Shanghai Institute of Organic Chemistry

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.

Most protein phosphatases have little intrinsic substrate specificity, making selective pharmacological inhibition of specific dephosphorylation reactions a challenging problem. In a screen for small molecules that protect cells from endoplasmic reticulum (ER) stress, we identified salubrinal, a selective inhibitor of cellular complexes that dephosphorylate eukaryotic translation initiation factor 2 subunit alpha (eIF2alpha). Salubrinal also blocks eIF2alpha dephosphorylation mediated by a herpes simplex virus protein and inhibits viral replication. These results suggest that selective chemical inhibitors of eIF2alpha dephosphorylation may be useful in diseases involving ER stress or viral infection. More broadly, salubrinal demonstrates the feasibility of selective pharmacological targeting of cellular dephosphorylation events.

This Review summarizes the development of catalytic asymmetric dearomatization (CADA) reactions. The CADA reactions discussed herein include oxidative dearomatization reactions, dearomatization by Diels-Alder and related reactions, the alkylative dearomatization of electron-rich arenes, transition-metal-catalyzed dearomatization reactions, cascade sequences involving asymmetric dearomatization as the key step, and nucleophilic dearomatization reactions of pyridinium derivatives. Asymmetric dearomatization reactions with chiral auxiliaries and catalytic asymmetric reactions of dearomatized substrates are also briefly introduced. This Review intends to provide a concept for catalytic asymmetric dearomatization.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTGood Partnership between Sulfur and Fluorine: Sulfur-Based Fluorination and Fluoroalkylation Reagents for Organic SynthesisChuanfa Ni, Mingyou Hu, and Jinbo Hu*View Author Information Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling−Ling Road, Shanghai City, Shanghai 200032, China*E-mail: [email protected]Cite this: Chem. Rev. 2015, 115, 2, 765–825Publication Date (Web):August 21, 2014Publication History Received1 May 2014Published online21 August 2014Published inissue 28 January 2015https://doi.org/10.1021/cr5002386Copyright © 2014 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views30150Altmetric-Citations919LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (16 MB) Get e-AlertscloseSUBJECTS:Anions,Chemical reactions,Reagents,Salts,Sulfones Get e-Alerts

For green and sustainable chemistry, molecular oxygen is considered as an ideal oxidant due to its natural, inexpensive, and environmentally friendly characteristics, and therefore offers attractive academic and industrial prospects. This critical review introduces the recent advances over the past 5 years in transition-metal catalyzed reactions using molecular oxygen as the oxidant. This review highlights the scope and limitations, as well as the mechanisms of these oxidation reactions (184 references).

Allenes are the simplest class of cumulenes, with two contiguous C=C bonds, and show unique physical and chemical properties. These features make allenes particularly attractive in modern organic chemistry. In this Review, attention is paid to the advances made in catalytic asymmetric synthesis and natural product syntheses based on well-established reactions of allenes, such as propargylation, addition, cycloaddition, cycloisomerization, cyclization, etc., with or without catalysts. Their versatile reactivity, substituent-loading ability, axial to center chirality transfer, and controllable selectivity allow access to target molecules by unique and efficient approaches. The main topics in this Review are presented with selected examples from 2003 to 2011.

Copper-assisted Ullmann-type coupling reactions are valuable transformations for organic synthesis. Researchers have extensively applied these reactions in both academic and industrial settings. However, two important issues, the high reaction temperatures (normally above 150 degrees C) and the stoichiometric amounts of copper necessary, have greatly limited the reaction scope. To solve these problems, we and other groups have recently explored the use of special ligands to promote these coupling reactions. We first showed that the structure of alpha-amino acids can accelerate Cu-assisted Ullmann reactions, leading to the coupling reactions of aryl halides and alpha-amino acids at 80-90 degrees C. In response to these encouraging results, we also discovered that an l-proline ligand facilitated the following transformations: (1) coupling of aryl halides with primary amines, cyclic secondary amines, and N-containing heterocycles at 40-90 degrees C; (2) coupling of aryl halides with sulfinic acid salts at 80-95 degrees C; (3) azidation of aryl halides and vinyl halides with sodium azide at 40-95 degrees C; (4) coupling of aryl halides with activated methylene compounds at 25-50 degrees C. In addition, we found that N,N-dimethylglycine as a ligand facilitated Cu-catalyzed biaryl ether formation at 90 degrees C. Moreover, Sonogashira reactions worked in the absence of palladium and phosphine ligands, forming enamides from vinyl halides and amides at temperatures ranging from ambient temperature up to 80 degrees C. Furthermore, we discovered that an ortho-amide group can accelerate some Ullmann-type reactions. This functional group in combination with other ligand effects allowed for aryl amination or biaryl ether formation at ambient temperature. The coupling between aryl halides and activated methylene compounds even proceeded at -45 degrees C to enantioselectively form a quaternary carbon center. Taking advantage of these results, we developed several novel approaches for the synthesis of pharmaceutically important heterocycles: 1,2-disubstituted benzimidazoles, polysubstituted indoles, N-substituted 1,3-dihydrobenzimidazol-2-ones, and substituted 3-acyl oxindoles. Our results demonstrate that an l-proline or N,N-dimethylglycine ligand can facilitate most typical Ullmann-type reactions, with reactions occurring under relatively mild conditions and using only 2-20 mol % copper catalysts. These conveniently available and inexpensive catalytic systems not only accelerate the reactions but also tolerate many more functional groups. Thus, they should find considerable application in organic synthesis.

