A versatile synthetic approach to peptidyl privileged structures using a "safety-catch" linker

Peptidyl privileged structures have been widely used by many groups to discover biologically active molecules. In this context, privileged substructures are used as "hydrophobic anchors", to which peptide functionality is appended to gain specificity. Utilization of this concept has led to the discovery of many different active compounds at a wide range of biological receptors. A synthetic approach to these compounds has been developed on a "safety-catch" linker that allows rapid preparation of large libraries of these molecules. Importantly, amide bond formation/cleavage through treatment with amines is the final step; it is a linker strategy that allows significant diversification to be easily incorporated, and it only requires the inclusion of an amide bond. In addition, chemistry has been developed that permits the urea moiety to be inserted at the N-terminus of the peptide, allowing the same set of amines (either privileged substructures or amino acid analogues) to be used at both the N- and C-termini of the molecule. To show the robustness of this approach, a small library of peptidyl privileged structures were synthesized, illustrating that large combinatorial libraries can be synthesized using these technologies.     

Emerging chemical patterns: a new methodology for molecular classification and compound selection

A concept termed Emerging Chemical Patterns (ECPs) is introduced as a novel approach to molecular classification. The methodology makes it possible to extract key molecular features from very few known active compounds and classify molecules according to different potency levels. The approach was developed in light of the situation often faced during the early stages of lead optimization efforts: too few active reference molecules are available to build computational models for the prediction of potent compounds. The ECP method generates high-resolution signatures of active compounds. Predictive ECP models can be built based on the information provided by sets of only three molecules with potency in the nanomolar and micromolar range. In addition to individual compound predictions, an iterative ECP scheme has been designed. When applied to different sets of active molecules, iterative ECP classification produced compound selection sets with increases in average potency of up to 3 orders of magnitude.     

The Development of "Caged" Substrates for the Studies of Rapid Electron Transfer and Early Events in Protein Folding

In recent years,the applications of photolabile compounds, or compounds that unmask a function group upon absorption of light, have become more diverse. Since such compounds can provide an effective means of orthogonal protection, they have been used to facilitate the synthesis of complex, polyfunctional organic molecules. These materials have also been used to "cage" compounds by protection of an essential functional group, so that a chemical reaction may be initiated by a pulse of light. In this manner, mixing difficulties can be circumvented in kinetics measurements. Applications of this method include the photolysis of caged ATP for studies of muscle fiber contraction, where diffusion of ATP into the muscle fiber is, slow; of caged fluorescent probes that only emit light after photolysis; and even of caged enzymes by incorporating photolabile groups on essential side chains.     

Fragment-based drug design: computational & experimental state of the art

Fragment-based screening is an emerging technology which is used as an alternative to high-throughput screening (HTS), and often in parallel. Fragment screening focuses on very small compounds. Because of their small size and simplicity, fragments exhibit a low to medium binding affinity (mM to μM) and must therefore be screened at high concentration in order to detect binding events. Since some issues are associated with high-concentration screening in biochemical assays, biophysical methods are generally employed in fragment screening campaigns. Moreover, these techniques are very sensitive and some of them can give precise information about the binding mode of fragments, which facilitates the mandatory hit-to-lead optimization. One of the main advantages of fragment-based screening is that fragment hits generally exhibit a strong binding with respect to their size, and their subsequent optimization should lead to compounds with better pharmacokinetic properties compared to molecules evolved from HTS hits. In other words, fragments are interesting starting points for drug discovery projects. Besides, the chemical space of low-complexity compounds is very limited in comparison to that of drug-like molecules, and thus easier to explore with a screening library of limited size. Furthermore, the "combinatorial explosion" effect ensures that the resulting combinations of interlinked binding fragments may cover a significant part of "drug-like" chemical space. In parallel to experimental screening, virtual screening techniques, dedicated to fragments or wider compounds, are gaining momentum in order to further reduce the number of compounds to test. This article is a review of the latest news in both experimental and in silico virtual screening in the fragment-based discovery field. Given the specificity of this journal, special attention will be given to fragment library design.     

固态"绝对"不对称合成

光学活性生物分子的形成是世界进化历史中一个重要过程。"绝对"不对称合成, 即在没有任何外界手性诱导试剂作用下或在圆偏振光影响下的封闭体系中的不对称合成, 为前生物时期天然手性的成因提供了解释。本文将综述通过非手性分子形成的手性晶体的固相反应进行的"绝对"不对称合成。     

Determination of "heavy" organotin pollution of water and shellfish by a modified hydride atomic absorption procedure

