide antibiotic, is the D-Ala-D-Ala dipeptide subunit on the bacterial cell wall. The molecular basis of interaction between vancomycin and D-Ala-D-Ala in solution is well-known. However, there is no structural data on vancomycin, and its interaction with D-Ala-D-Ala when the drug is tethered to a solid support. In this Article, vancomycin was directly coupled onto TentaGel or PEGA resin through its C terminus. High-resolution magic angle spinning NMR studies indicated that conformation of PEGA bead-bound vancomycin is identical to that of the free drug. Broadening and shifts of the same proton resonances were observed in solution-phase vancomycin or PEGA-bound vancomycin when complexed with Ac(2)-L-Lys-D-Ala-D-Ala. This study demonstrates that bead-bound molecules can behave the same as solution-phase molecules in terms of molecular interaction with its target molecule, thus validating the on-bead screening approach of the "one-bead-one-compound" combinatorial library method.     

Competition between reactivity and relaxation in free electron attachment to molecules

The reactivity of the C₆F₅X (X=F, Cl, Br, I) molecules following low energy (0–15 eV) electron attachment is studied in the gas phase under single collision conditions, free molecular clusters and condensed molecules by means of crossed beams and surface experiments. All four molecules exhibit a very prominent resonance for low energy electron attachment (<1 eV, attachment cross section >10⁻¹⁴ cm²). Under collision free conditions thermal electron capture generates long lived molecular parent anions C₆F₅X^−*. Along the line Cl, Br, I dissociation into X⁻+C₆F₅ and X+C₆F₅-increasingly competes until for X=1 only chemical fragmentation is observed on the mass spectrometric time scale. In free molecular clusters chemical fragmentation is quantitatively quenched at low energies in favour of associative attachment yielding undissociated, relaxed ions (C₆F₅X)⁻ _n,n≥1. A further dissociative resonance at 6.5 eV in C₆F₅Cl is considerably enhanched in clusters. If these molecules are finally condensed on a solid surface, one observes a prominent Cl⁻ desorption resonance at 6.5 eV. While the quantitative quenching of the chemical reactivity at low energies is due to the additional possibilities of energy dissipation under aggregation, the enhanched reactivity at 6.5 eV is interpreted by the conversion of a core excited open channel resonance in single molecules into a closed channel (Feshbach) resonance when it is coupled to environmental molecules.     

Establishment of correlations between the structure and reactivity of molecules in the gas phase based on information theory

A general approach to revealing correlations between the structure of molecules and their reactivity in fragmentation processes under electron impact conditions based on the use of generalized structural and mass spectral characteristics is suggested. The characteristics were obtained using information theory, molecular graphs, and absolute reaction rates. Information topological indices of molecular graphs were used as generalized structural characteristics of molecules. They are a quantitative measure of the structural complexity of molecules and are expressed in information units. The gas-phase process of fragmentation of molecules under electron impact was used as a general reaction series for all volatiles. In terms of information theory, the mass spectrum represents the distribution of probabilities of the formation of ions of each type, and the information entropy of this distribution appears to be an integral characteristic of the reactivity of a molecule during fragmentation under electron impact in the gas phase. Using organic and organometallic compounds of several classes (ferrocene derivatives, arylsilanes, aromatic azo compounds,etc.) as examples, linear correlations between the information indices of the mass spectra and the information topological indices of the appropriate molecular graphs or electronic parameters of molecules have been found, which testifies that the approach suggested is adequate.Translated fromIzvestiya Akodemii Nouk. Seriya Khimicheskaya, No. 11, pp. 2683–2688, November, 1996.     

Watching photoinduced chemistry and molecular energy flow in solution in real time

Energized molecules are the essential actors in chemical transformations in solution. As the rearrangement of bonds requires a movement of nuclei, vibrational energy is often the driving force for a reaction. Vibrational energy can be redistributed within the "hot" molecule, or relaxation can occur when molecules interact. Both processes govern the rates, pathways, and quantum yields of chemical transformations in solution. Unfortunately, energy transfer and the breaking, formation, and rearrangement of bonds take place on ultrafast timescales. This Review highlights experimental approaches for the direct, ultrafast measurement of photoinduced femtochemistry and energy flow in solution. In the first part of this Review, we summarize recent experiments on intra- and intermolecular energy transfer. The second part discusses photoinduced decomposition of large organic peroxides, which are used as initiators in free radical polymerization. The mechanisms and timescales of their decarboxylation determine the initial steps of polymerization and the microstructure of the polymer product.     

