1
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Huang F, Chen L, Yang X, Jeyakumar P, Wang Z, Sun S, Qiu T, Zeng Y, Chen J, Huang M, Wang H, Fang L. Unveiling the impacts of microplastics on cadmium transfer in the soil-plant-human system: A review. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135221. [PMID: 39096630 DOI: 10.1016/j.jhazmat.2024.135221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/02/2024] [Accepted: 07/14/2024] [Indexed: 08/05/2024]
Abstract
The co-contamination of soils by microplastics (MPs) and cadmium (Cd), one of the most perilous heavy metals, is emerging as a significant global concern, posing risks to plant productivity and human health. However, there remains a gap in the literature concerning comprehensive evaluations of the combined effects of MPs and Cd on soil-plant-human systems. This review examines the interactions and co-impacts of MPs and Cd in soil-plant-human systems, elucidating their mechanisms and synergistic effects on plant development and health risks. We also review the origins and contamination levels of MPs and Cd, revealing that sewage, atmospheric deposition, and biosolid applications are contributors to the contamination of soil with MPs and Cd. Our meta-analysis demonstrates that MPs significantly (p<0.05) increase the bioavailability of soil Cd and the accumulation of Cd in plant shoots by 6.9 and 9.3 %, respectively. The MPs facilitate Cd desorption from soils through direct adsorption via surface complexation and physical adsorption, as well as indirectly by modifying soil physicochemical properties, such as pH and dissolved organic carbon, and altering soil microbial diversity. These interactions augment the bioavailability of Cd, along with MPs, adversely affect plant growth and its physiological functions. Moreover, the ingestion of MPs and Cd through the food chain significantly enhances the bioaccessibility of Cd and exacerbates histopathological alterations in human tissues, thereby amplifying the associated health risks. This review provides insights into the coexistence of MPs and Cd and their synergistic effects on soil-plant-human systems, emphasizing the need for further research in this critical subject area.
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Affiliation(s)
- Fengyu Huang
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Chen
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xing Yang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Environmental Science and Engineering, Hainan University, Haikou 570228, China.
| | - Paramsothy Jeyakumar
- Environmental Sciences Group, School of Agriculture and Environment, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Zhe Wang
- College of Environment and Resources, Southwest University of Science & Technology, Mianyang 621010, China
| | - Shiyong Sun
- College of Environment and Resources, Southwest University of Science & Technology, Mianyang 621010, China
| | - Tianyi Qiu
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China
| | - Yi Zeng
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China
| | - Jing Chen
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Huang
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China
| | - Hailong Wang
- School of Environmental and Chemical Engineering, Foshan University, Foshan 528000, China; Guangdong Provincial Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Linchuan Fang
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
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2
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Chen X, Wang G, Zeng X, Li W, Zhou M. Unveiling the Role of Water on π-π Stacking Through Microwave Spectroscopy of (Thiophene) 2-(Water) 1-2 Clusters. J Am Chem Soc 2024; 146:1484-1490. [PMID: 38057276 DOI: 10.1021/jacs.3c10887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
There has been an ongoing debate about whether water enhances or hinders π-π stacking, a phenomenon crucial in various biological and chemical systems. In this study, the influence of water on π-π stacking is investigated by microwave spectroscopic observation of gas-phase hydrated clusters of thiophene dimers. Two isomers of (C4H4S)2-H2O and two isomers of (C4H4S)2-(H2O)2 have been unambiguously identified. These identifications are supported by quantum chemistry calculations and isotopic measurements. In each of these conformations, water molecules are situated between aromatic pairs, forming distinctive interactions. Water molecules engage with thiophene molecules either as hydrogen bond donors through OH···π interactions or as hydrogen bond acceptors through CH···O interactions. The energy decomposition analysis indicates that the bonding pattern of water molecules significantly affects the π···π interactions between aromatic rings. These findings offer valuable structural insights into the role of water in shaping π-π stacking.
