TargetNet: a web service for predicting potential drug–target interaction profiling via multi-target SAR models

Drug–target interactions (DTIs) are central to current drug discovery processes and public health fields. Analyzing the DTI profiling of the drugs helps to infer drug indications, adverse drug reactions, drug–drug interactions, and drug mode of actions. Therefore, it is of high importance to reliably and fast predict DTI profiling of the drugs on a genome-scale level. Here, we develop the TargetNet server, which can make real-time DTI predictions based only on molecular structures, following the spirit of multi-target SAR methodology. Naïve Bayes models together with various molecular fingerprints were employed to construct prediction models. Ensemble learning from these fingerprints was also provided to improve the prediction ability. When the user submits a molecule, the server will predict the activity of the user’s molecule across 623 human proteins by the established high quality SAR model, thus generating a DTI profiling that can be used as a feature vector of chemicals for wide applications. The 623 SAR models related to 623 human proteins were strictly evaluated and validated by several model validation strategies, resulting in the AUC scores of 75–100 %. We applied the generated DTI profiling to successfully predict potential targets, toxicity classification, drug–drug interactions, and drug mode of action, which sufficiently demonstrated the wide application value of the potential DTI profiling. The TargetNet webserver is designed based on the Django framework in Python, and is freely accessible at http://targetnet.scbdd.com.     

Structure-based grafting and identification of kinase–inhibitors to target mTOR signaling pathway as potential therapeutics for glioblastoma

Mammalian target of rapamycin (mTOR), a key mediator of PI3K/Akt/mTOR signaling pathway, has recently emerged as a compelling molecular target in glioblastoma. The mTOR is a member of serine/threonine protein kinase family that functions as a central controller of growth, proliferation, metabolism and angiogenesis, but its signaling is dysregulated in various human diseases especially in certain solid tumors including the glioblastoma. Here, considering that there are various kinase inhibitors being approved or under clinical or preclinical development, it is expected that some of them can be re-exploited as new potent agents to target mTOR for glioblastoma therapy. To achieve this, a synthetic pipeline that integrated molecular grafting, consensus scoring, virtual screening, kinase assay and structure analysis was described to systematically profile the binding potency of various small-molecule inhibitors deposited in the protein kinase–inhibitor database against the kinase domain of mTOR. Consequently, a number of structurally diverse compounds were successfully identified to exhibit satisfactory inhibition profile against mTOR with IC₅₀ values at nanomolar level. In particular, few sophisticated kinase–inhibitors as well as a flavonoid myricetin showed high inhibitory activities, which could thus be considered as potential lead compounds to develop new potent, selective mTOR–inhibitors. Structural examination revealed diverse nonbonded interactions such as hydrogen bonds, hydrophobic forces and van der Waals contacts across the complex interface of mTOR with myricetin, conferring both stability and specificity for the mTOR–inhibitor binding.     

Synthesis of new potential chelating agents: Catechol–bisphosphonate conjugates for metal intoxication therapy

In a quest for better chelating therapy drugs for the treatment of intoxication by Fe, Al, or actinides, three new series of bisphosphonates conjugated with catechol were synthesized. © 2004 Wiley Periodicals, Inc. Heteroatom Chem 15:251–257, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20013     

Water-Mediated Strecker Reaction: An Efficient and Environmentally Friendly Approach for the Synthesis of α-Aminonitriles via a Three-Component Condensation

The synthesis of α-aminonitriles by a direct three component Strecker reaction has been achieved in water, which is found to be an inexpensive, non-toxic and eco-friendly reaction medium for the nucleophilic addition. This protocol is effective to a wide variety of substrates with different functional groups and does not require the use any other catalyst.     

Construction of highly functional α-amino nitriles via a novel multicomponent tandem organocatalytic reaction: a facile access to α-methylene γ-lactams

The first tertiary amine-catalyzed multicomponent tandem Strecker-allylic-alkylation (SAA) reaction has been developed, which provides a facile access to functionalized α-amino nitriles, which could be readily converted into α-methylene-γ-butyrolactams.     

Noncovalent organocatalysis: a powerful tool for the nucleophilic epoxidation of α-ylideneoxindoles

A novel asymmetric nucleophilic epoxidation for α-ylideneoxindole esters has been successfully devised, resulting in enantioenriched spiro compounds with two new contiguous stereocenters. The employed (S)-α,α-diphenylprolinol functions as a bifunctional catalyst, creating a complex H-bond network in conjunction with a substrate and an oxidant.     