Tin speciation in aquatic environment is very complex. To the natural SnIV and methylated compounds, human activities add mainly butylated, octylated, phenylated or even methylated derivatives. The most environmentally significant, due to their high toxicity and direct introduction in water through biocidal use, are the trisubstituted ones. Several sophisticated speciation procedures have been proposed, they are not susceptible of common use. We propose a simple and fast procedure allowing routine global distinction of "heavy" tin species that are most susceptible of exerting harmful effects. This AA method use the differences in volatility of stannanes generated by reduction with NaBH4. SnIV and the methylated species have very close response coefficients whereas "heavy" compounds respond very slightly at room temperature and are eliminated in a -40 degrees C cold trap. "Heavy" tin determination in water is thus obtained by the difference between two hydride AA experiments, one performed on the untreated sample ("light tin") and the other on a UV mineralised subsample (total tin). (The mineralisation of organotins is realised by UV irradiation-2 hours--in a quartz container--yields 95-100%.) The analysis of shellfish tissue relies also on two experiments. Total tin is measured on a mineralised sample and "light tin" is obtained on a subsample "solubilised" with an Ultra Turrax homogeneizer in a diluted HCl solution.     

Photoisomerization of the Graft Copolymer of Starch and Azo-dye

Optical data storage materials are mainly based on organic molecules. To be suited for as an optical data storage material, molecules have to be photochromatic, they must be capable of being reversibly switched be. tween two spectroscopically distinct forms by use of light[1].Photoisome rization (trans ～cis) of azoaromatic compounds has been investigated extensively using UV-Vis spectroscopy. In 1972[2], the isomerization of various azobenzenes bound on the side chain or within the main chain of poly (methyl methacrylate), poly(ethyl methacrylate),polystyrene, a polyamide, and polyester had. been demonstrated. There are three processes: a trans-cis photochemical isomerization, a cis-trans photochemical isomerization, and a cis-trans thermal isomerization, which occurs due to the higher stability of the trans configuration, since that pioneering study, two main directions of research developed and are very active in the eurrent literature.     

Conformation Design of Open-Chain Compounds

At the brink of the 21st century, chemistry is increasingly concerned with the function that molecules fulfil as drugs, receptors, or-as ensemble of molecules-as materials. The capability of compounds to fulfil such functions cannot sufficiently be described by using only the terms composition and configuration. A decisive role is played in addition by the conformation of the molecules, which serves as the link between molecular composition and molecular function. Expressions such as "active conformation" or "competent conformation" allude to this aspect. Chemists have to develop an understanding how a flexible molecule adopts the conformation (a distinct shape) which is optimal for the function in question and how this process can be controlled. On the outset of such considerations, we may ask how nature succeeded in the process of evolution to endow flexible molecules with a preference to adopt the conformation which is optimal for the function it has to serve. In this review, I report on how we have reached a crude level of understanding of conformation design in nature with reference to the class of polyketide natural products, how we developed these insights into a conformation design of open-chain compounds, and which applications are already in sight.     

“推-拉”型巯基偶氮苯衍生物的合成

分子电子器件的研究是近期基础研究中受到极大关注的前沿热点[1-4]。带巯基的有机分子在金电极表面形成的自组装单分子膜(SAMs)及其电活性,是分子电子学领域具有代表性和研究最多的体系之一[5-13]。由于结构的特殊性和特征的光致异构化,偶氮苯衍生物具有对光和电的双重活性[14]     

Novel chiral conjugated macromolecules for potential electrical and optical applications

Optically active 1,1′‐binaphthyl molecules have been used to construct novel chiral dendrimers and linear polymers. Efficient light harvesting effects of the dendrimers have been observed. They have shown enantioselective fluorescence responses in the presence of chiral amino alcohol quenchers. They are potentially useful as fluorescent sensors for the recognition of chiral organic compounds. Linear binaphthyl polymers have shown strong light emitting properties. Their colors of emission can be systematically tuned by incorporating linkers of various conjugation length. A very efficient light emitting diode has been prepared from the binaphthyl‐based conjugated polymers. Nonlinear optical chromophores have been organized in the chiral binaphthyl polymer chains to construct noncentrosymmetric and multipolar materials. These novel propeller‐like polymers have shown significant second‐order nonlinear optical effects.     

Synthesis of a novel macrocyclic library: discovery of an IGF-1R inhibitor

We present a new approach for the conversion of active sequences of proteins and peptides into small molecules. A library of macrocyclic disulfide molecules was made, in which the active pharmacophores of the parent peptide are preserved while the size of the macromolecular scaffold on which the pharmacophores are arranged is varied. This enables a systematic search for macromolecules in which the pharmacophores are in an appropriate conformation for biological activity. We developed two procedures for the synthesis of such libraries from building blocks that include commercial amino acids and functionalized aldehydes. Chemical synthesis using the "tea-bag" method gave a library with higher diversity, but low yields, compared to the manual synthesis of the library, in which the compounds were synthesized in individual vessels and the yield and purity improved dramatically. As a proof of concept, we synthesized a 34-member library derived from the sequence of the activation loop of insulin-like growth factor-1 receptor. Selected compounds were screened, and one was found to be biologically active in the low micromolar range. The concept presented here may prove particularly useful in cases where the pharmacophores are known but need to be systematically screened for a spatial arrangement that will enable biological activity.     

