Predicting key example compounds in competitors' patent applications using structural information alone

In drug discovery programs, predicting key example compounds in competitors' patent applications is important work for scientists working in the same or in related research areas. In general, medicinal chemists are responsible for this work, and they attempt to guess the identity of key compounds based on information provided in patent applications, such as biological data, scale of reaction, and/or optimization of the salt form for a particular compound. However, this is sometimes made difficult by the lack of such information. This paper describes a method for predicting key compounds in competitors' patent applications by using only structural information of example compounds. Based on the assumption that medicinal chemists usually carry out extensive structure--activity relationship (SAR) studies around key compounds, the method identifies compounds located at the centers of densely populated regions in the patent examples' chemical space, as represented by Extended Connectivity Fingerprints (ECFPs). For the validation of the method, a total of 30 patents containing structures of launched drugs were selected to test whether or not the method is able to predict key compounds (the launched drugs). In 17 out of the 30 patents (57%), the method was able to successfully predict the key compounds. The result indicates that our method could provide an alternative approach to predicting key compounds in cases where the conventional medicinal chemist's approach does not work well. This method could also be used as a complement to the traditional medicinal chemist's approach.     

Enantioselective total synthesis of FD-891

The enantioselective synthesis of FD-891 has been achieved with a longest linear sequence of 21 steps. The synthetic strategy involves the use of aldol additions of a chlorotitanium enolate of N-acylthiazolidinethiones as the key reaction to establish 6 of the 10 stereogenic centers. A key cross-metathesis and a late-stage Julia olefination serve to assemble three key subunits.     

Chromene "lock", thiol "key", and mercury(II) ion "hand": a single molecular machine recognition system

A regenerative, molecular machine-like "ON-OFF-ON" chemosensor based on a chromene molecule with the pyran ring "OFF-ON-OFF" cycle is reported for the first time. It behaves as a molecular lock that requires a thiol "key" to open the lock and a mercury(II) ion "hand" that unlatches the key for unsheathing the key to close the lock.     

Efficient Synthesis of Beraprost Sodium

An efficient and straightforward synthesis of beraprost sodium was developed with dicyclopentadiene as a starting material, a one-pot reaction product 5 as key intermediate and the Prins reaction and the Horner-Wads- worth-Emmons reaction as key steps. The structures of the key intermediate and the target compound were confirmed by ¹H NMR, ¹³C NMR and MS. The purity of beraprost sodium identified by high performance liquid chromatography(HPLC) was identical to that of Japanese Pharmacopoeia(16^th). This development will be used for the industrial synthesis of beraprost sodium.     

Formal total synthesis of (±)-cortistatin A

A second-generation synthesis of the pentacyclic core of the cortistatins, a family of rearranged steroidal alkaloids that have recently attracted much attention, is reported. The improved sequence provides access to significant quantities of this key compound, which enabled a formal total synthesis of (±)-cortistatin A by conversion to the key Nicolaou/Hirama dienone. It is anticipated that this new, robust route to the pentacyclic core will facilitate the total synthesis of a range of natural products in the cortistatin family, as well as the construction of key structural analogs to probe the promising biological activity of these important compounds.     

Proline organocatalysis as a new tool for the asymmetric synthesis of ulosonic acid precursors

PEP and aldolase mimicry is the key for a direct organocatalytic entry to precursors of ulosonic acids, biomolecules of enormous importance in biology, chemistry and medicine; in the key aldol reaction the dimethylacetal of pyruvic aldehyde is used as phosphoenolpyruvate (PEP) equivalent and the amino acid proline functions as an organocatalyst, imitating the enzyme.     