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Affiliation(s)
- Xinlei Chen
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Songhu Road 2005, Shanghai 200438, China
| | - Guanjun Wang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Songhu Road 2005, Shanghai 200438, China
| | - Xiaoqing Zeng
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Songhu Road 2005, Shanghai 200438, China
| | - Weixing Li
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Songhu Road 2005, Shanghai 200438, China
| | - Mingfei Zhou
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Songhu Road 2005, Shanghai 200438, China
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3
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Ding Y, Chen S, Zhang F, Li W, Ge G, Liu T, Yang Q. Chitinase is a Potent Insecticidal Molecular Target of Camptothecin and Its Derivatives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1845-1851. [PMID: 36655791 DOI: 10.1021/acs.jafc.2c06607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Camptothecin (CPT) is a prominent molecule in natural product research because of its application prospects in medicine and agriculture. In this study, CPT and its derivatives were discovered to be competitive inhibitors of group II and group h insect chitinases, both of which are key components of insect chitinolytic systems. CPT and 7-ethyl-10-hydroxycamptothecin (SN-38) inhibited group II chitinase from Ostrinia furnacalis (OfChtII) with Ki values of 5.1 and 2.0 μM, respectively. Results from tryptophan fluorescence spectroscopy, molecular docking analysis, and molecular dynamics simulations revealed that both CPT and SN-38 inhibit OfChtII-C1 by interacting with solvent-exposed tryptophan residues in a substrate-binding cleft. CPT exhibited high insecticidal activity toward the orthopteran pest Locusta migratoria, possibly because of the midgut metabolism of CPT, with only moderate activities toward lepidopteran pests. Even though SN-38 exhibited much lower insecticidal activities than CPT, it still showed higher inhibitory activity toward chitinase. This study reports a new molecular target of CPT and provides insights into molecular design of CPT-based insecticides against different kinds of pests.
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Affiliation(s)
- Yi Ding
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Sizhe Chen
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Feng Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wenda Li
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Tian Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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4
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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5
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Strom A, Shah R, Dolot R, Rogers MS, Tong CL, Wang D, Xia Y, Lipscomb JD, Wagner CR. Dynamic Long-Range Interactions Influence Substrate Binding and Catalysis by Human Histidine Triad Nucleotide-Binding Proteins (HINTs), Key Regulators of Multiple Cellular Processes and Activators of Antiviral ProTides. Biochemistry 2022; 61:2648-2661. [PMID: 36398895 PMCID: PMC9854251 DOI: 10.1021/acs.biochem.2c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human histidine triad nucleotide-binding (hHINT) proteins catalyze nucleotide phosphoramidase and acyl-phosphatase reactions that are essential for the activation of antiviral proTides, such as Sofosbuvir and Remdesivir. hHINT1 and hHINT2 are highly homologous but exhibit disparate roles as regulators of opioid tolerance (hHINT1) and mitochondrial activity (hHINT2). NMR studies of hHINT1 reveal a pair of dynamic surface residues (Q62, E100), which gate a conserved water channel leading to the active site 13 Å away. hHINT2 crystal structures identify analogous residues (R99, D137) and water channel. hHINT1 Q62 variants significantly alter the steady-state kcat and Km for turnover of the fluorescent substrate (TpAd), while stopped-flow kinetics indicate that KD also changes. hHINT2, like hHINT1, exhibits a burst phase of adenylation, monitored by fluorescent tryptamine release, prior to rate-limiting hydrolysis and nucleotide release. hHINT2 exhibits a much smaller burst-phase amplitude than hHINT1, which is further diminished in hHINT2 R99Q. Kinetic simulations suggest that amplitude variations can be accounted for by a variable fluorescent yield of the E·S complex from changes in the environment of bound TpAd. Isothermal titration calorimetry measurements of inhibitor binding show that these hHINT variants also alter the thermodynamic binding profile. We propose that these altered surface residues engender long-range dynamic changes that affect the orientation of bound ligands, altering the thermodynamic and kinetic characteristics of hHINT active site function. Thus, studies of the cellular roles and proTide activation potential by hHINTs should consider the importance of long-range interactions and possible protein binding surfaces far from the active site.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rachit Shah
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rafal Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Cher-Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David Wang
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Youlin Xia
- Department of Structural Biology, St. Jude’s Research Hospital, Memphis, Tennessee 38105, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Carston R. Wagner
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States,Address correspondence to: Carston R. Wagner, University of Minnesota, Department of Medicinal Chemistry, 2231 6th Street S.E., Cancer & Cardiovascular Research Building, Minneapolis, Minnesota 55455, USA,
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6
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Paik D, Lee H, Kim H, Choi JM. Thermodynamics of π–π Interactions of Benzene and Phenol in Water. Int J Mol Sci 2022; 23:ijms23179811. [PMID: 36077201 PMCID: PMC9456204 DOI: 10.3390/ijms23179811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The π–π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π–π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy–entropy compensation. Our comprehensive computational study of the solvation effect on π–π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.
