2-Methoxy-2,4-diphenyl-3(2H)-furanone-labeled gelatin zymography and reverse zymography: a rapid real-time method for quantification of matrix metalloproteinases-2 and -9 and tissue inhibitors of metalloproteinases

Measurement of matrix metalloproteinases (MMPs) and their specific tissue inhibitors of metalloproteinases (TIMPs) by the techniques of zymography and reverse zymography provide useful information regarding the status of matrix accumulation or breakdown. This report describes the use of 2-methoxy-2,4-diphenyl-3(2H)-furanone (MDPF), a fluorescent compound which can be used to label gelatin as a substrate for detection of the gelatin degrading MMP-2 and -9 by zymography. In addition, a modification of the zymographic technique by addition of excess MMPs enables the use of the MDPF-labeled gelatin substrate for the identification and quantification of TIMPs by reverse zymography. Both systems are real-time sensitive reliable quantification techniques, easily used for measurement of these MMPs and TIMPs in clinical, biological, and tissue culture samples.     

A Versatile Approach to CF3‐Containing 2‐Pyrrolidones by Tandem Michael Addition–Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors

The synthesis of new fluorinated pyrrolidones starting from unprotected amino esters and amino nitriles through a Michael addition–lactamization sequence is described. The resulting CF₃‐containing building blocks, bearing a quaternary stereogenic center adjacent to the fluorinated group, have been converted into amino pyrrolidines that display potent β‐secretase 1 (BACE1) inhibitory activity. This work constitutes an example of selective fluorination as a valid strategy for the modulation of physicochemical and biological properties of lead compounds in drug discovery.     

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded a previously used diverse "cross-docking" benchmark to thirty ligand-protein pairs extracted from different crystal structures. The algorithm systematically scans pairs of neighbouring side chains, replaces them by alanines, and docks the ligand to each 'gapped' version of the pocket. All docked positions are scored, refined with original side chains and flexible backbone and re-scored. In the optimal version of the protocol pairs of residues were replaced by alanines and only one best scoring conformation was selected from each 'gapped' pocket for refinement. The optimal SCARE (SCan Alanines and REfine) protocol identifies a near native conformation (under 2 angstroms RMSD) as the lowest rank for 80% of pairs if the docking bounding box is defined by the predicted pocket envelope, and for as many as 90% of the pairs if the bounding box is derived from the known answer with approximately 5 angstroms margin as used in most previous publications. The presented fully automated algorithm takes about 2 h per pose of a single processor time, requires only one pocket structure and no prior knowledge about the binding site location. Furthermore, the results for conformationally conserved pockets do not deteriorate due to substantial increase of the pocket variability.     

Evaluation of designed ligands by a multiple screening method: Application to glycogen phosphorylase inhibitors constructed with a variety of approaches

Glycogen phosphorylase (GP) is an important enzyme that regulates blood glucose level and a key therapeutic target for the treatment of type II diabetes. In this study, a number of potential GP inhibitors are designed with a variety of computational approaches. They include the applications of MCSS, LUDI and CoMFA to identify additional fragments that can be attached to existing lead molecules; the use of 2D and 3D similarity-based QSAR models (HQSAR and SMGNN) and of the LUDI program to identify novel molecules that may bind to the glucose binding site. The designed ligands are evaluated by a multiple screening method, which is a combination of commercial and in-house ligand-receptor binding affinity prediction programs used in a previous study (So and Karplus, J. Comp.-Aid. Mol. Des., 13 (1999), 243–258). Each method is used at an appropriate point in the screening, as determined by both the accuracy of the calculations and the computational cost. A comparison of the strengths and weaknesses of the ligand design approaches is made.     

Protein Alpha Shape Similarity Analysis (PASSA): a new method for mapping protein binding sites. Application in the design of a selective inhibitor of tyrosine kinase 2

We have developed a method that we have called Protein Alpha Shape Similarity Analysis (PASSA), that identifies interaction sites that can be utilised to achieve selectivity towards a protein. We have shown that this method is able to identify residues of tyrosine kinases that interact with known selective inhibitors using the following test cases: Abelson (Abl) kinase in complex with STI-571 and Janus kinase 2 (Jak2) in complex with AG-490. The 3D structures of the tyrosine kinase domains of Tyrosine kinase 2 (Tyk2) and Jak2 have been predicted by homology modelling. Computational docking of AG-490 and a set of tyrphostins known not to inhibit Jak2 indicated that our homology models are able to separate inhibitors from non-inhibitors. PASSA has also been used to identify unique properties of Tyk2. According to our results, interactions with hydrogen acceptors and donors on the following residues can be utilised to achieve selectivity towards Tyk2: Y955, E1053, D1062 and S1063. These residues are placed close to non-conserved hydrophobic pockets. The PASSA results, together with results from Multiple Copy Simultaneous Search (MCSS) were used to suggest functional groups of a selective Tyk2 inhibitor.     

