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Teaching Green Chemistry Through Student-Generated Open Educational Resources

Journal of College Science Teaching 2023年第4期52卷 3-5页

作者： Grieger, Krystal Leontyev, Alexey Department of Chemistry and Biochemistry North Dakota State University in Fargo ND United States Department of Chemistry and Biochemistry and Discipline-Based Education Research PhD Program North Dakota State University Fargo ND United States

This article describes the implementation of a student-generated open educational resource project into a majors ’ organic chemistry laboratory. This scaffolded semester-long project was organized into six phases and designed to promote the goals of teaching students about both green chemistry and real-life applications of the reactions covered in the course while simultaneously creating open educational resources for future students. A project-based learning approach was utilized to promote student engagement, especially during remote instruction. To further promote engagement, multiple opportunities for peer feedback were provided using web-based software that supports anonymous feedback. The effect of the project on cognitive learning gains and student perceptions was assessed and is reported. Overall, positive learning gains on green chemistry knowledge and skills were observed, and most students viewed the project favorably. © 2023 National Science Teaching Association.

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Variations in kinase and effector signaling logic in a bacterial two component signaling network

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Journal of Biological Chemistry 2025年第6期301卷 108534页

作者： Swingle, Danielle Epstein, Leah Aymon, Ramisha Isiorho, Eta A. Abzalimov, Rinat R. Favaro, Denize C. Gardner, Kevin H. Structural Biology Initiative CUNY Advanced Science Research Center New YorkNY United States PhD. Program in Biochemistry The Graduate Center – City University of New York New YorkNY United States Department of Chemistry and Biochemistry City College of New York New YorkNY United States PhD. Programs in Biochemistry Biology and Chemistry The Graduate Center – City University of New York New YorkNY United States

The general stress response (GSR) protects bacteria from a wide range of stressors. In Alphaproteobacteria, GSR activation is coordinated by HWE/HisKA2 family histidine kinases (HKs), which can exhibit noncanonical structure and function. For example, while most light-oxygen-voltage sensor-containing HKs are light-activated dimers, the Rubellimicrobium thermophilum RT-HK has inverted "dark on, light off" signaling logic with a tunable monomer/dimer equilibrium. Here, we further investigate these atypical behaviors of RT-HK and characterize its downstream signaling network. Using hydrogen-deuterium exchange mass spectrometry, we find that RT-HK uses a signal transduction mechanism similar to light-activated systems, despite its inverted logic. Mutagenesis reveals that RT-HK autophosphorylates in trans, with changes to the Jα helix linking sensor and kinase domains affecting autophosphorylation levels. Exploring downstream effects of RT-HK, we identified two GSR genetic regions, each encoding a copy of the central regulator PhyR. In vitro measurements of phosphotransfer from RT-HK to the two putative PhyRs revealed that RT-HK signals only to one and does so at an increased intensity in the dark, consistent with its reversed logic. X-ray crystal structures of both PhyRs revealed a substantial shift within the receiver domain of one, suggesting a basis for RT-HK specificity. We probed further down the pathway using nuclear magnetic resonance to determine that the single NepR homolog interacts with both unphosphorylated PhyRs, and this interaction is decoupled from activation in one PhyR. This work expands our understanding of HWE/HisKA2 family signal transduction, revealing marked variations from signaling mechanisms previously identified in other GSR networks. © 2025 The Authors

关键词： Signaling

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Taming Multiple Binding Poses in Alchemical Binding Free Energy Prediction: the β-cyclodextrin Host-Guest SAMPL9 Blinded Challenge

arXiv

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arXiv 2023年

作者： Khuttan, Sheenam Azimi, Solmaz Wu, Joe Z. Dick, Sebastian Wu, Chuanjie Xu, Huafeng Gallicchio, Emilio Department of Chemistry Brooklyn College The City University of New York United States PhD Program in Biochemistry Graduate Center of the City University of New York United States PhD Program in Chemistry Graduate Center of the City University of New York United States Roivant Sciences New YorkNY United States

We apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force field to the SAMPL9 bCD host-guest binding free energy prediction challenge that comprises a combination of complexes formed between five phenothiazine guests and two cyclodextrin hosts. Multiple chemical forms, competing binding poses, and computational modeling challenges pose significant obstacles to obtaining reliable computational predictions for these systems. The phenothiazine guests exist in solution as racemic mixtures of enantiomers related by nitrogen inversions that bind the hosts in various binding poses, each requiring an individual free energy analysis. Due to the large size of the guests and the conformational reorganization of the hosts, which prevent a direct absolute binding free energy route, binding free energies are obtained by a series of absolute and relative binding alchemical steps for each chemical species in each binding pose. Metadynamics-accelerated conformational sampling was found to be necessary to address the poor convergence of some numerical estimates affected by conformational trapping. Despite these challenges, our blinded predictions quantitatively reproduced the experimental affinities for the β-cyclodextrin host, less one case of the methylated derivative being an outlier. The work illustrates the challenges of obtaining reliable free energy data in in-silico drug design for even seemingly simple systems and introduces some of the technologies available to tackle them. © 2023, CC BY.

关键词： Cyclodextrins

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DNA-damage-associated protein co-expression network in cardiomyocytes informs on tolerance to genetic variation and disease

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iScience 2025年第5期28卷

作者： Johnson, Omar Darrel Paul, Sayan Gutiérrez, José Angel Russell, William Kent Ward, Michelle Claire Biochemistry Cellular and Molecular Biology Graduate Program University of Texas Medical Branch Galveston 77555 TX United States MD-PhD Combined Degree Program University of Texas Medical Branch Galveston 77555 TX United States Department of Biochemistry and Molecular Biology University of Texas Medical Branch Galveston 77555 TX United States

Cardiovascular disease (CVD) is associated with genetic variants and environmental factors. A consequence of multiple risk factors is DNA damage. To examine how DNA damage influences the cardiomyocyte proteome and its relationship to CVD risk, we treated human induced pluripotent stem cell (iPSC)-derived cardiomyocytes with the DNA-damaging agent doxorubicin (DOX). A network constructed from 4,178 proteins reveals 12 co-expressed modules with 403 hub proteins. Five modules correlate with DOX and associate with RNA processing, chromatin regulation, and metabolism. DOX-correlated hub proteins are depleted for proteins that vary in expression across individuals due to genetic variation but are enriched for proteins encoded by loss-of-function intolerant genes. While not enriched for known CVD risk proteins, DOX-correlated hub proteins are enriched for the physical protein interactors of CVD risk proteins. These data demonstrate that protein connectivity in DNA-damage-associated modules influences the tolerance to genetic variation and supports the use of dynamic networks to explore complex traits. © 2025 The Author(s)

关键词： Integrative aspects of cell biology Molecular network Proteomics

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Kinetics of primary mechanochemical covalent-bond-forming reactions

RSC Mechanochemistry

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RSC Mechanochemistry 2024年第1期1卷 11-32页

作者： Yerzhan S. Zholdassov Ryan W. Kwok Milan A. Shlain Monil Patel Mateusz Marianski Adam B. Braunschweig Advanced Science Research Center at the Graduate Center of the City University of New York 85 St Nicholas Terrace New York NY 10031 USA abraunschweig@gc.cuny.edu Department of Chemistry Hunter College 695 Park Ave New York NY 10065 USA PhD Program in Chemistry Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA PhD Program in Biochemistry Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA

Mechanical activation of reactions can reduce significantly the amounts of solvent and energy required to form covalent organic bonds. Despite growing interest in the field of mechanochemistry and increasing reports of mechanochemical synthesis of organic molecules, the fundamental question of how stresses activate covalent-bond-forming (CBF) reactions remains unresolved. This question remains unresolved because of the difficulties involved in measuring the applied forces and the reaction times in mechanochemical reactors, and the challenges related to deconvoluting microscopic (primary) and macroscopic (secondary) processes in the analysis of reaction kinetics. Here we discuss the use nanoscopic probe-microscope tips to explore the kinetics of CBF reactions. Because these experiments examine reactions on monolayers, surfaces, or nanoscopic particles, they circumvent secondary processes to isolate how stress affects the rates of the primary, CBF events. The major result of these studies is an emerging consensus that stress accelerates reactions by distorting organic molecules and in doing so, lowers reaction activation energies and alters reaction trajectories. This new understanding of how stresses activate reactions can be used to predict the outcomes of CBF mechanochemical reactions, which will lead to the wider adoption of sustainable mechanochemical processes by the synthetic community.

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A good gut feeling on Sarml-mediated axon degeneration

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Protein & Cell 2021年第8期12卷 596-598页

作者： Victoria E.von Saucken David J.Simon Department of Biochemistry Weill Cornell Medical College1300 York AvenueNew YorkNY 10065USA Tri-lnstitutional MD-PhD Program Weill Cornell MedicineRockefeller UniversityMemorial Sloan Kettering Cancer Center1300 York AvenueNew YorkNY 10065USA

Axons,the cable-like projections of neurons,experience a wide range of stressors throughout their *** result of any one of these challenges can be catastrophic,promoting degeneration of the *** degeneration is an active signaling process observed in traumatic brain injury,chemotherapy-induced peripheral neuropathies,and neu-rodegenerative disease(Simon and Watkins,2018;Coleman and Hoeke,2020).

关键词： degeneration chemotherapy traumatic

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Enhancing Protein-Ligand Binding Affinity Predictions using Neural Network Potentials

arXiv

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arXiv 2024年

作者： Zariquiey, Francesc Sabanés Galvelis, Raimondas Gallicchio, Emilio Chodera, John D. Markland, Thomas E. De Fabritiis, Gianni C Dr. Aiguader 88 Barcelona08003 Spain Acellera Labs C Dr Trueta 183 Barcelona08005 Spain Department of Chemistry Brooklyn College of the City University of New York PhD Program in Chemistry Graduate Center of the City University of New York PhD Program in Biochemistry Graduate Center of the City University of New York NY11210 United States Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Department of Chemistry Stanford University 337 Campus Drive StanfordCA94305 United States Passeig Lluis Companys 23 Barcelona08010 Spain

This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology (NNP/MM). We compute relative binding free energies (RBFE) with the Alchemical Transfer Method (ATM) and validate its performance against established benchmarks and find significant enhancements compared to conventional MM force fields like GAFF2. Copyright © 2024, The Authors. All rights reserved.

关键词： Molecular dynamics

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Mechanistic insights of evaporation-induced actuation in supramolecular crystals (Sept, 10.1038/s41563-020-0799-0, 2020)

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NATURE MATERIALS 2021年第3期20卷 434-434页

作者： Piotrowska, Roxana Hesketh, Travis Wang, Haozhen Martin, Alan R. G. Bowering, Deborah Zhang, Chunqiu Hu, Chunhua T. McPhee, Scott A. Wang, Tong Park, Yaewon Singla, Pulkit McGlone, Thomas Florence, Alastair Tuttle, Tell Ulijn, Rein V. Chen, Xi Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York New York NY USA PhD Program in Chemistry The Graduate Center of the City University of New York New York NY USA Department of Pure and Applied Chemistry University of Strathclyde Glasgow UK PhD Program in Physics The Graduate Center of the City University of New York New York NY USA EPSRC Continuous Manufacturing and Crystallisation Future Research Hub c/o Strathclyde Institute of Pharmacy and Biomedical Sciences Technology Innovation Centre University of Strathclyde Glasgow UK Department of Chemistry New York University New York NY USA Department of Chemistry and Biochemistry Hunter College City University of New York New York NY USA Department of Chemical Engineering The City College of New York New York NY USA

A Correction to this paper has been published: https://***/10.1038/s41563-021-00950-3.