Molecularly Precise Dendrimer–Drug Conjugates with Tunable Drug Release for Cancer Therapy

The structural preciseness of dendrimers makes them perfect drug delivery carriers, particularly in the form of dendrimer–drug conjugates. Current dendrimer–drug conjugates are synthesized by anchoring drug and functional moieties onto the dendrimer peripheral surface. However, functional groups exhibiting the same reactivity make it impossible to precisely control the number and the position of the functional groups and drug molecules anchored to the dendrimer surface. This structural heterogeneity causes variable pharmacokinetics, preventing such conjugates to be translational. Furthermore, the highly hydrophobic drug molecules anchored on the dendrimer periphery can interact with blood components and alter the pharmacokinetic behavior. To address these problems, we herein report molecularly precise dendrimer–drug conjugates with drug moieties buried inside the dendrimers. Surprisingly, the drug release rates of these conjugates were tailorable by the dendrimer generation, surface chemistry, and acidity.     

Mechanochemical activation of disulfide-based multifunctional polymers for theranostic drug release

Drug delivery systems responsive to physicochemical stimuli allow spatiotemporal control over drug activity to overcome limitations of systemic drug administration. Alongside, the non-invasive real-time tracking of drug release and uptake remains challenging as pharmacophore and reporter function are rarely unified within one molecule. Here, we present an ultrasound-responsive release system based on the mechanochemically induced 5-exo-trig cyclization upon scission of disulfides bearing cargo molecules attached via β-carbonate linker within the center of a water soluble polymer. In this bifunctional theranostic approach, we release one reporter molecule per drug molecule to quantitatively track drug release and distribution within the cell in real-time. We use N-butyl-4-hydroxy-1,8-naphthalimide and umbelliferone as fluorescent reporter molecules to accompany the release of camptothecin and gemcitabine as clinically employed anticancer agents. The generality of this approach paves the way for the theranostic release of a variety of probes and drugs by ultrasound.

A theranostic approach for the mechanochemically induced release of drugs is presented to track drug release and uptake in real-time.     

Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method

Localized water molecules in the binding pockets of proteins play an important role in noncovalent association of proteins and small drug compounds. At times, the dominant contribution to the binding free energy comes from the release of localized water molecules in the binding pockets of biomolecules. Therefore, to quantify the energetic importance of these water molecules for drug design purposes, we have used the double-decoupling approach to calculate the standard free energy of tying up a water molecule in the binding pockets of two protein complexes. The double-decoupling approach is based on the underlying principle of statistical thermodynamics. We have calculated the standard free energies of tying up the water molecule in the binding pockets of these complexes to be favorable. These water molecules stabilize the protein-drug complexes by interacting with the ligands and binding pockets. Our results offer ideas that could be used in optimizing protein-drug interactions, by designing ligands that are capable of targeting localized water molecules in protein binding sites. The resulting free energy of ligand binding could benefit from the potential free energy gain accompanying the release of these water molecules. Furthermore, we have examined the theoretical background of the double-decoupling method and its connection to the molecular dynamics thermodynamic integration techniques.     

Structure of Charged Poly(propylene imine) Dendrimers: Theoretical Investigation

A mean‐field model for charged dendrimers has been elaborated and applied to Astramol dendrimers of 5^th generation in salt‐free solution. The free energy of a dendrimer molecule was minimized with respect to the dendrimer size and to the profile of counterion distribution. The model of highly stretched freely jointed chain was used to describe the elasticity of long branches, the dissociated groups were assumed to be localized mostly on the periphery of the molecule, and the electrostatic interactions were described in the Poisson‐Boltzmann approximation. It was found that the osmotic pressure of counterions leads to moderate expansion of dendrimer molecules upon charging, and a significant fraction of counterions is localized within the dendrimer molecule under typical experimental conditions.

The schematic structure of poly(propylene imine) dendrimers for the 4^th generation.     