Biofilm-i: A Platform for Predicting Biofilm Inhibitors Using Quantitative Structure—Relationship (QSAR) Based Regression Models to Curb Antibiotic Resistance

Antibiotic drug resistance has emerged as a major public health threat globally. One of the leading causes of drug resistance is the colonization of microorganisms in biofilm mode. Hence, there is an urgent need to design novel and highly effective biofilm inhibitors that can work either synergistically with antibiotics or individually. Therefore, we have developed a recursive regression-based platform “Biofilm-i” employing a quantitative structure–activity relationship approach for making generalized predictions, along with group and species-specific predictions of biofilm inhibition efficiency of chemical(s). The platform encompasses eight predictors, three analysis tools, and data visualization modules. The experimentally validated biofilm inhibitors for model development were retrieved from the “aBiofilm” resource and processed using a 10-fold cross-validation approach using the support vector machine and andom forest machine learning techniques. The data was further sub-divided into training/testing and independent validation sets. From training/testing data sets the Pearson’s correlation coefficient of overall chemicals, Gram-positive bacteria, Gram-negative bacteria, fungus, Pseudomonas aeruginosa, Staphylococcus aureus, Candida albicans, and Escherichia coli was 0.60, 0.77, 0.62, 0.77, 0.73, 0.83, 0.70, and 0.71 respectively via Support Vector Machine. Further, all the QSAR models performed equally well on independent validation data sets. Additionally, we also checked the performance of the random forest machine learning technique for the above datasets. The integrated analysis tools can convert the chemical structure into different formats, search for a similar chemical in the aBiofilm database and design the analogs. Moreover, the data visualization modules check the distribution of experimentally validated biofilm inhibitors according to their common scaffolds. The Biofilm-i platform would be of immense help to researchers engaged in designing highly efficacious biofilm inhibitors for tackling the menace of antibiotic drug resistance.     

二羰基二茂钛和酚类的反应: 合成二芳氧基二环戊二烯基钛的新途径

本文介绍在缓和条件下, 二羰基二茂钛和酚类反应是合成二芳氧基二环戊二烯基钛的新途径, 得到的新化合物都经过元素分析和^1HNMR测定。     

Total synthesis of (-)-balanol, all stereoisomers, their N-tosyl analogues, and fully protected ophiocordin: an easy route to hexahydroazepine cores from garner aldehydes

Total syntheses of (-)-balanol and all of its stereoisomers starting from easily available Garner aldehydes are described. Diastereoselective Grignard reactions on Garner aldehydes and ring-closing metatheses are the key steps for the construction of hexahydroazepine subunits. The benzophenone subunits were constructed through coupling of suitably functionalized aromatic aldehyde and bromo components. The synthetic route constitutes a convenient and scalable reaction sequence to generate all of the stereoisomers of balanol. The methodology is explored further for the synthesis of N-tosyl analogues of balanol and of fully protected ophiocordin.     

To the Knowledge of Interpseudohalogens: A Contribution to Cyanogen Isocyanate (NC–NCO)

Cyanogen isocyanate (NC–NCO) has been prepared and studied using a combined experimental and theoretical approach. A crystalline film of the interpseudohalogen species was stabilized by vapor deposition on a cold substrate (T = –100 °C). From IR spectroscopy on the “free” molecule, trapped in a matrix of solid argon, the connectivity and geometry of this unstable interpseudohalogen was deduced and substantiated by theoretical calculations. With this information, the crystal structure of NCNCO in the solid state could be analysed using powder X‐ray diffraction [Pbca (No. 61), a = 7.63(1) Å, b = 6.50(2) Å, c = 6.03(6) Å; V = 299.5(1) ų]. The compound transforms into amorphous polymeric C₂N₂O at T > –68 °C. The results obtained were compared with recent findings and further discussed in the general context of C–N–(O) chemistry.     

Photochemistry of 5-aryl-2(3H)-furanones. : A new route to the synthesis of chromones

The photochemistry of 5-phenyl-, 5-(2',5'-dimethoxyphenyl)-, 5-(2'-acetoxy-5'-methoxyphenyl)- and 5- (2',5'-diacetoxyphenyl)- 2(3H)-furanone (1a-d) has been investigated. Compound 1a yields phenyl vinyl ketone as expected. Similarly, 1b affords the corresponding aryl vinyl ketone but, in this case, photodimerization also occurs. Irradiation of the two o-acetoxyaryl furanones 1c and 1d gives rise to the formation of chromones as the main products. This interesting result can be accounted for in terms of a photochemical opening of the lactonic ring followed by radical addition to the acetoxy group.     

A Practical Manufacturing Synthesis of 1-(R)-Hydroxymethyl-Dtpa: An Important Intermediate in the Synthesis of MRI Contrast Agents

An efficient synthesis of alcohol 2 is described from L-Serine (OMe) in four synthetic steps. The process uses readily available reagents and is suitable for manufacturing.