ACS Publications最新文献

{"title":"Insights into Chemical Bonding Modes and Heat Transport at the Molecular Level.","authors":"Shintaro Fujii, Yoshiaki Shoji, Yuma Masuda, Takanori Fukushima, Tomoaki Nishino","doi":"10.1021/acs.jpclett.4c02325","DOIUrl":"10.1021/acs.jpclett.4c02325","url":null,"abstract":"<p><p>Despite the demand for nanoscale thermal management technologies of material surfaces and interfaces using organic molecules, heat transport properties at the single molecular level remain elusive due to the experimental difficulty of measuring temperature at the nanoscopic scale. Here we show how chemical bonding modes can affect the heat transport properties of single molecules. We focused on four molecular systems: benzylthiol linked to another phenyl group by either a triple (compound <b>1</b>), double (<b>3</b>), or amide (<b>4</b>) bond and a common linear alkanethiol (<b>2</b>), all of which are nearly identical in molecular length. We prepared binary self-assembled monolayers (SAMs) using <b>1</b> as a common reference in combination with <b>2</b>-<b>4</b> and investigated their relative heat transport properties using scanning thermal microscopy (SThM). Two-dimensional temperature mapping of the binary SAMs showed that C≡C and C=C bonds provide more effective pathways for heat transport compared to C-C bonds. Since the amide molecule has resonance structures with C=N double bond character, we expected that its heat transport properties would be comparable to those of the thiols containing triple or double bonds. However, the heat transport properties of this molecule prevailed over the others, most likely due to the formation of additional heat transport pathways caused by intermolecular hydrogen bonding. These findings may provide important guidelines for the design of organic materials for nanoscale thermal management.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Modeling of Glycosylated Catalytic Domain of Human Carbonic Anhydrase IX.","authors":"Ritwika Dey, Srabani Taraphder","doi":"10.1021/acs.jpcb.4c03514","DOIUrl":"10.1021/acs.jpcb.4c03514","url":null,"abstract":"<p><p>Glycans exhibit significant structural diversity due to the flexibility of glycosidic bonds linking their constituent monosaccharides and the formation of numerous hydrogen bonds. The present work searches a simulated ensemble of glycan chain conformations attached to the catalytic domain of N-glycosylated human carbonic anhydrase IX (HCA IX-c) to identify conformations pointed away or back-folded toward the protein surface guided by different amino acid residues. A series of classical molecular dynamics (MD) simulation studies for a total of 30 μs followed by accelerated MD simulations for a total of 2 μs have been performed using two different force fields to capture varying degrees of fluctuations of both glycan chain and HCA IX. From the underlying free energy profile and kinetics derived using hidden Markov state model, several stable glycan orientations are identified that extend away from the protein surface and convert among each other with rate constants of the order 10⁷-10¹⁰ _S^-1. Most importantly, we have identified a <i>rare</i> glycan conformation which reaches close to a catalytically important amino acid residue, Glu-106. We further enlist the protein residues that couple such less frequent event of the glycan chain back-folding toward the surface of the protein.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Slope of the Delocalization Function Is Proportional to Analytical Hardness.","authors":"Bin Wang, Paul Geerlings, Farnaz Heidar-Zadeh, Paul W Ayers, Frank De Proft","doi":"10.1021/acs.jpclett.4c02263","DOIUrl":"10.1021/acs.jpclett.4c02263","url":null,"abstract":"<p><p>Conceptual Density Functional Theory (CDFT) has been extended beyond its traditional role in elucidating chemical reactivity to the development of density functional theory methods, e.g., the investigation of the delocalization error. This delocalization error causes the dependence of the energy on the number of electrons (<i>N</i>) to deviate from its exact piecewise linear behavior, an error which is the basis of many well-known limitations of commonly used density-functional approximations (DFAs). Following our previous work on the analytical hardness η^± for pure functionals, we extend its application to hybrid and range-separated functionals. A comparison is made between the analytical hardness and the slope of the delocalization function introduced by Hait and Head-Gordon. Our results show that there is a linear relationship between its slope and the analytical hardness. An approximate scheme is presented to construct the energy vs <i>N</i> curve without fractional occupation number calculations. The extension to densities is discussed.