Identifying condition specific key genes from basal-like breast cancer gene expression data

Mining patterns of co-expressed genes across the subset of conditions help to narrow down the search space for the analysis of gene expression data. Identifying conditions specific key genes from the large-scale gene expression data is a challenging task. The conditions specific key gene signifies functional behavior of a group of co-expressed genes across the subset of conditions and can be act as biomarkers of the diseases. In this paper, we have propose a novel approach for identification of conditions specific key genes from Basal-Like Breast Cancer (BLBC) disease using biclustering algorithm and Gene Co-expression Network (GCN). The proposed approach is a two-stage approach. In the first stage, significant biclusters have been extracted with the help of ‘runibic’ biclustering algorithm. The second stage identifies conditions specific key genes from the extracted significant biclusters with the help of GCN. By using difference matrix and gene correlation matrix, we have constructed biologically meaningful and statistically strong GCN. Also, presented the proposed approach with the help of a process diagram and demonstrated the procedure with an example of bicluster number 93 (Bic93). From the experimental results, we observed that 95% and 85% of the extracted biclusters are found to be biologically significant at the p-values less than 0.05 and 0.01 respectively. We have compared proposed approach with the Weighted Gene Co-expression Network Analysis (WGCNA) based approach. From the comparison, our approach has performed effectively and extracted biologically significant biclusters. Also, identified conditions specific key genes which cannot be extracted using the WGCNA based approach. Some of the important identified known key genes are PIK3CA, SHC3, ERBB2, SHC4, PTOV1, STAG1, ZNF215 etc. These key genes can be used as a diagnostic and prognostic biomarker for the BLBC disease after the rigorous analysis. The identified conditions specific key genes can be helpful to reduce the analysis time and increase the accuracy of further research such as biomarker identification, drug target discovery etc.     

Identification of key classification features of early cervical squamous cell carcinoma

Despite the tremendous progress in molecular analysis of pan-cancer, little is known regarding molecular classification of cervical squamous cell carcinoma. In this study, we adopted a multi-omics approach to identify potential key classification features of cervical squamous cell carcinoma. Specifically, we analyzed mRNA, and microRNA (miRNA) expression data, as well as DNA methylation and copy number variation in cervical squamous cell carcinoma cases, using datasets obtained from The Cancer Genome Atlas (TCGA). Moreover, we identified molecules in each dimension, as well as integrated and clustered filtered classification features, and used them to distinguish different subtypes. The resulting key classification features were used to establish a classification model for cervical squamous cell carcinoma. Our results revealed two cervical squamous cell carcinoma subtypes, with significant differences across clinical survival levels, as well as 8 key classification features of cervical squamous cell carcinomas. These findings are expected to provide important references for early classification of cervical squamous cell carcinoma and identification of classification markers.     

Progress towards the total synthesis of 2,3-dihydroxytrinervitanes

Intramolecular Diels-Alder approach to construct the fused AB ring of trinervitane has been demonstrated efficiently. The key intermediate for the Diels-Alder cyclization has been achieved following highly stereoselective Julia-Kocienski olefination, Sharpless epoxidation and Evan’s asymmetric alkylation as the key reactions.     

Stereoselective synthesis of functionalized 1,3 diols through the tandem isomerization-aldolization reaction mediated by nickel catalysts

A new approach to functionalized 1,3 diols, such as 15, is described using as the key step the tandem isomerization-aldolization reaction of allylic alcohols 1. The chiral imidazolidine group is shown to play a key role for the stereocontrol during aldolization and reduction steps.     

Chemoenzymatic approaches toward dechloroansamitocin P-3

[reaction: see text] The enantioselective total synthesis of proansamitocin, a key biosynthetic intermediate of the highly potent antitumor agent ansamitocin P-3, is described which bears a diene-ene RCM as the key macrocyclization step. Feeding of proansamitocin to an AHBA block mutant Actinosynnema pretiosum (HGF073) yielded ansamitocin P-3 as well as dechloroansamitocin P-3, the latter also being formed upon fermentation in the presence of 3-amino-5-methoxybenzoic acid.     

Regioselective double Boekelheide reaction: first synthesis of 3,6-dialkylpyrazine-2,5-dicarboxaldehydes from dl-alanine

Pyrazine-2,5-dicarboxaldehyde was synthesized on a multi-gram scale by MnO₂ oxidation of 2,5-bis(hydroxymethyl)pyrazine, which in turn was obtained from 2,5-dimethylpyrazine employing double Boekelheide reaction as a key step as reported previously. This reaction was subsequently utilized in a regioselective fashion as a key step to synthesize efficiently, for the first time, 3,6-di(long-chain)alkylpyrazine-2,5-dicarboxaldehydes starting from dl-alanine. These monomers are certain to have importance as electron deficient and chemically versatile components for new materials development.     