International audience

ADVERTISEMENT RETURN TO ISSUEPREVReviewTransition-Metal-Free Coupling ReactionsChang-Liang Sun and Zhang-Jie Shi*View Author Information Beijing National Laboratory of Molecular Sciences (BNLMS) and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Green Chemistry Center, Peking University, 202 Chengfu Road, 098#, Beijing 100871, China State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 200060, China*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 18, 9219–9280Publication Date (Web):September 3, 2014Publication History Received18 May 2013Published online3 September 2014Published inissue 24 September 2014https://pubs.acs.org/doi/10.1021/cr400274jhttps://doi.org/10.1021/cr400274jreview-articleACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views34901Altmetric-Citations908LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aromatic compounds,Cross coupling reaction,Hydrocarbons,Reagents,Substitution reactions Get e-Alerts

The development of some new synthetic reactions derived from nucleophilic addition of phosphines to electron-deficient carbon-carbon triple bonds is described. These reactions show that the phosphine plays the role of a nucleophile as well as an excellent leaving group. The central problem is to generate a 1,3-dipole from alkynoates or allenoates (2,3-butadienoates) by interaction with various phosphines. This study illuminates the unusual phenomena and shows how this understanding allows control of the reaction.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTRecent Advances in Transition-Metal-Catalyzed Functionalization of Unstrained Carbon–Carbon BondsFeng Chen†, Teng Wang†, and Ning Jiao*†‡View Author Information† State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China‡ State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 17, 8613–8661Publication Date (Web):July 25, 2014Publication History Received1 November 2013Published online25 July 2014Published inissue 10 September 2014https://pubs.acs.org/doi/10.1021/cr400628shttps://doi.org/10.1021/cr400628sreview-articleACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views19417Altmetric-Citations786LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aldehydes,Bond cleavage,Catalysts,Chemical reactions,Hydrocarbons Get e-Alerts

Carbon dioxide is an important carbon source in the atmosphere and is "problematic" toward the activities of human beings. Although carbon dioxide is a cheap, abundant and relatively nontoxic C1 source, its chemical transformations have not been widely developed so far and are still far from synthetic applications, especially in the construction of the C-C bond. This critical review summarizes the recent advances on transition-metal-catalyzed C-C bond formation through the fixation of carbon dioxide and their synthetic applications (124 references).

We have developed a new method, i.e., XLOGP3, for logP computation. XLOGP3 predicts the logP value of a query compound by using the known logP value of a reference compound as a starting point. The difference in the logP values of the query compound and the reference compound is then estimated by an additive model. The additive model implemented in XLOGP3 uses a total of 87 atom/group types and two correction factors as descriptors. It is calibrated on a training set of 8199 organic compounds with reliable logP data through a multivariate linear regression analysis. For a given query compound, the compound showing the highest structural similarity in the training set will be selected as the reference compound. Structural similarity is quantified based on topological torsion descriptors. XLOGP3 has been tested along with its predecessor, i.e., XLOGP2, as well as several popular logP methods on two independent test sets: one contains 406 small-molecule drugs approved by the FDA and the other contains 219 oligopeptides. On both test sets, XLOGP3 produces more accurate predictions than most of the other methods with average unsigned errors of 0.24-0.51 units. Compared to conventional additive methods, XLOGP3 does not rely on an extensive classification of fragments and correction factors in order to improve accuracy. It is also able to utilize the ever-increasing experimentally measured logP data more effectively.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric Ylide Reactions: Epoxidation, Cyclopropanation, Aziridination, Olefination, and Rearrangement†An-Hu Li, Li-Xin Dai, and Varinder K. AggarwalView Author Information Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China Department of Chemistry, Dainton Building, The University of Sheffield, Sheffield S3 7HF, The United KingdomCite this: Chem. Rev. 1997, 97, 6, 2341–2372Publication Date (Web):October 1, 1997Publication History Received10 March 1997Revised28 May 1997Published online1 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/cr960411rhttps://doi.org/10.1021/cr960411rresearch-articleACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views12579Altmetric-Citations775LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Cyclopropanation,Organic reactions,Rearrangement,Salts,Sulfides Get e-Alerts

Developing recyclable polymers provides a solution to materials' end-of-life issues and also an approach to establish a circular materials economy.

