Flexible Analogue Research Articles

O6-[(2″,3″-O-Isopropylidene-5″-O-tbutyldimethylsilyl)pentyl]-5′-O-tbutyldiphenylsilyl-2′,3′-O-isopropylideneinosine

Cyclic adenosine diphosphate ribose (cADPR) is a cyclic nucleotide involved in the Ca2+ homeostasis. In its structure, the northern ribose, bonded to adenosine through an N1 glycosidic bond, is connected to the southern ribose through a pyrophosphate bridge. Due to the chemical instability at the N1 glycosidic bond, new bioactive cADPR derivatives have been synthesized. One of the most interesting analogues is the cyclic inosine diphosphate ribose (cIDPR), in which the hypoxanthine replaced adenosine. The efforts for synthesizing new linear and cyclic northern ribose modified cIDPR analogues led us to study in detail the inosine N1 alkylation reaction. In the last few years, we have produced new flexible cIDPR analogues, where the northern ribose has been replaced by alkyl chains. With the aim to obtain the closest flexible cIDPR analogue, we have attached to the inosine N1 position a 2″,3″-dihydroxypentyl chain, possessing the two OH groups in a ribose-like fashion. The inosine alkylation reaction afforded also the O6-alkylated regioisomer, which could be a useful intermediate for the construction of new kinds of cADPR mimics.

Cover Feature: A N‐Heterocyclic Carbene‐Palladacycle with Constrained Aliphatic Linker: Synthesis, Characterization and Its Catalytic Application towards Suzuki‐Miyaura Cross‐Coupling (Asian J. Org. Chem. 12/2021)

Two robust structure-defined NHC-Palladacycle complexes with N/O-aliphatic substituents have been successfully developed, which acted as catalysts in the Suzuki-Miyaura coupling of various (hetero)aryl chlorides with a wide range of substrate adaptability under the aqueous and mild reaction conditions. Their structures are very similar, just like the Real and Fake Monkey King. Among them, the constrained complex exhibited higher catalytic efficiency than its flexible analogue. More information can be found in the Communication by Dong-Yuan Yang, Qinyue Deng, Tao Tu et al.

Flexible nickel Prussian blue analogue films for electrochromic and H2O2 sensing

We showed that nickel Prussian blue analogue (NiPBA) films were electrochemically deposited onto a conducting transparent indium tin oxide coated with polyethylene terephthalate electrodes. The flexible NiPBA films were characterized by means of scanning electron microscopy–energy dispersive X-ray spectroscopy (SEM–EDS), X-ray photoelectronspectroscopy technique and X-ray diffraction analyses. Electrochromic performance of the flexible NiPBA films was investigated using cyclic voltammetry, chronoamperometry and chronocoulometry methods. The coloration, bleaching times and reversibility of the NiPBA film were calculated as 5.8 s, 2.7 s, and 97.37% in KCl liquid electrolyte medium, respectively. Electrocatalytic behavior of the NiPBA film towards H2O2 sensor was also evaluated by chronoamperometry technique. The flexible NiPBA film showed a linear response to H2O2 in concentration range of 3.92 to 15.68 mM (R2 = 0.9906), sensitivity of 1.6272 µAmM−1 cm−2. After performing repeated bended cycle tests, the flexible NiPBA films showed good mechanical stability in terms of both electrochromic and H2O2 sensing properties. The presented results can promote its potential application in wearable devices, displays, which are flexible states for monitoring.

Synthesis and Characterization of Acid-Responsive Luminescent Fe(II) Metallopolymers of Rigid and Flexible Backbone N-Donor Multidentate Conjugated Ligands.

In this report we have disclosed the syntheses and properties of two new conjugated organic moieties bearing the same coordination sites but possessing different backbone rigidities and rotational flexibilities. Two new metallopolymers have been synthesized from the corresponding ligands under identical reaction conditions, and they have been thoroughly characterized through different techniques to understand the effect of backbone rigidity on the evolution of different properties in these metallopolymers. A FESEM micrograph of the rigid metallopolymer confirms the formation of a rigid nanorod type structure, while long agglomerated nanofiber strands are visible on the substrate in the case of the flexible analogue. All of the newly synthesized materials are fluorescence active. An Fe(II) metallopolymer of the flexible ligand showed huge changes in emission properties in the presence of different acids and showed a possibility of it being used as a thin film acid vapor sensor. All of the materials showed reversible electrochemical activity, and both of these polymers have shown electroluminescence when an appropriate potential is applied.