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimization of Antiproliferative Properties of Triimine Copper(II) Complexes.","authors":"Katarzyna Choroba, Bartosz Zowiślok, Sławomir Kula, Barbara Machura, Anna M Maroń, Karol Erfurt, Cristiana Marques, Sandra Cordeiro, Pedro V Baptista, Alexandra R Fernandes","doi":"10.1021/acs.jmedchem.4c01806","DOIUrl":"10.1021/acs.jmedchem.4c01806","url":null,"abstract":"<p><p>Cu(II) complexes with 2,2':6',2″-terpyridines (terpy) and 2,6-bis(thiazol-2-yl)pyridines (dtpy) with 1- or 2-naphtyl and methoxy-naphtyl were synthesized to elucidate the impact of the triimine core, naphtyl linking mode, and presence of methoxy groups on the antiproliferative activity of [CuCl₂(L^<i>n</i>)]. Their antiproliferative effect was analyzed in ovarian (A2780) and colorectal (HCT116) carcinomas and colorectal carcinoma resistant to doxorubicin (HCT116-DoxR) cell lines and in normal human fibroblasts. Among all complexes, the 1- and 2-naphtyl substituted terpy Cu(II) complexes (<b>Cu1a</b> and <b>Cu1b</b>) showed the strongest cytotoxicity, namely, in HCT116-DoxR 2Dcells and were also capable of inducing the loss of cell viability in 3D HCT116-DoxR spheroids. Their intracellular localization, capability to increase reactive oxygen species (ROS), and interaction with DNA (nonintercalative mode) trigger oxidative DNA cleavage leading to cell death by apoptosis and autophagy. <b>Cu1a</b> and <b>Cu1b</b> do not show in vivo toxicity in a chicken embryo and can interact with bovine serum albumin (BSA).</p>","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":null,"pages":null},"PeriodicalIF":6.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Dynamics and Self-Assembly in Double Hydrophilic Block and Random Copolymers.","authors":"Achilleas Pipertzis, Angeliki Chroni, Stergios Pispas, Jan Swenson","doi":"10.1021/acs.jpcb.4c05398","DOIUrl":"10.1021/acs.jpcb.4c05398","url":null,"abstract":"<p><p>We investigate the self-assembly and dynamics of double hydrophilic block copolymers (DHBCs) composed of densely grafted poly[oligo(ethylene glycol) methacrylate] (POEGMA) and poly(vinyl benzyl trimethylammonium chloride) (PVBTMAC) parent blocks by means of calorimetry, small- and wide-angle X-ray scattering (SAXS/WAXS), and dielectric spectroscopy. A weak segregation strength is evident from X-ray measurements, implying a disordered state and reflecting the inherent miscibility between the host homopolymers. The presence of intermixed POEGMA/PVBTMAC nanodomains results in homogeneous molecular dynamics, as evidenced through isothermal dielectric and temperature-modulated DSC measurements. The intermixed process undergoes a glass transition at a temperature approximately 40 K higher than the vitrification of bulk POEGMA segments, and it shifts to an even higher temperature by increasing the content of the hard block. At temperatures below the intermixed glass transition temperature, the confined POEGMA segments between the glassy intermixed regions contribute to a segmental process featuring (i) reduced glass transition temperature (<i>T</i>_g), (ii) reduced dielectric strength, (iii) broader distribution of relaxation times, and (iv) reduced fragility compared to the POEGMA homopolymer. We also observe two glass transition temperatures of dry PVBTMAC, which we attribute to the backbone and side chain segmental relaxation. To the best of our knowledge, this is the first time in the literature that these glass transitions of dry PVBTMAC have been reported. Finally, this study shows that excellent mixing of the two homopolymers is obtained, and this implies that different properties of this copolymer system can be tailored by adjusting the concentration of each homopolymer.