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Affiliation(s)
- Dooam Paik
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hankyul Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Correspondence: (H.K.); (J.-M.C.)
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
- Correspondence: (H.K.); (J.-M.C.)
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7
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Uppala S, Vullendula SKA, Yarlagadda DL, Dengale SJ. Exploring the utility of co-amorphous materials to concurrently improve the solubility and permeability of Fexofenadine. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Volarić J, Szymanski W, Simeth NA, Feringa BL. Molecular photoswitches in aqueous environments. Chem Soc Rev 2021; 50:12377-12449. [PMID: 34590636 PMCID: PMC8591629 DOI: 10.1039/d0cs00547a] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 12/17/2022]
Abstract
Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.
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Affiliation(s)
- Jana Volarić
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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9
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Loeffler JR, Fernández-Quintero ML, Waibl F, Quoika PK, Hofer F, Schauperl M, Liedl KR. Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning. Front Chem 2021; 9:641610. [PMID: 33842433 PMCID: PMC8032969 DOI: 10.3389/fchem.2021.641610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Stacking interactions play a crucial role in drug design, as we can find aromatic cores or scaffolds in almost any available small molecule drug. To predict optimal binding geometries and enhance stacking interactions, usually high-level quantum mechanical calculations are performed. These calculations have two major drawbacks: they are very time consuming, and solvation can only be considered using implicit solvation. Therefore, most calculations are performed in vacuum. However, recent studies have revealed a direct correlation between the desolvation penalty, vacuum stacking interactions and binding affinity, making predictions even more difficult. To overcome the drawbacks of quantum mechanical calculations, in this study we use neural networks to perform fast geometry optimizations and molecular dynamics simulations of heteroaromatics stacked with toluene in vacuum and in explicit solvation. We show that the resulting energies in vacuum are in good agreement with high-level quantum mechanical calculations. Furthermore, we show that using explicit solvation substantially influences the favored orientations of heteroaromatic rings thereby emphasizing the necessity to include solvation properties starting from the earliest phases of drug design.
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Affiliation(s)
- Johannes R Loeffler
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Patrick K Quoika
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Florian Hofer
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Michael Schauperl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Center of Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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10
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Khalilinia E, Ebrahimi A. π-Stacking effects on acid capacity of p-aminobenzoic acid. Struct Chem 2020. [DOI: 10.1007/s11224-020-01530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Li W, Ding G, Gao H, Zhuang Y, Gu X, Peijnenburg WJGM. Prediction of octanol-air partition coefficients for PCBs at different ambient temperatures based on the solvation free energy and the dimer ratio. CHEMOSPHERE 2020; 242:125246. [PMID: 31704525 DOI: 10.1016/j.chemosphere.2019.125246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/19/2019] [Accepted: 10/27/2019] [Indexed: 06/10/2023]
Abstract
Temperature-dependent octanol-air partition coefficients (KOA) are of great importance in assessing the environmental behavior and fate of persistent organic pollutants including polychlorinated biphenyls (PCBs). Due to the tremendous amounts of time, effort and cost needed for the experimental determination of KOA, it is desirable to develop a rapid and precise predictive method to estimate KOA just based on molecular structure. In the present study, a predictive model for log KOA of PCBs at ambient temperatures was developed based on the thermodynamic relationship between KOA and the solvation free energy from air to octanol (ΔGOA). For the calculation of ΔGOA of PCBs, the optimal combination of theoretical method and basis-set was identified to be HF/MIDI!6D for both geometry optimization and energy calculation. Dimer formation could affect the partition behavior and promote the apparent KOA values of PCBs. After taking the effect of dimer formation into account, the goodness-of-fit, predictive ability, and robustness of the predictive model were significantly improved. Apparent log KOA values of PCBs at different ambient temperatures ranging from 283.15 to 303.15 K were predicted. Compared with other reported models, the model developed in the present study had not only comparable goodness-of-fit and predictive ability, but also a universal application domain and the relative independency of experimental data. Therefore, the solvation free energy method could be a promising method for the prediction of KOA.