Characterizing the "shell phase" formed from amphiphilic picolinates

The shell phase forms when certain picolinates are subjected to energy input (via sonication or vortexing) while exposed to a water/toluene mixture. A shell, about 600 A thick and containing the picolinate and (very likely) toluene, surround the water droplets that are always produced during the mixing process. Solubility in either phase appears to be deleterious to shell formation. The shells, stable for months, are not easily distorted but can be punctured, even skewered, with a syringe needle without destroying the sphere, yet there is enough mobility among the molecules to repair the physical damage after the needle is removed. This, plus the absence of evidence for crystallinity, suggests a solid or semisolid film forms when picolinates, with the aid of an aromatic solvent, are provided the energy to rearrange themselves on water droplet surfaces. Structure-activity comparisons among the 10 compounds studied indicate that chain-chain association and intermolecular hydrogen bonding are dominant forces in a side-by-side self-assembly of the molecules within the shells.     

Tetrahedral boron chemistry for the preparation of highly efficient "cascatelle" devices

The replacement of the two fluorine atoms on the boron center of the well-known Bodipy fluorophore by functionalized acetylenic groups opens the way to a new family of highly luminescent, redox active, and stable fluorophores termed "E-Bodipy" species. The substitution is effective for ethynyl-lithium reagents incorporating tolyl, naphthyl, pyrenyl, fluorenyl, and terpyridinyl units. The protocol also tolerates the presence of various functional groups in the dipyrromethene meso position such as pyrene, phenylethynylpyrene, 4'-terpyridine, and iodophenyl. The last of these is particularly useful for a further coupling reaction enabling introduction of a flexible arm bearing a succinimidyl unit reactive toward primary amines. X-ray structure determinations of two E-Bodipy compounds confirm the introduction of the ethynyl units and show the boron atoms to have a distorted tetrahedral environment, with B-C(ethynyl) approximately 1.59 A and both boron atoms lying essentially in the mean planes of the dipyrromethene units. All the new compounds show intense electronic absorption bands (epsilon 60,000-70,000 M-1 cm-1), high quantum yields (>80%), and slow rates of nonradiative decay. Absorption by the aromatic substituents results in a "cascatelle" process leading to emission exclusively through the boradiazaindacene entity and thus large virtual Stokes' shift (>10,000 cm-1). The new compounds are also redox active, with the formation of both Bodipy+* and Bodipy-* occurring more readily than for F-Bodipy species. The molecules in their excited states are strong reducing agents.     

Recent applications of ring-closing metathesis in the synthesis of lactams and macrolactams

Lactams are an important class of compounds owing to their presence in numerous biologically active molecules of natural and unnatural nature. They are also highly versatile intermediates that can be elaborated into interesting compounds for potential use in organic and medicinal chemistry endeavors. In this feature article, the reader will be given a background to olefin metathesis followed by concise discussions (with selected examples) to report recent applications of ring-closing metathesis to form lactams and macrolactams from acyclic diene precursors, an area which continues to deposit attractive applications in the chemical literature en route or in the final step to the target molecules.     

SHAFTS: a hybrid approach for 3D molecular similarity calculation. 1. Method and assessment of virtual screening

We developed a novel approach called SHAFTS (SHApe-FeaTure Similarity) for 3D molecular similarity calculation and ligand-based virtual screening. SHAFTS adopts a hybrid similarity metric combined with molecular shape and colored (labeled) chemistry groups annotated by pharmacophore features for 3D similarity calculation and ranking, which is designed to integrate the strength of pharmacophore matching and volumetric overlay approaches. A feature triplet hashing method is used for fast molecular alignment poses enumeration, and the optimal superposition between the target and the query molecules can be prioritized by calculating corresponding "hybrid similarities". SHAFTS is suitable for large-scale virtual screening with single or multiple bioactive compounds as the query "templates" regardless of whether corresponding experimentally determined conformations are available. Two public test sets (DUD and Jain's sets) including active and decoy molecules from a panel of useful drug targets were adopted to evaluate the virtual screening performance. SHAFTS outperformed several other widely used virtual screening methods in terms of enrichment of known active compounds as well as novel chemotypes, thereby indicating its robustness in hit compounds identification and potential of scaffold hopping in virtual screening.     

Synthesis of new mixed phenol/heterocyclic derivatives and studies of their activity as inhibitors of Bax/Bcl-xL interaction

We describe here the synthesis of a series of new molecules containing phenol and heteroaromatic moieties, compounds, which have been evaluated for their ability to inhibit Bax/Bcl-xL interactions in BRET assays. Among them, a triazole derivative 13, exhibit a very promising activity, being more potent than the reference compounds acylpyrogallol 1 and ABT 737. These preliminary results demonstrate that derivatives of this family can be attractive to develop new molecules with potent anticancer activity.