Expeditious Synthesis of a Trisubstrate Analogue for α(1→3)Fucosyltransferase

Abstract

The synthesis of cyclohexyl 2-acetamido-2-deoxy-3-O-{2-O-[2-(guanosine 5′-O-phosphate)ethyl]-α-L-fucopyranosyl}-β-D-glucopyranoside (1), a potential inhibitor of α(1→3)fucosyltransferases, is described. Target compound 1 was assembled via fucosylation of cyclohexyl 2-acetamido-2-deoxy-4,6-O-isopropylidene-β-D-glucopyranoside (6) with ethyl 2-O-[2-(benzoylhydroxy)ethyl]-3,4-O-isopropylidene-1-thio-β-L-fucopyranoside (5) followed by debenzoylation, subsequent condensation of the resulting compound with 3′,4′ -di-O-benzoyl-5′ -O-(2-cyanoethyl-N,N-diisopropylphosphoramidite)-2-N-diphenylacetylguanosine (10) and deprotection.     

The first total synthesis of ganglioside GalNAc-GD1a, a target molecule for autoantibodies in Guillain-Barré syndrome

The first synthesis of ganglioside GalNAc-GD1a, featuring efficient glycan assembly and a cyclic glucosyl ceramide as a versatile unit for ganglioside synthesis is described. Although ganglioside GalNAc-GD1a was first found as a brain ganglioside, IgG autoantibodies to GalNAc-GD1a were subsequently found to be closely related to a human peripheral-nerve disorder, Guillain-Barré syndrome, which is the commonest cause of acute flaccid paralysis worldwide. In this study, the characteristic hexasaccharide part carrying two sialic acid residues was synthesized efficiently by use of a readily accessible GM2-core unit as a common unit. The potentially difficult coupling of the oligosaccharide and ceramide moieties was carried out by using a cyclic glucosyl ceramide as a coupling partner for the hexasaccharide part, thereby successfully providing the framework of the target compound. Global deprotection delivered the homogenous ganglioside GalNAc-GD1a. An enzyme-linked immunosorbent assay showed that sera from patients with Guillain-Barré syndrome reacted both with natural and with synthetic GalNAc-GD1a.     

Practical synthesis of C1–8 fragment of autolytimycin via a chelation-controlled diastereoselective addition of diisopropenylzinc to α-methoxy aldehyde

The C1–8 fragment of autolytimycin was synthesized via a reliable 10-step route capable of delivering 41% overall yield at multi-gram scale. As a key step, a chelation-controlled isopropenylation of α-oxygenated aldehydes was established with a reagent combination of diisopropenylzinc, magnesium halide, and a dichloromethane/toluene mixed solvent. Cram-chelate isopropenylation products dominated for aldehydes with a small α-substituents, such as –OMe and –OBn groups, while the Felkin product could be obtained with a bulky –OTBS group.     

Modification strategies of TiO2 for potential applications in photocatalysis: a critical review

TiO₂ has received tremendous attention owing to its potential applications in the field of photocatalysis for solar fuel production and environmental remediation. This review mainly describes various modification strategies and potential applications of TiO₂ in efficient photocatalysis. In past few years, various strategies have been developed to improve the photocatalytic performance of TiO₂, including noble metal deposition, elemental doping, inorganic acids modification, heterojunctions with other semiconductors, dye sensitization and metal ion implantation. The enhanced photocatalytic activities of TiO₂-based material for CO₂ conversion, water splitting and pollutants degradation are highlighted in this review.     

N-Chlorosuccinimide as a versatile reagent for the sulfenylation of ketones: a facile synthesis of α-ketothioethers

The sulfenylation of ketones having α-hydrogens has been achieved using N-chlorosuccinimide (NCS) under mild reaction conditions to produce α-ketothioethers in excellent yields with high selectivity. The use of NCS makes this method quite simple, convenient and practical.     

Metal-amyloid-β peptide interactions: a preliminary investigation of molecular mechanisms for Alzheimer''''s disease

Although humans have spent exactly 100 years combating Alzheimer's disease (AD), the molecular mechanisms of AD remain unclear. Owing to the rapid growth of the oldest age groups of the population and the continuous increase of the incidence of AD, it has become one of the crucial problems to modern sciences. It would be impossible to prevent or reverse AD at the root without elucidating its molecular mechanisms. From the point of view of metal-amyloid-β peptide (Aβ) interactions, we review the molecular mechanisms of AD, mainly including Cu2 and Zn2 inducing the aggregation of Aβ, catalysing the production of active oxygen species from Aβ, as well as interacting with the ion-channel-like structures of Aβ. Moreover, the development of therapeutic drugs on the basis of metal-Aβ interactions is also briefly introduced. With the increasingly rapid progress of the molecular mechanisms of AD, we are now entering a new dawn that promises the delivery of revolutionary developments for the control of dementias.     

