Article
Biochemistry & Molecular Biology
Bing Bai, Rongfeng Zou, H. C. Stephen Chan, Hongchun Li, Shuguang Yuan
Summary: Protein-ligand interaction analysis is crucial for drug discovery and rational protein design. MolADI, an online tool, provides detailed analysis of these interactions and allows easy viewing with 2D graphs and 3D representations. It focuses on interactions that evolve over time.
Article
Chemistry, Medicinal
Matthew D. Shortridge, Gabriele Varani
Summary: This scalable NMR screening approach allows for the identification of small molecule fragments binding to structured RNAs, providing initial hits for further drug discovery efforts. Using the pre-miR-21 stem-loop as a demonstration, a thiadiazole fragment was identified to bind the Dicer cleavage site of pre-miR-21.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Review
Biochemistry & Molecular Biology
Michael A. Erb
Summary: YEATS domains are protein folds that bind to acylated lysines and are important for regulating chromatin and transcription. Development of small-molecule tools for YEATS domains has facilitated the study of their function and biological significance.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Physical
Hahnbeom Park, Guangfeng Zhou, Minkyung Baek, David Baker, Frank DiMaio
Summary: The accurate and rapid calculation of protein-small molecule interaction free energies is crucial for computational drug discovery. A new approach was developed in this study that optimized small molecule force field parameters based on information from available small molecule crystal structures. The resulting energy model, implemented in Rosetta with a genetic algorithm docking method, significantly improved the success rate of bound structure recapitulation in cross-docking on 1112 complexes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Chemistry, Medicinal
Joshua W. Conner, Daniel P. Poole, Manuela Jorg, Nicholas A. Veldhuis
Summary: This review addresses the key challenges, synthesis approaches, and structure-activity relationships in recent fluorescent small molecule studies for GPCRs, and discusses the advantages of using high-resolution GPCR structures to inform conjugation strategies.
FUTURE MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Minghui Zhu, Shicheng Han, Junrui Liu, Mengjin Tan, Wei Wang, Kosuke Suzuki, Panchao Yin, Debin Xia, Xikui Fang
Summary: This study reports the formation of giant {Mo126W30} polyoxometalate cages templated by pi-conjugated planar ligands, with inorganic shells containing arrays of stacked aromatic carboxylates stabilized by multiple pi-pi interactions. NMR data confirmed the stability of the cages in solution, and showed that the inner aromatic templates can be postsynthetically replaced by selected aliphatic dicarboxylates. This paves the way for endo-functionalization and exploration of reactivities within the cage cavities.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Viktor A. Urban, Alexander Davidovskii, Valery G. Veresov
Summary: The programmed cell death ligand protein 1 (PD-L1) is an important immunosuppressive molecule that can be targeted for cancer treatment. Antibody-based immunotherapy against the PD-1/PD-L1 pathway has shown unprecedented therapeutic responses, but has limitations. This study explores small-molecule inhibitors as an alternative or complementary therapeutic option, and identifies potential compounds that can target the PD-1/PD-L1 interaction.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Review
Biochemistry & Molecular Biology
Wan Gi Byun, Donghyun Lim, Seung Bum Park
Summary: This review discusses the potential of targeting PRIs using small molecules, the tools for observing PRIs in biochemical and cell-based experiments, and various PRI modulators. Emerging technologies and challenges in the development of PRI modulators are also highlighted.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Monika Conrad, Guenther Proll, Esteban Builes-Muenden, Andreas Dietzel, Sven Wagner, Guenter Gauglitz
Summary: Antibody gold nanoparticle conjugates play a crucial role in lateral flow assays. Different methods for immobilizing antibodies on gold nanoparticles were investigated to select the most appropriate conjugate for quantitative lateral flow test. Direct adsorption of UV-light irradiated antibody to gold nanoparticles was shown to be the best conjugate for quantification of amitriptyline.
Review
Virology
Vladimir Chulanov, Anastasiya Kostyusheva, Sergey Brezgin, Natalia Ponomareva, Vladimir Gegechkori, Elena Volchkova, Nikolay Pimenov, Dmitry Kostyushev
Summary: CRISPR/Cas technology plays a crucial role in studying viral infections and identifying potential antiviral genes through screening methods. The development of CRISPR screens has helped in uncovering novel drug candidates for treating viral infections.
Article
Chemistry, Multidisciplinary
Zhaofei Chai, Qiong Wu, Kai Cheng, Xiaoli Liu, Ling Jiang, Maili Liu, Conggang Li
Summary: The study established a F-19 NMR platform for simultaneous detection of various thiols and generating unique two-dimensional codes in different environments. This method can reliably quantify thiol drug content in tablets, discriminate thiols in living cells, and monitor thiol-related metabolism pathways at the atomic level. This versatile platform can be extended to detect the activity of thiol-related enzymes such as gamma-glutamyl transpeptidase.
