Article
Chemistry, Multidisciplinary
Stefan M. Kohlbacher, Thierry Langer, Thomas Seidel
Summary: QSAR methods are commonly used in drug discovery, where pharmacophores provide advantageous properties for building quantitative SAR models that can generalize to different datasets with low requirements.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Chemistry, Medicinal
Stefan Michael Kohlbacher, Matthias Schmid, Thomas Seidel, Thierry Langer
Summary: Pharmacophores are abstract representations of stereoelectronic molecular features used for modeling ligand-receptor interactions and widely applied in fast virtual screening. While much effort has been made to enhance the computational efficiency of the screening process, little attention has been given to automated procedures for optimizing pharmacophores with higher discriminatory power. In this study, an algorithm is proposed that automatically selects features driving pharmacophore model quality using SAR information from validated QPhAR models, leading to a fully automated method for deriving high-quality pharmacophores. Additionally, the QPhAR-generated models are shown to provide insights into (un-)favorable interactions for compounds of interest, guiding researchers.
Article
Chemistry, Organic
Amal Al-Azmi, Mona A. Shalaby
Summary: This paper describes a novel, last, and straightforward procedure for the synthesis of di- and tri-functionalized isoxazoles, which features the availability of starting materials, moderate reaction conditions, and simplicity of workup. Characterization of the structures is done through various spectroscopic studies, and theoretical calculations are performed to determine NMR chemical shift values and molecular properties of the synthesized isoxazoles.
CURRENT ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Tsuyoshi Oikawa, Shinya Fujii, Shuichi Mori, Hiroyuki Masuno, Emiko Kawachi, Hiroyuki Kagechika
Summary: A series of retinobenzoic acids were synthesized to investigate the structure-activity relationship of retinoids at the hydrophobic moiety. Compound 24c with a t-butyldimethylsilyl group showed potent retinoid activity, especially towards RARγ. This study provides insights for the development of new RARγ ligands.
Article
Chemistry, Medicinal
Tianxiao Wu, Qiaohua Qin, Nian Liu, Chu Zhang, Ruicheng Lv, Wenbo Yin, Yin Sun, Yixiang Sun, Ruifeng Wang, Dongmei Zhao, Maosheng Cheng
Summary: In this study, a series of 2,4-diaminopyrimidine derivatives were synthesized to explore their activity against TRK. Compound 19k was identified as a potent pan-TRK inhibitor that inhibits cell proliferation and induces apoptosis. It exhibited good stability and oral bioavailability, making it a potential lead compound for NTRK-fusion cancer treatment.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Pharmacology & Pharmacy
Yanhong Sun, Xiaoyan Duan, Fenghe Wang, Huixin Tan, Jiahuan Hu, Wanting Bai, Xinbo Wang, Baolian Wang, Jinping Hu
Summary: Glucose transporter 1 (GLUT1) plays a crucial role in the energy metabolism of tumor cells and inhibiting GLUT1 can decrease tumor growth and enhance drug sensitivity. This study screened flavonoids for their ability to inhibit GLUT1 and found that sinensetin and nobiletin showed strong sensitizing effects on HepG2 cells, enhancing the efficacy of sorafenib. The pharmacophore model identified the key pharmacophores of flavonoid inhibitors. These findings provide valuable information for designing novel GLUT1 inhibitors and overcoming drug resistance in cancer treatment.
Article
Biochemistry & Molecular Biology
Tian-Yun Fan, Yu-Xin Yang, Qing-Xuan Zeng, Xue-Lei Wang, Wei Wei, Xi-Xi Guo, Li-Ping Zhao, Dan-Qing Song, Yan-Xiang Wang, Li Wang, Bin Hong
Summary: In this study, 40 berberine derivatives were synthesized and evaluated for their potential as PCSK9 transcriptional inhibitors. Among them, compound 9k showed the strongest activity in downregulating PCSK9 protein levels and promoting LDLR expression with a mechanism targeting HNF1 alpha and/or Sp1 cluster modulation upstream of PCSK9. This compound may hold promise as a novel treatment for atherosclerosis.