4,2':6',4"- and 3,2':6',3"-Terpyridines: The Conflict between Well-Defined Vectorial Properties and Serendipity in the Assembly of 1D-, 2D- and 3D-Architectures.

A comparative investigation of the coordination assemblies formed between Co(NCS)2 and two monotopic 4,2’:6’,4’’-terpyridine (4,2’:6’,4”-tpy) ligands or two related ditopic ligands is reported. Crystals were grown by layering MeOH solutions of Co(NCS)2 over a CHCl3 or 1,2-C6H4Cl2 solution of the respective ligand at room temperature. With 4’-(2-methylpyrimidin-5-yl)-4,2’:6’,4”-terpyridine (6), the 1D-coordination polymer {[Co2(NCS)4(MeOH)4(6)2]∙2MeOH∙8H2O}n assembles with 6 coordinating only through the outer N-donors of the 4,2’:6’,4”-tpy unit; coordination by the MeOH solvent blocks two cobalt coordination sites preventing propagation in a higher-dimensional network. A combination of Co(NCS)2 and 1-(4,2‘:6’,4”-terpyridin-4’-yl)ferrocene (7) leads to {[Co(NCS)2(7)2]∙4CHCl3}n which contains a (4,4) net; the 2D-sheets associate through π-stacking interactions between ferrocenyl and pyridyl units. A 3D-framework is achieved through use of the ditopic ligand 1,4-bis(npropoxy)-2,5-bis(4,2’:6’,4”-terpyridin-4’-yl)benzene (8) which acts as a 4-connecting node in {[Co(NCS)2(8)2]∙2C6H4Cl2}n; the combination of metal and ligand planar 4-connecting nodes results in a {65.8} cds net. For a comparison with the coordinating abilities of the previously reported 1,4-bis(noctoxy)-2,5-bis(4,2’:6’,4”-terpyridin-4’-yl)benzene (3), a more flexible analogue 9 was prepared. {[Co(NCS)2(9)]∙2CHCl3}n contains a (4,4) net defined by both metal and ligand planar 4-connecting nodes. The noctoxy tails of 9 protrude from each side of the (4,4) net and thread through adjacent sheets; the arene-attached noctoxy chains associate through a combination of van der Waals and C–H...π interactions.

Asymmetric Phase-Transfer Catalysis with Homo- and Heterochiral Quaternary Ammonium Salts: A Theoretical Study

A thorough theoretical study of phase-transfer quaternary ammonium catalysts designed by the Maruoka group has been performed in an attempt to gain better understanding of the properties and catalytic behavior of the homo- and heterochiral forms of these systems. The conformationally flexible analogue is found to easily undergo interconversion from the homo- to the heterochiral form driven by the higher thermodynamic stability of the heterochiral isomer and resulting in alternation in catalytic behavior. Theoretical calculations of (1)H NMR spectra of the two isomers for different model systems are in good agreement with the experimental data, allowing us to conclude that the upfield shift of signals for the benzylic protons in the heterochiral form could be explained by an increase in the shielding effect of the aromatic parts of the system around these protons due to the conformational changes. By applying the automated transition state (TS) search procedure for the alkylation of glycine derivatives catalyzed by the homo-/heterochiral form of a conformationally rigid analogue, we were able to locate more than 40 configurations of the TS structures. In brief, the homochiral form was theoretically confirmed to catalyze the formation of the predominant R-product, while for the heterochiral form the catalytic activity is found to depend on two factors: (i) formation of a tight ion pair between the catalyst and the glycine derivative, which results in a decrease in the reaction rate, in agreement with the experimental data, and formation of only the R-product, and (ii) the possibility that the reaction occurs without the initial formation of the ion pair or after its dissociation, in which case the formation of an S-product is predominant. The combined effects of both factors would explain the lower reaction rate and the poor enantioselectivity observed experimentally for the heterochiral form.

P‐tert‐Butylcalix[8]arene: An Extremely Versatile Platform for Cluster Formation

p-tert-Butylcalix[4]arene is a bowl-shaped molecule capable of forming a range of polynuclear metal clusters under different experimental conditions. p-tert-Butylcalix[8]arene (TBC[8]) is a significantly more flexible analogue that has previously been shown to form mono- and binuclear lanthanide (Ln) metal complexes. The latter (cluster) motif is commonly observed and involves the calixarene adopting a near double-cone conformation, features of which suggested that it may be exploited as a type of assembly node in the formation of larger polynuclear lanthanide clusters. Variation in the experimental conditions employed for this system provides access to Ln(1), Ln(2), Ln(4), Ln(5), Ln(6), Ln(7) and Ln(8) complexes, with all polymetallic clusters containing the common binuclear lanthanide fragment. Closer inspection of the structures of the polymetallic clusters reveals that all but one (Ln(8)) are in fact based on metal octahedra or the building blocks of octahedra, with the identity and size of the final product dependent upon the basicity of the solution and the deprotonation level of the TBC[8] ligand. This demonstrates both the versatility of the ligand towards incorporation of additional metal centres, and the associated implications for tailoring the magnetic properties of the resulting assemblies in which lanthanide centres may be interchanged.