Dearomatization reactions serve as powerful methods for the synthesis of highly functionalized, three-dimensional structures starting with simple planar aromatic compounds. Among processes of this type, catalytic asymmetric dearomatization (CADA) reactions are attractive owing to the large number of aromatic compounds that are readily available and the fact that they enable direct access to enantiopure polycycles and spirocycles, which frequently are key structural motifs in biologically active natural products and pharmaceuticals. However, as a consequence of their high stabilities, arenes only difficultly participate in dearomatization reactions that take place with high levels of enantioselectivity. Transition-metal-catalyzed asymmetric allylic substitution reactions have been demonstrated to be powerful methods for enantioselective formation of C-C and C-X (X = O, N, S, etc.) bonds. However, the scope of these processes has been explored mainly using soft carbon nucleophiles, some hard carbon nucleophiles such as enolates and preformed organometallic reagents, and heteroatom nucleophiles. Readily accessible aromatic compounds have been only rarely used directly as nucleophiles in these reactions. In this Account, we present the results of studies we have conducted aimed at the development of transition-metal-catalyzed asymmetric allylic dearomatization reactions. By utilizing this general process, we have devised methods for direct dearomatization of indoles, pyrroles, phenols, naphthols, pyridines, and pyrazines, which produce various highly functionalized structural motifs bearing all-carbon quaternary stereogenic centers in a straightforward manner. In mechanistic investigations of the dearomatization process, we found that the five-membered spiroindolenines serve as intermediates, which readily undergo stereospecific allylic migration to form corresponding tetrahydro-1H-carbazoles upon treatment with a catalytic amount of TsOH. It is worth noting that no notable loss of the enantiomeric excess of the spiroindolenine derivatives takes place during the rearrangement process as a consequence of the intervention of a "three-center-two-electron"-type transition state, a proposal that has gained support from the results of DFT calculations. Equally intriguing, upon tuning of the electronic nature of the tethers, pyrroles or indoles undergo unprecedented Ir or Ru catalyzed intramolecular allylic alkylation promoted dearomatization/migration reactions. The operation of this novel reaction pathway provides additional information leading to a greater mechanistic understanding of the transition-metal-catalyzed enantioselective intramolecular functionalizations of pyrroles and indoles. The combined results of this effort provide not only methods for the efficient synthesis of highly enantioenriched fused and spiro polycycles but also novel strategies in the field of asymmetric catalysis.

In structure-based drug design, scoring functions are often employed to evaluate protein–ligand interactions. A variety of scoring functions have been developed so far, and thus, some objective benchmarks are desired for assessing their strength and weakness. The comparative assessment of scoring functions (CASF) benchmark developed by us provides an answer to this demand. CASF is designed as a “scoring benchmark”, where the scoring process is decoupled from the docking process to depict the performance of scoring function more precisely. Here, we describe the latest update of this benchmark, i.e., CASF-2016. Each scoring function is still evaluated by four metrics, including “scoring power”, “ranking power”, “docking power”, and “screening power”. Nevertheless, the evaluation methods have been improved considerably in several aspects. A new test set is compiled, which consists of 285 protein–ligand complexes with high-quality crystal structures and reliable binding constants. A panel of 25 scoring functions are tested on CASF-2016 as a demonstration. Our results reveal that the performance of current scoring functions is more promising in terms of docking power than scoring, ranking, and screening power. Scoring power is somewhat correlated with ranking power, so are docking power and screening power. The results obtained on CASF-2016 may provide valuable guidance for the end users to make smart choices among available scoring functions. Moreover, CASF is created as an open-access benchmark so that other researchers can utilize it to test a wider range of scoring functions. The complete CASF-2016 benchmark will be released on the PDBbind-CN web server (http://www.pdbbind-cn.org/casf.asp/) once this article is published.

In this review, we summarize the origin and advancements of iridium-catalyzed asymmetric allylic substitution reactions during the past two decades. Since the first report in 1997, Ir-catalyzed asymmetric allylic substitution reactions have attracted intense attention due to their exceptionally high regio- and enantioselectivities. Ir-catalyzed asymmetric allylic substitution reactions have been significantly developed in recent years in many respects, including ligand development, mechanistic understanding, substrate scope, and application in the synthesis of complex functional molecules. In this review, an explicit outline of ligands, mechanism, scope of nucleophiles, and applications is presented.

In this tutorial review, we will summarize our recent efforts in transition metal-catalyzed oxidative coupling via C-H functionalization of aromatic, benzylic and allylic C-H bonds. Related works from other laboratories will be cited where suitable, aiming to give the readers a flavor of this field. Special emphasis is placed on the reaction design and development.