关键词： Condensed-matter physics Materials science Soft materials

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Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series

arXiv

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arXiv 2023年

作者： Zariquiey, Francesc Sabanés Pérez, Adrià Majewski, Maciej Gallicchio, Emilio De Fabritiis, Gianni C Dr. Aiguader 88 Barcelona08003 Spain Acellera Labs C Dr Trueta 183 Barcelona08005 Spain Department of Chemistry Brooklyn College of the City University of New York PhD Program in Chemistry Graduate Center of the City University of New York PhD Program in Biochemistry Graduate Center of the City University of New York United States Acellera Devonshire House 582 Honeypot Lane Stanmore Middlesex HA7 1JS United Kingdom Passeig Lluis Companys 23 Barcelona08010 Spain

The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. Alchemical free energy calculations have become a popular tool for this purpose. However, the accuracy and reliability of these methods can vary depending on the methodology. In this study, we evaluate the performance of a relative binding free energy protocol based on the alchemical transfer method (ATM), a novel approach based on a coordinate transformation that swaps the positions of two ligands. The results show that ATM matches the performance of more complex free energy perturbation (FEP) methods in terms of Pearson correlation, but with marginally higher mean absolute errors. This study shows that the ATM method is competitive compared to more traditional methods in speed and accuracy and offers the advantage of being applicable with any potential energy function. Copyright © 2023, The Authors. All rights reserved.

关键词： Ligands

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Directed discovery of high-loading nanoaggregates enabled by drug-matched oligo-peptide excipients

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Chem 2025年

作者： Berisha, Naxhije Farahpour, Atena Ramakrishnan, Maithreyi Chen, Chen McPhee, Scott A. Wang, Tong Li, Tai-De Hema, Kuntrapakam Panagiotakopoulou, Magdalini Athiyarath, Vignesh Coste, Maeva Marciano, Yaron Sherman, Emmet Ulijn, Rein V. Heller, Daniel A. Nanoscience Initiative Advanced Science Research Center CUNY Graduate Center City University of New York New York 10031 NY United States Department of Chemistry and Biochemistry Hunter College City University of New York New York 10065 NY United States PhD Program in Chemistry CUNY Graduate Center City University of New York New York 10016 NY United States Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New York 10065 NY United States Tri-Institutional PhD Program in Chemical Biology Memorial Sloan Kettering Cancer Center New York 10065 NY United States Department of Physics City College of New York City University of New York New York 10031 NY United States Department of Chemistry Brooklyn College City University of New York 2900 Bedford Avenue Brooklyn 11210 NY United States PhD Program in Biochemistry CUNY Graduate Center City University of New York New York 10016 NY United States Weill Cornell Medicine Cornell University New York 10065 NY United States

Nanoparticles can improve drug pharmacokinetics, but low loading efficiencies can limit treatment efficacy. Drug-aggregation-based nanoparticles have demonstrated improved loadings of up to 90%, but few excipients facilitate efficient co-assembly. We investigated peptides as designer excipients because of their diverse chemical space and inherent biodegradability. We designed pentapeptide scaffolds to mimic the structure of known indocyanine excipients by modulating aromaticity, rigidity, and charge. We screened 184 formulations by using diverse drug cargoes. We found drug-peptide combinations that formed nanoparticles with up to 98% drug loading. Molecular dynamics simulations and mass spectrometry analysis demonstrated that tryptophan-drug interactions and solvent exposure of charged amino acid residues drove the formation of core-shell structures. Peptide-drug formulations containing the JAK2/FLT3 inhibitor lestaurtinib were investigated in acute myeloid leukemia models, resulting in enhanced anti-tumor efficacy. This work found that oligopeptides can be designed to efficiently co-assemble with therapeutic cargoes to result in high-loading nanoparticles that improve anti-tumor efficacy. © 2024

关键词： co-assembly directed discovery drug delivery excipient nanocarrier design nanoparticle oligopeptides SDG3: Good health and well-being

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