Stationarity of generalized autoregressive moving average models

Time series models are often constructed by combining nonstationary effects such as trends with stochastic processes that are believed to be stationary. Although stationarity of the underlying process is typically crucial to ensure desirable properties or even validity of statistical estimators, there are numerous time series models for which this stationarity is not yet proven. A major barrier is that the most commonly-used methods assume φ-irreducibility, a condition that can be violated for the important class of discrete-valued observation-driven models. We show (strict) stationarity for the class of Generalized Autoregressive Moving Average (GARMA) models, which provides a flexible analogue of ARMA models for count, binary, or other discrete-valued data. We do this from two perspectives. First, we show conditions under which GARMA models have a unique stationary distribution (so are strictly stationary when initialized in that distribution). This result potentially forms the foundation for broadly showing consistency and asymptotic normality of maximum likelihood estimators for GARMA models. Since these conclusions are not immediate, however, we also take a second approach. We show stationarity and ergodicity of a perturbed version of the GARMA model, which utilizes the fact that the perturbed model is φ-irreducible and immediately implies consistent estimation of the mean, lagged covariances, and other functionals of the perturbed process. We relate the perturbed and original processes by showing that the perturbed model yields parameter estimates that are arbitrarily close to those of the original model.

Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy−Entropy Compensation in SH2−Ligand Binding

NMR spectroscopy and molecular dynamics (MD) simulations were used to probe the structure and dynamics of complexes of three phosphotyrosine-derived peptides with the Src SH2 domain in an effort to uncover a structural explanation for enthalpy-entropy compensation observed in the binding thermodynamics. The series of phosphotyrosine peptide derivatives comprises the natural pYEEI Src SH2 ligand, a constrained mimic, in which the phosphotyrosine (pY) residue is preorganized in the bound conformation for the purpose of gaining an entropic advantage to binding, and a flexible analogue of the constrained mimic. The expected gain in binding entropy of the constrained mimic was realized; however, a balancing loss in binding enthalpy was also observed that could not be rationalized from the crystallographic structures. We examined protein dynamics to evaluate whether the observed enthalpic penalty might be the result of effects arising from altered motions in the complex. (15)N-relaxation studies and positional fluctuations from molecular dynamics indicate that the main-chain dynamics of the protein show little variation among the three complexes. Root mean squared (rms) coordinate deviations vary by less than 1.5 A for all non-hydrogen atoms for the crystal structures and in the ensemble average structures calculated from the simulations. In contrast to this striking similarity in the structures and dynamics, there are a number of large chemical shift differences from residues across the binding interface, but particularly from key Src SH2 residues that interact with pY, the "hot spot" residue, which contributes about one-half of the binding free energy. Rank-order correlations between chemical shifts and ligand binding enthalpy for several pY-binding residues, coupled with available mutagenesis and calorimetric data, suggest that subtle structural perturbations (<1 A) from the conformational constraint of the pY residue sufficiently alter the geometry of enthalpically critical interactions in the binding pocket to cause the loss of binding enthalpy, leading to the observed enthalpy-entropy compensation. We find no evidence to support the premise that enthalpy-entropy compensation is an inherent property and conclude that preorganization of Src SH2 ligand residues involved in binding hot spots may eventuate in suboptimal interactions with the domain. We propose that introducing constraints elsewhere in the ligand could minimize enthalpy-entropy compensation effects. The results illustrate the utility of the NMR chemical shift to highlight small, but energetically significant, perturbations in structure that might otherwise go unnoticed in an apparently rigid protein.

Synthesis and conformational analysis of locked carbocyclic analogues of 1,3-diazepinone riboside, a high-affinity cytidine deaminase inhibitor.