One-pot synthesis of α-aminonitriles from alkyl and aryl cyanides: a Strecker reaction via aldimine alanes

A one-pot Strecker reaction using various alkyl, arylalkyl and arylnitriles is developed. Aldimine alanes were generated in situ from nitriles by the addition of diisobutylaluminium hydride, and were converted into the corresponding imines on reaction with (S)-(−)-1-phenylethylamine. Nucleophilic addition to the imines in the presence of catalytic triethylamine, using acetone cyanohydrin as a cyanide source, provided α-aminonitriles.     

Chiral symmetry breaking via crystallization of the glycine and α-amino acid system: a mathematical model

We introduce and numerically solve a mathematical model of the experimentally established mechanisms responsible for the symmetry breaking transition observed in the chiral crystallization experiments reported by I. Weissbuch, L. Addadi, L. Leiserowitz and M. Lahav, J. Am. Chem. Soc., 1988, 110, 561-567. The mathematical model is based on five basic processes: (1) the formation of achiral glycine clusters in solution, (2) the nucleation of oriented glycine crystals at the air/water interface in the presence of hydrophobic amino acids, (3) a kinetic orienting effect which inhibits crystal growth, (4) the enantioselective occlusion of the amino acids from solution, and (5) the growth of oriented host glycine crystals at the interface. We translate these processes into differential rate equations. We first study the model with the orienting process (2) without (3) and then combine both allowing us to make detailed comparisons of both orienting effects which actually act in unison in the experiment. Numerical results indicate that the model can yield a high percentage orientation of the mixed crystals at the interface and the consequent resolution of the initially racemic mixture of amino acids in solution. The model thus leads to separation of enantiomeric territories, the generation and amplification of optical activity by enantioselective occlusion of chiral additives through chiral surfaces of glycine crystals.     

Asymmetric Synthesis of α-Methylene-γ-Butyrolactones via Tandem Allylboration/Lactonization: a Kinetic Resolution Process

The α-methylene-γ-butyrolactone motif is a widely encountered unit in many natural products and pharmaceutical compounds. Herein, a practical and efficient synthesis of α-methylene-γ-butyrolactones from readily available allylic boronates and benzaldehyde derivatives was developed with chiral N,N′-dioxide/Al^III complex as the catalyst. The key success of this transformation was the kinetic resolution of allylboration intermediate via asymmetric lactonization. This protocol enabled to assemble all of four stereoisomers from the same set of starting materials upon variable lactonization. Taking advantage of the current method as the key step, catalytic asymmetric total synthesis of eupomatilones 2 , 5 , and 6 was accomplished. Control experiments were carried out to probe into the tandem reaction as well as the origin of stereoselectivities.     

Syntheses and pyrolyses of furan analogues of α-oxo-o-quinodimethanes. Formation of methylenecyclobutenone and 1-buten-3-yne via a vinylcarbene-cyclopropene rearrangement

Flash vacuum pyrolyses (FVP) of benzoic 2-methyl-3-furoic anhydride (12) and benzoic 3-methyl-2-furoic anhydride (13) at 550 °C and ca. 10(-2) Torr both give methylenecyclobutenone (16) and 1-buten-3-yne (17) as the main products. A mechanism involving generation of furan analogues of α-oxo-o-quinodimethane, 10 and 11, from FVP of 12 and 13, respectively, followed by elimination of a CO molecule to give the respective carbenes 34 and 36 is proposed. Carbenes 34 and 36 are interconvertible via a cyclopropene intermediate 35. A ring contraction from 36 will give 16, whereas a ring-opening of 34 followed by elimination of a CO molecule then leads to 17. The proposed mechanism is supported by substituent- and deuterium-labeling study on FVP of the derivatives of 12.     

1-(1-Alkenyl)benzotriazoles: Novel α-Hydroxyacyl Anion Equivalents for the Synthesis of α-Hydroxy Ketones

α-Lithiated 1-(1-alkenyl)benzotriazoles, generated from the reactions of 1-(1-alkenyl)benzotriazoles with n-BuLi, react with a variety of electrophiles to afford α-substituted 1-(1-alkenyl)benzotriazoles which undergo epoxidation with m-CPBA followed by hydrolysis to give α-hydroxy ketones in good yields. Thus, 1-(1-alkenyl)benzotriazoles behave as α-hydroxyacyl anion equivalents.     

Synthesis of novel zerumbone derivatives via regioselective palladium catalyzed decarboxylative coupling reaction: a new class of α-glucosidase inhibitors

A new strategy for the synthesis of novel zerumbone derivatives via a regioselective palladium catalyzed decarboxylative coupling reaction using arene carboxylic acids is described. The current methodology involves the repositioning of endocyclic double bond to exocyclic double bond of zerumbone. Preliminary in vitro analysis revealed that most of the newly synthesized derivatives are potent α-glucosidase enzyme inhibitors.