Article
Chemistry, Multidisciplinary
Yongjin Xu, Chunxia Gao, Liliana Haversen, Thomas Lundback, Joakim Andreasson, Morten Grotli
Summary: In this study, the synthesis and characterization of a photoswitchable DFG-out kinase inhibitor were reported, and the photocontrol of the target kinase was demonstrated in both enzymatic and living cell assays.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Bharath Srinivasan
Summary: The kinetics parameters during the interaction between drugs and targets play an important role in drug optimization and dosing decisions.
Article
Chemistry, Physical
Alexander Grandjean, J. Luis Perez Lustres, Stephan Muth, Daniel Maus, Gregor Jung
Summary: This study investigates the solvent dependence on proton transfer reactions using a probe system of a pyrene-based photoacid and a phosphine oxide. By triggering excited-state proton transfer along the hydrogen bond through photon excitation, the complex system was analyzed via fluorescence spectroscopy, revealing changes in emission bands and hydrogen bond configurations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Multidisciplinary Sciences
Hyun-Kyu Choi, Peiwen Cong, Chenghao Ge, Aswin Natarajan, Baoyu Liu, Yong Zhang, Kaitao Li, Muaz Nik Rushdi, Wei Chen, Jizhong Lou, Michelle Krogsgaard, Cheng Zhu
Summary: Catch bonds form when T cell receptors (TCR) interact with agonist peptide-MHC (pMHC) complexes, with the lifetime of the bond increasing with applied force. In this study, the authors develop two models and analyze 55 datasets to quantitatively integrate and classify different bond behaviors and biological activities. The models can distinguish class I from class II MHCs and correlate their structural parameters with TCR/pMHC potency to trigger T cell activation, providing insights into the mechanisms of TCR mechanosensing.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yaohui Huang, Jiarun Geng, Zhuoliang Jiang, Meng Ren, Bo Wen, Jun Chen, Fujun Li
Summary: This study attempts a solvation-regulated strategy in tetraethylene glycol dimethyl ether (G4) based electrolyte to achieve stable lithium anodes in Li-O-2 batteries. By incorporating trifluoroacetate anions (TFA(-)) with strong Li+ affinity into the lithium bis(fluorosulfonyl)imide (LiTFSI)/G4 electrolyte, the Li+-G4 interaction is attenuated and anion-dominant solvates are formed. The bisalt electrolyte with 0.5 M LiTFA and 0.5 M LiTFSI mitigates G4 decomposition and induces an inorganic-rich solid electrolyte interphase (SEI), leading to improved Li+ diffusion and extended lifespan in Li-O-2 batteries.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Pharmacology & Pharmacy
Hongli Liu, Haoran Zhang, Adriaan P. Ijzerman, Dong Guo
Summary: Research on residence time contributes to the translation of in vitro potency to in vivo efficacy and safety, serving as a method to predict drug pharmacological activity and side effects. Integrating residence time into the early stages of drug discovery and development aids in obtaining promising clinical candidates. Further research and optimization of residence time measurement will facilitate the development of safer and more effective drugs.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Chemistry, Medicinal
Noam Morningstar-Kywi, Kaichen Wang, Thomas R. Asbell, Zhaohui Wang, Jason B. Giles, Jiawei Lai, Dab Brill, Brian T. Sutch, Ian S. Haworth
Summary: The retention and displacement of water molecules during formation of ligand-protein interfaces play a major role in determining ligand binding. This article describes an algorithm for water placement and the calculation of ligand-driven water displacement in protein-ligand complexes. The algorithm predicts a significant number of experimental water positions and can form water networks that were not detected in crystallographic structures. Additionally, this method can evaluate water displacement upon ligand binding, which is important in drug design.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Astronomy & Astrophysics
Jessica Tennis, Jean-Christophe Loison, Eric Herbst
Summary: This study investigates the gas-phase formation of dimethyl ether in interstellar space and finds that the process of radiative association can rapidly produce dimethyl ether at low temperatures. However, adding this reaction into the network model still cannot fully explain the abundance of dimethyl ether in cold and prestellar cores.