Cytidine deaminase (CDA) catalyzes the deamination of cytidine via a hydrated transition-state intermediate that results from the nucleophilic attack of zinc-bound water at the active site. Nucleoside analogues where the leaving NH3 group is replaced by a proton and prevent conversion of the transition state to product are very potent inhibitors of the enzyme. However, stable carbocyclic versions of these analogues are less effective as the role of the ribose in facilitating formation of hydrated species is abolished. The discovery that a 1,3-diazepinone riboside (4) operated as a tight-binding inhibitor of CDA independent of hydration provided the opportunity to study novel inhibitors built as conformationally locked, carbocyclic 1,3-diazepinone nucleosides to determine the enzyme’s conformational preference for a specific form of sugar pucker. This work describes the synthesis of two target bicyclo[3.1.0]hexane nucleosides, locked as north (5) and south (6) conformers, as well as a flexible analogue (7) built with a cyclopentane ring. The seven-membered 1,3-diazepinone ring in all the three targets was built from the corresponding benzoyl-protected carbocyclic bis-allyl ureas by ring-closing metathesis. The results demonstrate CDA’s binding preference for a south sugar pucker in agreement with the high-resolution crystal structures of other CDA inhibitors bound at the active site.

Sequence-Specific Unusual (1→2)-Type Helical Turns in α/β-Hybrid Peptides

This article describes novel conformationally ordered alpha/beta-hybrid peptides consisting of repeating l-proline-anthranilic acid building blocks. These oligomers adopt a compact, right-handed helical architecture determined by the intrinsic conformational preferences of the individual amino acid residues. The striking feature of these oligomers is their ability to display an unusual periodic pseudo beta-turn network of nine-membered hydrogen-bonded rings formed in the forward direction of the sequence by 1-->2 amino acid interactions both in solid-state and in solution. Conformational investigations of several of these oligomers by single-crystal X-ray diffraction, solution-state NMR, and ab initio MO theory suggest that the characteristic steric and dihedral angle restraints exerted by proline are essential for stabilizing the unusual pseudo beta-turn network found in these oligomers. Replacing proline by the conformationally flexible analogue alanine (Ala) or by the conformationally more constrained alpha-amino isobutyric acid (Aib) had an adverse effect on the stabilization of this structural architecture. These findings increase the potential to design novel secondary structure elements profiting from the steric and dihedral angle constraints of the amino acid constituents and help to augment the conformational space available for synthetic oligomer design with diverse backbone structures.

Feature Extraction Using Molecular Planes for Fuzzy Relational Clustering of a Flexible Dopamine Reuptake Inhibitor

Six rigid-body parameters (Shift, Slide, Rise, Tilt, Roll, Twist) are commonly used to describe the relative displacement and orientation of successive base pairs in a nucleic acid structure. The present work adapts this approach to describe the relative displacement and orientation of any two planes in an arbitrary molecule-specifically, planes which contain important pharmacophore elements. Relevant code from the 3DNA software package (Nucleic Acids Res. 2003, 31, 5108-5121) was generalized to treat molecular fragments other than DNA bases as input for the calculation of the corresponding rigid-body (or "planes") parameters. These parameters were used to construct feature vectors for a fuzzy relational clustering study of over 700 conformations of a flexible analogue of the dopamine reuptake inhibitor, GBR 12909. Several cluster validity measures were used to determine the optimal number of clusters. Translational (Shift, Slide, Rise) rather than rotational (Tilt, Roll, Twist) features dominate clustering based on planes that are relatively far apart, whereas both types of features are important to clustering when the pair of planes are close by. This approach was able to classify the data set of molecular conformations into groups and to identify representative conformers for use as template conformers in future Comparative Molecular Field Analysis studies of GBR 12909 analogues. The advantage of using the planes parameters, rather than the combination of atomic coordinates and angles between molecular planes used in our previous fuzzy relational clustering of the same data set (J. Chem. Inf. Model. 2005, 45, 610-623), is that the present clustering results are independent of molecular superposition and the technique is able to identify clusters in the molecule considered as a whole. This approach is easily generalizable to any two planes in any molecule.