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Affiliation(s)
- Wanran Li
- College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China
| | - Guanghui Ding
- College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China.
| | - Hong Gao
- Department of Physics, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China
| | - Yuting Zhuang
- College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China
| | - Xiaoyue Gu
- College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China
| | - Willie J G M Peijnenburg
- Center for Safety of Substances and Products, National Institute of Public Health and the Environment, P.O. Box 1, Bilthoven, the Netherlands; Institute of Environmental Sciences (CML), Leiden University, Leiden, 2300, the Netherlands
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12
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Kumar A, Mahato J, Dixit M, Patwari GN. Progressive Hydrophobicity of Fluorobenzenes. J Phys Chem B 2019; 123:10083-10088. [PMID: 31661279 DOI: 10.1021/acs.jpcb.9b08057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potentials of mean force for the dimers of fluorobenzenes sample both π-stacked and T-shaped structures for partially fluorinated benzenes, namely, 1,4-difluorobenzene, 1,3,5-trifluorobenzene, and 1,2,4,5-tetrafluorobenzene, and sample only the T-shaped structures for benzene and hexafluorobenzene. While the free energy for the dimerization in water is very weakly dependent on the number of fluorine atoms, the formation of π-stacked structures is entropy-driven and the T-shaped structures appear due to an enthalpic minimum. Interestingly, the solvation behavior suggests that the accumulation of water around the contact and solvent-separated pairs decreases with the increase in the number of fluorine atoms, which signifies progressive hydrophobicity of fluorobenzenes.
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Affiliation(s)
- Anuj Kumar
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India.,Prithwi Chand Vigyan College, Jai Prakash Vishwavidyalaya , Chapra , Saran, Bihar 841301 , India
| | - Jaladhar Mahato
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
| | - Mayank Dixit
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
| | - G Naresh Patwari
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
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13
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Loeffler JR, Schauperl M, Liedl KR. Hydration of Aromatic Heterocycles as an Adversary of π-Stacking. J Chem Inf Model 2019; 59:4209-4219. [PMID: 31566975 PMCID: PMC7032848 DOI: 10.1021/acs.jcim.9b00395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydration is one of the key players in the protein-ligand binding process. It not only influences the binding process per se, but also the drug's absorption, distribution, metabolism, and excretion properties. To gain insights into the hydration of aromatic cores, the solvation thermodynamics of 40 aromatic mono- and bicyclic systems, frequently occurring in medicinal chemistry, are investigated. Thermodynamics is analyzed with two different methods: grid inhomogeneous solvation theory (GIST) and thermodynamic integration (TI). Our results agree well with previously published experimental and computational solvation free energies. The influence of adding heteroatoms to aromatic systems and how the position of these heteroatoms impacts the compound's interactions with water is studied. The solvation free energies of these heteroaromatics are highly correlated to their gas phase interaction energies with benzene: compounds showing a high interaction energy also have a high solvation free energy value. Therefore, replacing a compound with one having a higher gas phase interaction energy might not result in the expected improvement in affinity. The desolvation costs counteract the higher stacking interactions, hence weakening or even inverting the expected gain in binding free energy.
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Affiliation(s)
- Johannes R Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Tyrol , Austria
| | - Michael Schauperl
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92039-0736 , United States
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Tyrol , Austria
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Structure, Dynamics, and Wettability of Water at Metal Interfaces. Sci Rep 2019; 9:14805. [PMID: 31616006 PMCID: PMC6794260 DOI: 10.1038/s41598-019-51323-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022] Open
Abstract
The water/metal interface often governs important chemophysical processes in various technologies. Therefore, from scientific and engineering perspectives, the detailed molecular-level elucidation of the water/metal interface is of high priority, but the related research is limited. In experiments, the surface-science techniques, which can provide full structural details of the surface, are not easy to directly apply to the interfacial systems under ambient conditions, and the well-defined facets cannot be entirely free from contamination at the contact with water. To answer long-standing debates regarding the wettability, structure, and dynamics of water at metal interfaces, we here develop reliable first-principles-based multiscale simulations. Using the state-of-the-art simulations, we find that the clean metal surfaces are actually superhydrophilic and yield zero contact angles. Furthermore, we disclose an inadequacy of widespread ice-like bilayer model of the water adlayers on metal surfaces from both averaged structural and dynamic points of view. Our findings on the nature of water on metal surfaces provide new molecular level perspectives on the tuning and design of water/metal interfaces that are at the heart of many energy applications.
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