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unusual and Persistent Free Radical Intermediate Production from 2-Pyridyl Ketones via UV Irradiation: A Direct ESR Study.","authors":"Lin-Na Xie, Chun-Hua Huang, Dan Xu, Zhen-Huan Li, Li Qin, Bo Shao, Li Mao, Jie Shao, Zhi-Sheng Liu, Jing Chen, Zhi-Guo Sheng, Zhi-Hui Zhang, Ben-Zhan Zhu","doi":"10.1021/acs.jpclett.4c02657","DOIUrl":"10.1021/acs.jpclett.4c02657","url":null,"abstract":"<p><p>Aryl ketones are often used as photosensitizers and photoinitiators. Free radical intermediates have been suggested, but not confirmed, to be generated after photoirradiation. Here we found, unexpectedly, that a persistent radical was produced from di-2-pyridyl ketone after UV irradiation, which was detected by the direct ESR method. Interestingly, the persistent radical was very sensitive to oxygen and the pH of the reaction medium. A similar persistent radical was also observed from phenyl-2-pyridyl ketone, but not from 3-benzoylpyridine, 4-benzoylpyridine, and benzophenone, suggesting that the presence of a carbonyl group connected to the <i>ortho</i>-position of the pyridine ring is critical for such radical production. By complementary applications of ESR, HPLC, and ESI-Q-TOF-MS, the possible chemical structures of the persistent radical and final product were identified, and the possible underlying reaction mechanism was proposed. This represents the first report on UV-induced persistent radical generation from 2-pyridyl ketones, which should be of great significance for future studies.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What Is the Protonation State of Proteins in Crystals? Insights from Constant pH Molecular Dynamics Simulations.","authors":"Noora Aho, Gerrit Groenhof, Pavel Buslaev","doi":"10.1021/acs.jpcb.4c05947","DOIUrl":"10.1021/acs.jpcb.4c05947","url":null,"abstract":"<p><p>X-ray crystallography is an important technique to determine the positions of atoms in a protein crystal. However, because the native environment in which proteins function, is not a crystal, but a solution, it is not a priori clear if the crystal structure represents the functional form of the protein. Because the protein structure and function often depend critically on the pH, the question arises whether proton affinities are affected by crystallization. X-ray diffraction usually does not reveal protons, which makes it difficult to experimentally measure p<i>K</i>_a shifts in crystals. Here, we investigate whether this challenge can be addressed by performing in silico titration with constant pH molecular dynamics (MD) simulations. We compare the computed p<i>K</i>_a values of proteins between solution and crystal environment and analyze these differences in the context of molecular interactions. For the proteins considered in this work, p<i>K</i>_a shifts were mostly found for residues at the crystal interfaces, where the environment is more apolar in the crystal than in water. Although convergence was an obstacle, our simulations suggest that in principle it is possible to apply constant pH MD to protein crystals routinely and assess the effect of crystallization on protein function more systematically than with standard MD simulations. We also highlight technical challenges that need to be addressed to make MD simulations of crystals more reliable.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of α-Helical Antimicrobial Peptides with Imperfect Amphipathicity for Superior Activity and Selectivity.","authors":"Zhongxiang Wu, Ying Cai, Yajun Han, Yunhan Su, Tianyu Zhang, Xingyu Wang, An Yan, Liunan Wang, Sijing Wu, Gan Wang, Zhiye Zhang","doi":"10.1021/acs.jmedchem.4c01855","DOIUrl":"10.1021/acs.jmedchem.4c01855","url":null,"abstract":"<p><p>The advancement of antimicrobial peptides (AMPs) as therapeutic agents is hindered by their poor selectivity. Recent evidence indicates that controlled disruption of the amphipathicity of α-helical AMPs may increase the selectivity. This study investigated the role of imperfect amphipathicity in optimizing AMPs with varied sequences to enhance their activity and selectivity. Among these, the lead peptide RI-18, characterized by an imperfectly amphipathic α-helical structure, demonstrated potent and broad-spectrum antibacterial activity without inducing hemolytic or cytotoxic effects. RI-18 effectively eliminated planktonic and biofilm-associated bacteria as well as persister cells and exhibited high bacterial plasma membrane affinity, inducing rapid membrane permeabilization and rupture. Notably, RI-18 significantly reduced bacterial loads without promoting bacterial resistance, highlighting its therapeutic potential. Overall, this study identified RI-18 as a promising antimicrobial candidate. The rational strategy of tuning imperfect amphipathicity to enhance the AMP activity and selectivity may facilitate the design and development of AMPs.