The influence of modifications in imide fragment structure on 5-HT 1A and 5-HT 7 receptor affinity and in vivo pharmacological properties of some new 1-( m-trifluoromethylphenyl)piperazines

New, flexible ( 7, 9, 11 and 13) and rigid (8, 10, 12 and 14) imides with a 1-( m-trifluorophenyl)piperazine fragment and a tetramethylene or a 1e,4e-cyclohexylene spacer, respectively, showed very high affinity ( K i = 0.3–34 nM) and agonistic in vivo activity for 5-HT 1A receptors. Flexible new compounds and the previously described 5 also bound to 5-HT 7 receptors ( K i = 21–134 nM). Selected glutarimide derivatives, that is, the most potent postsynaptic 5-HT 1A receptor agonist rigid compound 8 and its flexible analogue 7, as well as the previously described full agonist—rigid compound 6 and the partial agonist—its flexible counterpart 5 exhibited moderate affinity for α 1-adrenoceptors ( K i = 85–268 nM), but were practically devoid of any affinity for dopamine D 2 sites. Those glutarimides demonstrated anxiolytic- ( 5 and 7) and antidepressant-like ( 5, 6 and 8) activity in the four-plate and the swim tests in mice, respectively; at the same time, however, they inhibited the locomotor activity of mice. The antidepressant-like effect of 8 was significantly stronger than that induced by imipramine used as a reference antidepressant.

Novel Feature Extraction Technique for Fuzzy Relational Clustering of a Flexible Dopamine Reuptake Inhibitor.

This paper describes a novel clustering methodology for classifying over 700 conformations of a flexible analogue of GBR 12909, a dopamine reuptake inhibitor that has completed phase I clinical trials as a treatment for cocaine abuse. The major aspect of the clustering methodology includes an efficient data-conditioning scheme where a systematic feature extraction procedure based on the structural properties of the molecule was used to reduce the associated feature space. This allowed region-specific clustering that focused on individual pharmacophore elements of the molecule. For clustering of the reduced feature set, the fuzzy clustering partitional method was utilized. Due to the relational nature of the feature data, fuzzy relational clustering was employed, and it successfully detected natural groups defined by rotational minima around N(sp3)−C(sp3), O(sp3)−C(sp3), and C(sp3)−C(sp2) bonds. The proposed clustering methodology also employed several cluster validity measures, which corroborated the part...

Molecular Tectonics. Hydrogen-Bonded Networks Built from Tetra- and Hexaanilines

A series of compounds with multiple PhNH2 groups were synthesized and crystallized, and their structures were solved by X-ray diffraction to assess the ability of -NH2 groups in anilines to direct molecular crystallization. 2,2‘,7,7‘-Tetraamino-9,9‘-spirobi[9H-fluorene] (1c) forms an inclusion complex held together in part by donation of hydrogen bonds from -NH2 groups to guest molecules. Surprisingly, the -NH2 groups do not engage in hydrogen bonding with each other. Tetrakis(4-aminophenyl)methane (2c) crystallizes to form a guest-free close-packed diamondoid network in which each -NH2 group donates and accepts one N−H···N hydrogen bond. Tetrakis[(4-aminophenoxy)methyl]methane (3c), a more flexible analogue, also crystallizes as a close-packed structure maintained by an extensive network of N−H···N hydrogen bonds. Despite the structural similarity of tetraanilines 2c and 3c, their hydrogen-bonding patterns and network topologies are different. A flexible hexaaniline, 1,1‘-oxybis[3-(4-aminophenoxy)-2,2-bi...

Novel Feature Extraction Technique for Fuzzy Relational Clustering of a Flexible Dopamine Reuptake Inhibitor

This paper describes a novel clustering methodology for classifying over 700 conformations of a flexible analogue of GBR 12909, a dopamine reuptake inhibitor that has completed phase I clinical trials as a treatment for cocaine abuse. The major aspect of the clustering methodology includes an efficient data-conditioning scheme where a systematic feature extraction procedure based on the structural properties of the molecule was used to reduce the associated feature space. This allowed region-specific clustering that focused on individual pharmacophore elements of the molecule. For clustering of the reduced feature set, the fuzzy clustering partitional method was utilized. Due to the relational nature of the feature data, fuzzy relational clustering was employed, and it successfully detected natural groups defined by rotational minima around N(sp(3))-C(sp(3)), O(sp(3))-C(sp(3)), and C(sp(3))-C(sp(2)) bonds. The proposed clustering methodology also employed several cluster validity measures, which corroborated the partitions produced by the clustering technique and agreed with the results of hierarchical clustering using the XCluster program. Representative structures which exhibited a reasonable spread of energies and showed good spatial coverage of the conformational space were identified for use as putative bioactive conformations in a future Comparative Molecular Field Analysis of GBR 12909 analogues. The clustering methodology developed here is capable of handling other computational chemistry problems, and the feature extraction technique can be easily generalized to other molecules.

Evaluation of lactam-bridged neurotensin analogues adjusting psi(Pro10) close to the experimentally derived bioactive conformation of NT(8-13).