BIOORGANIC CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Petja Rosenqvist, Janne J. Makinen, Kaisa Palmu, Johanna Jokinen, Ranjit K. Prajapati, Heidi J. Korhonen, Pasi Virta, Georgiy A. Belogurov, Mikko Metsa-Ketela
Summary: Showdomycin is a C-nucleoside microbial natural product with antimicrobial and cytotoxic properties, its derivatives act as uridine mimics and inhibit RNA polymerases, with ethylthio derivative showing reduced cytotoxicity and antibacterial activity.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Xiaochen Chi, Fei Xie, Liping Li, Yumeng Hao, Hao Wu, Xianru Li, Guangxin Xia, Lan Yan, Dazhi Zhang, Yuanying Jiang, Tingjunhong Ni
Summary: In this study, 29 novel triazoles with benzyloxy phenyl isoxazole side chain were synthesized and tested. The majority of these compounds showed potent anti-fungal activity against eight pathogenic fungi. Compounds 13, 20, and 27 displayed outstanding activity against drug-resistant Candida auris isolates and inhibitory effects on biofilm formation. Compound 13 showed low risk of drug-drug interactions and will be further investigated as a promising candidate.
BIOORGANIC CHEMISTRY
(2023)
Article
Agriculture, Multidisciplinary
Xiang Wang, Yujia Cao, Siyu Chen, Jiachen Lin, Xin Yang, Dejian Huang
Summary: Flavones with double bonds and hydroxyl groups promote anti-inflammatory activity, while methoxy and certain hydroxyl groups attenuate overall anti-inflammatory and antioxidant activities. The most effective flavones are 3',4'-dihydroxyflavone and luteolin, which can effectively inhibit LPS-induced nitric oxide levels, suppress iNOS production, and inhibit IL-1 beta and IL-6 production.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Neha Sharma, Mala Sharma, Qazi Inamur Rahman, Salman Akhtar, Mohd Muddassir
Summary: The study focused on exploring novel natural compounds targeting VEGFR-2 through computational modeling and database screening. Among the screened compounds, Compound B demonstrated the highest binding energy and stable binding to the active site of VEGFR-2, suggesting its potential as a potent antiangiogenic agent.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Inorganic & Nuclear
Catalin Maxim, Cristian D. Ene, Ioana Nicolau, Lavinia L. Ruta, Ileana C. Farcasanu
Summary: Three pairs of copper(II) complexes with tridentate Schiff bases were synthesized and used for biological assessments. The structures, spectra, and biological activities of the complexes were analyzed, and the accumulation of 3-S was found to potentially disrupt the redox state of cells.
DALTON TRANSACTIONS
(2022)
Article
Chemistry, Physical
Adam A. Wallace, Yerbolat Dauletyarov, Andrei Sanov
Summary: Electron capture by the sigma* LUMO of isoxazole triggers the dissociation of the O-N bond and the opening of the ring, leading to the formation of a dense manifold of diradical states, which differs qualitatively from that of the analogous system in oxazole. The near degeneracy of the pi and sigma* orbitals in isoxazole, resulting from the placement of the N atom in the terminal position within the ring-open structure, favors a triplet-state configuration.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Integrative & Complementary Medicine
Chengyan Long, Yang Yang, Yong Yang, Sixing Huang, Xiaomei Zhang, Wei Du, Dajian Yang, Yanlei Guo, Li Zhang
Summary: Sesquiterpene pyridine alkaloids from Tripterygium exhibit potential therapeutic effects in treating various diseases and are predicted to target multiple proteins and pathways. The pharmacophore model-5 (Pm-05) was identified as the best model for these compounds, with the greatest structural difference in the pyridine ring. The 2-(carboxyalkyl) nicotinic acid portion containing a pyridine ring system is proposed as both a pharmacologically active center and a core of structural diversity.
EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE
(2021)
Article
Pharmacology & Pharmacy
Renkai Li, Winston Wing-Shum Mak, Jingjing Li, Chengwen Zheng, Polly Ho-Ting Shiu, Sai-Wang Seto, Simon Ming-Yuen Lee, George Pak-Heng Leung
Summary: This study identified compound 3c as a selective and irreversible non-competitive inhibitor of ENT1 and ENT2, which is a derivative of FPMINT. The structure-activity relationship analysis revealed the importance of the position of benzene moiety and the addition of halogen substitutes for the inhibitory effects. These findings contribute to the development of more potent and selective drugs.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Chemistry, Organic
Shikha Sharma, Trideep Rajale, Daniel K. Unruh, David M. Birney
JOURNAL OF ORGANIC CHEMISTRY
(2015)
Article
Biochemical Research Methods
Antonietta M. Lillo, Ciana L. Lopez, Trideep Rajale, Hung-Ju Yen, Harsha D. Magurudeniya, M. Lisa Phipps, Eva Rose M. Balog, Timothy C. Sanchez, Srinivas Iyer, Hsing-Lin Wang, Ryszard Michalczyk, Reginaldo C. Rocha, Jennifer S. Martinez
BIOCONJUGATE CHEMISTRY
(2018)
Article
Chemistry, Organic
Trideep Rajale, Shikha Sharma, Daniel K. Unruh, Daniel A. Stroud, David M. Birney
ORGANIC & BIOMOLECULAR CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Parminder Kaur, Walter Wever, Trideep Rajale, Guigen Li
CHEMICAL BIOLOGY & DRUG DESIGN
(2010)
Article
Chemistry, Multidisciplinary
Parminder Kaur, Suresh Pindi, Walter Wever, Trideep Rajale, Guigen Li
CHEMICAL COMMUNICATIONS
(2010)
Review
Chemistry, Multidisciplinary
Bo Jiang, Trideep Rajale, Walter Wever, Shu-Jiang Tu, Guigen Li
CHEMISTRY-AN ASIAN JOURNAL
(2010)
Article
Chemistry, Organic
Parminder Kaur, Suresh Pindi, Walter Wever, Trideep Rajale, Guigen Li
JOURNAL OF ORGANIC CHEMISTRY
(2010)
Article
Chemistry, Multidisciplinary
Shikha Sharma, Trideep Rajale, David B. Cordes, Fernando Hung-Low, David M. Birney
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2013)
Article
Chemistry, Organic
Shu-Liang Wang, Chuang Cheng, Fei-Yue Wu, Bo Jiang, Feng Shi, Shu-Jiang Tu, Trideep Rajale, Guigen Li
Article
Chemistry, Organic
Trideep Rajale, Shikha Sharma, Daniel A. Stroud, Daniel K. Unruh, Emily Miaou, Kimberly Lai, David M. Birney
TETRAHEDRON LETTERS
(2014)
Article
Chemistry, Multidisciplinary
Trideep Rajale, Jacob C. Miner, Ryszard Michalczyk, M. Lisa Phipps, Jurgen G. Schmidt, Robert D. Gilbertson, Robert F. Williams, Charlie E. M. Strauss, Jennifer S. Martinez
Summary: This research presents a novel method for the generation and characterization of peptoid hetero-oligomers, utilizing microwave-assisted synthesis to combine a library of sub-monomers with amine and carboxylate side-chains in different sequences. The sequence-structure propensity is confirmed by circular dichroism and NMR analysis, while biasing the psi-angle backbone to trans in Monte Carlo modelling enhances the i to i + 3 naphthyl-naphthyl stacking. Overall, the high-yield synthesis of hetero-oligomers and structure prediction using NMR enables rapid determination of sequences with secondary structural propensities for hydrophilic peptidomimetic foldamers.
CHEMICAL COMMUNICATIONS
(2021)
Meeting Abstract
Chemistry, Multidisciplinary
Trideep Rajale, Shikha Sharma, David M. Birney
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2014)
Meeting Abstract
Chemistry, Multidisciplinary
Trideep Rajale, Shikha Sharma, Deepali Butani, Daniel Stroud, David M. Birney
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2013)
Meeting Abstract
Chemistry, Multidisciplinary
Shikha Sharma, Trideep Rajale, David M. Birney
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2013)