Review
Chemistry, Multidisciplinary
Qiuran Wang, Sam H. Brooks, Tianchang Liu, Neil C. Tomson
Summary: Cluster complexes have recently been designed with ligand scaffolds specifically tailored to support multinuclear transition metal cores in order to facilitate cooperative small molecule activation. The incorporation of geometric flexibility and redox-active ligands in the ligand design allows for unique small molecule activation modes, providing significant analogies to heterogeneous and metalloenzyme catalysts.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biology
Li Shen, Hongsong Feng, Yuchi Qiu, Guo-Wei Wei
Summary: A sequence-based virtual screening method utilizes natural language processing algorithms and optimized deep K-embedding strategies to encode biomolecular interactions without relying on 3D structure-based docking. It outperforms current methods in multiple datasets and has significant potential in drug discovery and protein engineering.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Analytical
Clarice E. Froehlich, Jiayi He, Christy L. Haynes
Summary: Investigating the interactions between small, charged molecules and aptamers using surface plasmon resonance (SPR) is challenging due to the low response of small molecules and nonspecific electrostatic interactions. However, aptamers are increasingly used in sensors for small molecule detection. This study develops a method to characterize the interaction between the charged small molecule serotonin and an aptamer using streptavidin-biotin capture and a high-ionic-strength buffer. These techniques provide insight into working with small molecules and offer the potential for improving SPR sensors.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Haipeng Jiang, Yang Liu, Jian Guo
Summary: The study introduces an accurate and efficient strategy for discovering ligands from natural product extracts using NMR technology, which involves pre-purified subfraction libraries for screening, separation, and structural identification of biologically active components.
PHYTOCHEMICAL ANALYSIS
(2021)
Article
Biochemistry & Molecular Biology
Woonghee Lee, Chad M. Petit, Gabriel Cornilescu, Jaime L. Stark, John L. Markley
JOURNAL OF BIOMOLECULAR NMR
(2016)
Article
Cell Biology
Timothy W. Rhoads, Maggie S. Burhans, Vincent B. Chen, Paul D. Hutchins, Matthew J. P. Rush, Josef P. Clark, Jaime L. Stark, Sean J. McIlwain, Hamid R. Eghbalnia, Derek M. Pavelec, Irene M. Ong, John M. Denu, John L. Markley, Joshua J. Coon, Ricki J. Colman, Rozalyn M. Anderson
Article
Biochemistry & Molecular Biology
Jaime L. Stark, Kamiya Mehla, Nina Chaika, Thomas B. Acton, Rong Xiao, Pankaj K. Singh, Gaetano T. Monteione, Robert Powers
Article
Chemistry, Medicinal
Jaime L. Stark, Jennifer C. Copeland, Alexander Eletsky, Greg A. Somerville, Thomas Szyperski, Robert Powers
Article
Biochemistry & Molecular Biology
Woonghee Lee, Jaime L. Stark, John L. Markley
JOURNAL OF BIOMOLECULAR NMR
(2014)
Article
Biochemical Research Methods
Matthew D. Shortridge, Michael Bokemper, Jennifer C. Copeland, Jaime L. Stark, Robert Powers
JOURNAL OF PROTEOME RESEARCH
(2011)
Article
Chemistry, Multidisciplinary
Jaime Stark, Robert Powers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2008)
Article
Biochemistry & Molecular Biology
Jaime L. Stark, Kelly A. Mercier, Geoffrey A. Mueller, Thomas B. Acton, Rong Xiao, Gaetano T. Montelione, Robert Powers
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2010)
Article
Mathematical & Computational Biology
Thomas Triplet, Matthew D. Shortridge, Mark A. Griep, Jaime L. Stark, Robert Powers, Peter Revesz
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2010)
Article
Endocrinology & Metabolism
Sukru Serter Catav, Emine Sonay Elgin, Cagdas Dag, Jaime L. Stark, Koksal Kucukakyuz
Article
Biochemistry & Molecular Biology
Andrew G. Reidenbach, Zachary A. Kemmerer, Deniz Aydin, Adam Jochem, Molly T. McDevitt, Paul D. Hutchins, Jaime L. Stark, Jonathan A. Stefely, Thiru Reddy, Alex S. Hebert, Emily M. Wilkerson, Isabel E. Johnson, Craig A. Bingman, John L. Markley, Joshua J. Coon, Matteo Dal Peraro, David J. Pagliarini
CELL CHEMICAL BIOLOGY
(2018)