Synthesis of Onion‐Peel Nanodendritic Structures with Sequential Functional Phosphorus Diversity

The preparation of novel families of phosphorus‐based macromolecular architectures called “onion peel” phosphorus nanodendritic systems is reported. This construct is based on the versatility of methods of synthesis using several building blocks and on the capability of these systems to undergo regioselective reactions within the cascade structure. Sustainable metal‐free routes such as the Staudinger reaction or Schiff‐base condensation, involving only water and nitrogen as byproducts, allow access to several dendritic macromolecules bearing up to seven different phosphorus units in their backbone, each of them featuring specific reactivity. The presence of the highly aurophilic P?N?P?S fragment enables selective ligation of Au^I within the dendritic framework.     

Dynamic path bifurcation in the Beckmann reaction: support from kinetic analyses

The reactions of oximes to amides, known as the Beckmann rearrangement, may undergo fragmentation to form carbocations + nitriles when the migrating groups have reasonable stability as cations. The reactions of oxime sulfonates of 1-substituted-phenyl-2-propanone derivatives (7-X) and related substrates (8-X, 9a-X) in aqueous CH(3)CN gave both rearrangement products (amides) and fragmentation products (alcohols), the ratio of which depends on the system; the reactions of 7-X gave amides predominantly, whereas 9a-X yielded alcohols as the major product. The logk-logk plots between the systems gave excellent linear correlations with slopes of near unity. The results support the occurrence of path bifurcation after the rate-determining TS of the Beckmann rearrangement/fragmentation reaction, which has previously been proposed on the basis of molecular dynamics simulations. It was concluded that path-bifurcation phenomenon could be more common than thought and that a reactivity-selectivity argument based on the traditional TS theory may not always be applicable even to a well-known textbook organic reaction.     

Intermittent single-molecule interfacial electron transfer dynamics

We report on single-molecule studies of photosensitized interfacial electron transfer (ET) processes in Coumarin 343 (C343)-TiO(2) nanoparticles (NP) and Cresyl Violet (CV(+))-TiO(2) NP systems, using time-correlated single-photon counting coupled with scanning confocal fluorescence microscopy. Fluorescence intensity trajectories of individual dye molecules adsorbed on a semiconductor NP surface showed fluorescence fluctuations and blinking, with time constants distributed from milliseconds to seconds. The fluorescence fluctuation dynamics were found to be inhomogeneous from molecule to molecule and from time to time, showing significant static and dynamic disorders in the interfacial ET reaction dynamics. We attribute fluorescence fluctuations to the interfacial ET reaction rate fluctuations, associating redox reactivity intermittency with the fluctuations of molecule-TiO(2) electronic and Franck-Condon coupling. Intermittent interfacial ET dynamics of individual molecules could be characteristic of a surface chemical reaction strongly involved with and regulated by molecule-surface interactions. The intermittent interfacial reaction dynamics that likely occur among single molecules in other interfacial and surface chemical processes can typically be observed by single-molecule studies but not by conventional ensemble-averaged experiments.     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields

The widely used CHARMM additive all‐atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug‐like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug‐like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3‐phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform “all‐CHARMM” simulations on drug‐target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Using tandem mass spectrometry to predict chemical transformations of 2-pyrimidinyloxy-N-arylbenzyl amine derivatives in solution

Tandem mass spectrometry is used to predict the chemical transformations of 2-pyrimidinyloxy-N-arylbenzyl amine derivatives. Compound 1, N-2-2-4,6- dimethoxypyrimidin-2-yloxy benzylamino phenyl benzamide was selected as a model to present our idea. The CID reactions of protonated 1 include an intramolecular S(N)2 reaction and a cyclodehydration reaction. Under in-source CID conditions, deprotonated 1 undergoes a Smiles rearrangement reaction and then dissociates to the ion at m/z 349. Theoretical computations were invoked to shed light on the reaction mechanisms of 1 by the semiempirical PM3 method. These studies of gas-phase reactions show the reactivity of some potential reaction centers in this molecule, which inspired us to explore the solution phase analogous reactions of 1. Further experiments show that 1 has two analogous reactions in acidic solution: the acid-catalyzed cyclodehydration reaction and the acid-catalyzed Smiles rearrangement reaction. Moreover, 1 undergoes the base-catalyzed Smiles rearrangement under basic conditions. The present study demonstrates that mass spectrometry can play an important role in predicting the chemical solution phase transformations of 2-pyrimidinyloxy-N-arylbenzyl amine derivatives.