The neurotensin C-terminal hexapeptide, NT(8-13), which has been found to adopt a beta-strand-like conformation while bound to the NT1 receptor, was modified by the introduction of conformational constraints. Synthesis of the four stereoisomeric 4.4-spirolactams 1-4 and subsequent NT1 receptor binding studies showed that the restriction of psi(Pro10) to approximately 130 degrees leads to a more than 1000-fold increase of binding affinity for 1 (Ki = 12 nM) when compared to the more flexible analogue [NMeTyr11]NT(8-13).

Synthesis and supramolecular properties of conformationally restricted and flexible phospholipids.

Short synthetic routes are described to produce structurally related phospholipids that are either conformationally restricted or flexible. The conformationally restricted structures have a cyclopropyl ring in the interfacial region of the phospholipid. The key synthetic step is a cyclopropanation reaction between 2(5H)-furanone and a stabilized chloroallylic phosphonate anion. The synthetic routes enable the incorporation of different polar headgroups as well as nonpolar tails at late stages in the sequence. The phosphoethanolamine derivatives 1b and 2b readily form encapsulating vesicles, however, dye leakage from vesicles composed of the restricted phospholipid 1b is significantly slower than from vesicles composed of flexible analogue 2b. Physicochemical analyses using 31P NMR, differential scanning calorimetry, fluorescence anisotropy, and Langmuir-Blodgett films suggest that the decreased permeability of membranes composed of conformationally restricted 1b is due to its ability to pack more closely in a bilayer assembly.

Design, synthesis, and evaluation of matrix metalloprotease inhibitors bearing cyclopropane-derived peptidomimetics as P1' and P2' replacements.

We have previously used trisubstituted cyclopropanes as peptide replacements to induce conformational constraints in known pseudopeptide inhibitors of a number of important enzymes. Cyclopropane-derived peptide mimics are novel in that they are among the few replacements that locally orient the peptide backbone and the amino acid side chain in a predefined manner. Although these dipeptide isosteres have been employed to orient amino acid side chains mimicking the gauche(-) conformation of chi(1)-space, their ability to project the side chains into an anti orientation has not been evaluated. As a first step toward this goal, the conformationally constrained pseudopeptides 8 and 10 and their corresponding flexible analogues 9 and 11 were prepared and tested as inhibitors of matrix metalloproteinases (MMPs). These compounds are analogues of 4 and 5, which were known to be potent MMP inhibitors. The anti orientations of the isopropyl side chain in 8 and the aromatic ring in 10 relative to the peptide backbone substituents on the cyclopropane were predicted to correspond to the known orientations of the P1' and P2' side chains of 5 when bound to MMPs. Hence, 8 and 10 were designed explicitly to probe topological features of the S1' or the S2' binding pockets of the MMPs. They were also designed to explore the importance of the P1'-P2' amide group, which is known to form highly conserved hydrogen bonds in several MMP-inhibitor complexes, and the viability of introducing a retro amide linkage between P2' and P3'. Pseudopeptides 8 and 9 were found to be weak competitive inhibitors of a series of MMPs. Any entropically favorable conformational constraints that were induced by the cyclopropane in 8 were thus overwhelmed by the loss of the hydrogen bonding capability associated with the P1'-P2' amide group. On the other hand, compounds 10 and 11, which contain a P2'-P3' retro amide group, were modest competitive inhibitors of a series of MMPs. The results obtained for 10 and 11 suggest that there may be a loss of hydrogen bonding capability associated with introducing the P2'-P3' retro amide group. However, because the conformationally constrained pseudopeptide 10 was significantly more potent than its flexible analogue 11, trisubstituted cyclopropanes related to 3 may serve as useful rigid dipeptide replacements in some biologically active pseudopeptides.

Distributed structure-searchable toxicity (DSSTox) public database network: a proposal

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, Structure–Activity Relationship (SAR) model development, or building of chemical relational databases (CRD). The distributed structure-searchable toxicity (DSSTox) public database network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: (1) to adopt and encourage the use of a common standard file format (structure data file (SDF)) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; (2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure–toxicity data files, and that will effectively link knowledgeable toxicity data sources with potential users of these data from other disciplines (such as chemistry, modeling, and computer science); and (3) to engage public/commercial/academic/industry groups in contributing to and expanding this community-wide, public data sharing and distribution effort. The DSSTox project’s overall aims are to effect the closer association of chemical structure information with existing toxicity data, and to promote and facilitate structure-based exploration of these data within a common chemistry-based framework that spans toxicological disciplines.