ASTROPHYSICAL JOURNAL
(2021)
Article
Chemistry, Medicinal
Francesca Galvani, Daniele Pala, Alberto Cuzzolin, Laura Scalvini, Alessio Lodola, Marco Mor, Andrea Rizzi
Summary: In this study, two metadynamics protocols were used to estimate the residence times of muscarinic M3 receptor antagonists. The results showed that both computational methods were able to accurately rank compounds according to their experimental residence times.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Review
Pharmacology & Pharmacy
Kevin E. Knockenhauer, Robert A. Copeland
Summary: A dominant assumption in pharmacology has been that the systemic concentration of a drug relative to the equilibrium dissociation constant for the drug-target complex determines its in vivo target occupancy and pharmacodynamics. However, there are examples of drugs for which the pharmacodynamic effect persists even after the drug concentration has decreased. To explain this, the drug-target residence time model proposes that it is the lifetime of the drug-target complex, rather than its equilibrium affinity, that determines the extent and duration of drug pharmacodynamics. This review discusses the evolution of this model and its applications in natural ligand-macromolecule biology and synthetic drug-target pharmacology.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Chemistry, Physical
Saumyak Mukherjee, Subhajit Acharya, Sayantan Mondal, Puja Banerjee, Biman Bagchi
Summary: This article analyzes the processes of insulin oligomers in aqueous solution, focusing on the solvation of the insulin monomer in water, stability and dissociation of its dimer, and the structural integrity of the hexamer. The role of water in solvation of the dimer- and hexamer-forming surfaces, long-range interactions between the monomers, and the stability of the oligomers is discussed. The study also delves into how different order parameters can be used to understand the dissociation of the insulin dimer, and how calculation of the rate using multidimensional free energy provides insight into the interplay between protein and water dynamics.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Environmental Sciences
Qianting Ye, Zecong Ding, Rong Li, Zhenqing Shi
Summary: This study investigated the kinetics of Cd, Ni, and Pb release from a typical fulvic acid (FA) and developed a kinetics model for predicting metal release from dissolved organic matter (DOM). The study found that Cd showed the fastest release from FA while Ni and Pb had slower release rates. The study also demonstrated that metal-FA complexes undergo different rates of dissociation in the environment, affecting the dynamic speciation and transfer of metals to other biological processes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Physical
Navjeet Ahalawat, Jagannath Mondal
Summary: Computer simulation approaches have greatly advanced in biomolecular recognition processes, particularly through unbiased simulation and Markov state modeling methods. Enhanced sampling approaches are crucial in accelerating simulations of ligand recognition processes, but key issues such as force fields and sampling bottlenecks still need to be addressed to achieve quantitative reconstruction of experimental measurements. Adopting multiscale approaches and coarse-grained simulations may be a possible way forward for efficient elucidation of ligand binding kinetics.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Beata Wielgus-Kutrowska, Urszula Marcisz, Jan M. Antosiewicz
Summary: The study used stopped-flow fluorometry and Brownian dynamics simulations to investigate the binding anisotropy of NAG(3) with lysozyme, finding that hydrodynamic orienting effects are negligible in this system. While simulations suggest the presence of these effects in other molecular systems, the ionic strength dependence of rate constants did not provide conclusive evidence in this case.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Medicinal
Lane W. Votapka, Andrew M. Stokely, Anupam A. Ojha, Rommie E. Amaro
Summary: SEEKR2 is a computational method for estimating the kinetics and thermodynamics of molecular processes. It provides equivalent or improved results compared to previous versions, with increased speed and capabilities. SEEKR2 also offers improved usability and supports simulation using OpenMM and Browndye 2.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Pharmacology & Pharmacy
Fiona M. McRobb, Ana Negri, Thijs Beuming, Woody Sherman
CURRENT OPINION IN PHARMACOLOGY
(2016)
Article
Chemistry, Medicinal
Steven L. Dixon, Jianxin Duan, Ethan Smith, Christopher D. Von Bargen, Woody Sherman, Matthew P. Repasky
FUTURE MEDICINAL CHEMISTRY
(2016)
Article
Chemistry, Medicinal
Michelle Lynn Hall, David Calkins, Woody Sherman
Journal of Chemical Information and Modeling
(2016)
Article
Chemistry, Medicinal
Daniel Cappel, Michelle Lynn Hall, Eelke B. Lenselink, Thijs Beuming, Jun Qi, James Bradner, Woody Sherman
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2016)
Article
Biochemistry & Molecular Biology
Charles A. English, Woody Sherman, Wenli Meng, Lila M. Gierasch
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Chemistry, Medicinal
S. Roy Kimura, Hai Peng Hu, Anatoly M. Ruvinsky, Woody Sherman, Angelo D. Favia
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2017)
Article
Chemistry, Medicinal
Zoe Cournia, Bryce Allen, Woody Sherman
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2017)
Article
Biochemistry & Molecular Biology
Thomas Steinbrecher, Chongkai Zhu, Lingle Wang, Robert Abel, Christopher Negron, David Pearlman, Eric Feyfant, Jianxin Duan, Woody Sherman
JOURNAL OF MOLECULAR BIOLOGY
(2017)
Article
Chemistry, Multidisciplinary
Jean B. Bertoldo, Tiago Rodrigues, Lavinia Dunsmore, Francesco A. Aprile, Marta C. Marques, Leonardo A. Rosado, Omar Boutureira, Thomas B. Steinbrecher, Woody Sherman, Francisco Corzana, Hernan Terenzi, Goncalo J. L. Bernardes
Article
Chemistry, Medicinal
Phani Ghanakota, Herman van Vlijmen, Woody Sherman, Thijs Beuming
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2018)
Article
Chemistry, Physical
Angela N. Migues, Qinfang Sun, S. Vaitheeswaran, Woody Sherman, Scott M. Auerbach
JOURNAL OF PHYSICAL CHEMISTRY C
(2018)
Article
Chemistry, Multidisciplinary
Bas J. G. E. Pieters, Maud H. M. Wuts, Jordi Poater, Kiran Kumar, Paul B. White, Jos J. A. G. Kamps, Woody Sherman, Ger J. M. Pruijn, Robert S. Paton, Thijs Beuming, F. Matthias Bickelhaupt, Jasmin Mecinovic
COMMUNICATIONS CHEMISTRY
(2020)
Proceedings Paper
Computer Science, Hardware & Architecture
Chen Yang, Tong Geng, Tianqi Wang, Charles Lin, Jiayi Sheng, Vipin Sachdeva, Woody Sherman, Martin Herbordt
2019 IEEE 30TH INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES AND PROCESSORS (ASAP 2019)
(2019)
Review
Chemistry, Medicinal
Daniel Cappel, Woody Sherman, Thijs Beuming
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2017)
Article
Chemistry, Multidisciplinary
Jerome M. Fox, Kyungtae Kang, Madhavi Sastry, Woody Sherman, Banumathi Sankaran, Peter H. Zwart, George M. Whitesides
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2017)