</p>","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":null,"pages":null},"PeriodicalIF":6.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probing Functional Allosteric States and Conformational Ensembles of the Allosteric Protein Kinase States and Mutants: Atomistic Modeling and Comparative Analysis of AlphaFold2, OmegaFold, and AlphaFlow Approaches and Adaptations.","authors":"Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady Verkhivker","doi":"10.1021/acs.jpcb.4c04985","DOIUrl":"10.1021/acs.jpcb.4c04985","url":null,"abstract":"<p><p>This study reports a comprehensive analysis and comparison of several AlphaFold2 adaptations and OmegaFold and AlphaFlow approaches in predicting distinct allosteric states, conformational ensembles, and mutation-induced structural effects for a panel of state-switching allosteric ABL mutants. The results revealed that the proposed AlphaFold2 adaptation with randomized alanine sequence scanning can generate functionally relevant allosteric states and conformational ensembles of the ABL kinase that qualitatively capture a unique pattern of population shifts between the active and inactive states in the allosteric ABL mutants. Consistent with the NMR experiments, the proposed AlphaFold2 adaptation predicted that G269E/M309L/T408Y mutant could induce population changes and sample a significant fraction of the fully inactive I₂ form which is a low-populated, high-energy state for the wild-type ABL protein. We also demonstrated that other ABL mutants G269E/M309L/T334I and M309L/L320I/T334I that introduce a single activating T334I mutation can reverse equilibrium and populate exclusively the active ABL form. While the precise quantitative predictions of the relative populations of the active and various hidden inactive states in the ABL mutants remain challenging, our results provide evidence that AlphaFold2 adaptation with randomized alanine sequence scanning can adequately detect a spectrum of the allosteric ABL states and capture the equilibrium redistributions between structurally distinct functional ABL conformations. We further validated the robustness of the proposed AlphaFold2 adaptation for predicting the unique inactive architecture of the BSK8 kinase and structural differences between ligand-unbound apo and ATP-bound forms of BSK8. The results of this comparative study suggested that AlpahFold2, OmegaFold, and AlphaFlow approaches may be driven by structural memorization of existing protein folds and are strongly biased toward predictions of the thermodynamically stable ground states of the protein kinases, highlighting limitations and challenges of AI-based methodologies in detecting alternative functional conformations, accurate characterization of physically significant conformational ensembles, and prediction of mutation-induced allosteric structural changes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pan-Transcriptional Enhanced Associated Domain Palmitoylation Pocket Covalent Inhibitor.","authors":"Jinhyuk Kim, Hadong Kim, Jongwan Kim, Seon Yeon Cho, Sungho Moon, Youngki Yoo, Hanseong Kim, Jin Kwan Kim, Hyejin Jeon, Wan Namkung, Gyoonhee Han, Kyoung Tai No","doi":"10.1021/acs.jmedchem.4c01393","DOIUrl":"10.1021/acs.jmedchem.4c01393","url":null,"abstract":"<p><p>In the Hippo signaling pathway, the palmitoylated transcriptional enhanced associated domain (TEAD) protein interacts with the coactivator Yes-associated protein/PDZ-binding motif, leading to transcriptional upregulation of oncogenes such as Ctgf and Cyr61. Consequently, targeting the palmitoylation sites of TEAD has emerged as a promising strategy for treating TEAD-dependent cancers. Compound <b>1</b> was identified using a structure-based drug design approach, leveraging the molecular insights gained from the known TEAD palmitoylation site inhibitor, K-975. Optimization of the initial hit compound resulted in the development of compound <b>3</b>, a covalent pan-TEAD inhibitor characterized by high potency and oral bioavailability.</p>","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":null,"pages":null},"PeriodicalIF":6.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}