Stereoselective Synthesis of (+)-Nephrosteranic Acid by Ring-Closing Metathesis and Its Biological Evaluation

A simple and efficient approach to (+)-nephrosteranic acid from dodecanol as a starting material is described, employing Sharpless asymmetric epoxidation, ring-closing metathesis, and Gilman addition of a vinyl group as key steps. These key reactions allow fast access to trisubstituted γ-butyrolactone. The molecule synthesized exhibits potent antifungal, antibacterial, and cytotoxic activities against all the tested strains.     

A convergent synthesis of the right-hand fragment of ciguatoxin CTX3C

A convergent synthesis of the right-hand fragment of ciguatoxin CTX3C was investigated. The first and second generation stereocontrolled syntheses of the LM ring fragment were achieved via spiroacetalization as a key step, respectively. The polyether framework of the HIJKLM ring fragment was constructed in a convergent manner by using intramolecular allylation, ring-closing metathesis, and stereoselective hydrogenation to form the 36-methyl substituent as the key transformations.     

Second-generation total synthesis of haterumalide NA using B-alkyl Suzuki-Miyaura coupling

Second-generation total synthesis of haterumalide NA, a potent cytotoxic marine macrolide, was achieved by using B-alkyl Suzuki-Miyaura coupling and Nozaki-Hiyama-Kishi coupling as key steps (1.2% in 33 steps). Compared to our first-generation approach, the second-generation synthesis is much improved in the yield of key intermediate.     

Mukaiyama-Michael reactions with acrolein and methacrolein: a catalytic enantioselective synthesis of the C17-C28 fragment of pectenotoxins

Enantioselective iminium-catalyzed reactions with acrolein and methacrolein are rare. A catalytic enantioselective Mukaiyama-Michael reaction that readily accepts acrolein or methacrolein as substrates, affording the products in good yields and 91-97% ee, is presented. As an application of the methodology, an enantioselective route to the key C17-C28 segment of the pectenotoxin using the Mukaiyama-Michael reaction as the key step is described.     

A Facile Route for the Synthesis of Novel Heterocyclic Prostaglandin F2α Analogs

A general synthetic approach has been developed for heterocyclic prostaglandins (PGF_2α type) starting from the key intermediate ( 6 ). (±) 6 was obtained from (±) ‐Corey lactone. The key intermediate (±) 6 was, in turn, converted in to several new heterocyclic prostaglandins consisting of furan and thiophene moieties in ω‐side chain in two to three steps. Horner–Wadsworth–Emmons reaction and Grignard reaction as the key reactions in these transformations.     

Synthetic approach to cis and trans-decalins via Diels—Alder reaction and ring-closing metathesis as key steps: further extension to dioxapropellane derivative by ring-closing metathesis

9,10-Substituted cis and trans-decalins were synthesized by a simple route using the Diels-Alder reaction and ring-closing metathesis (RCM) as key steps. Later, the cis-decalin system has been extended to 3,8-dioxa[8.4.4]propellane derivative by RCM sequence as a key step.     

A gold-catalyzed domino process to the steroid framework

The facile formation of the B and C ring of rac-desoxyequilenin and of a chrysenone derivative in just one preparative step is demonstrated, applying a gold-catalyzed domino process, which involves a benzopyrylium cation as the key intermediate and an intramolecular [3 + 2] cycloaddition as the key step.     

浅谈几种同分异构体的质谱解析

Mass spectrometric analysis is a key and difficult issue in teaching of spectroscopic analysis course. Moreover, fragmentation patterns are the key points for mass spectrometric analysis. Understanding the dissociation rules of organic compounds will help the students to analyze the chemical structures. From the viewpoint of teaching practice, we review in this paper the fragmentation patterns of some common isomers such as acids-esters, alcoholsethers, and straight-chain and branched-chain alkyl groups. In addition, some classic examples were presented to help the students to grasp the fragmentation patterns as well as to improve their ability of mass spectrometric analysis.