1
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He M, Yao Y, Yang Z, Li B, Wang J, Wang Y, Kong Y, Zhou Z, Zhao W, Yang XJ, Tang J, Wu B. Biomimetic Charge-Neutral Anion Receptors for Reversible Binding and Release of Highly Hydrated Phosphate in Water. Angew Chem Int Ed Engl 2024; 63:e202406946. [PMID: 38802316 DOI: 10.1002/anie.202406946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
Control of phosphate capture and release is vital in environmental, biological, and pharmaceutical contexts. However, the binding of trivalent phosphate (PO4 3-) in water is exceptionally difficult due to its high hydration energy. Based on the anion coordination chemistry of phosphate, in this study, four charge-neutral tripodal hexaurea receptors (L1-L4), which were equipped with morpholine and polyethylene glycol terminal groups to enhance their solubility in water, were synthesized to enable the pH-triggered phosphate binding and release in aqueous solutions. Encouragingly, the receptors were found to bind PO4 3- anion in a 1 : 1 ratio via hydrogen bonds in 100 % water solutions, with L1 exhibiting the highest binding constant (1.2×103 M-1). These represent the first neutral anion ligands to bind phosphate in 100 % water and demonstrate the potential for phosphate capture and release in water through pH-triggered mechanisms, mimicking native phosphate binding proteins. Furthermore, L1 can also bind multiple bioavailable phosphate species, which may serve as model systems for probing and modulating phosphate homeostasis in biological and biomedical researches.
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Affiliation(s)
- Maolin He
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Yuhang Yao
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zihe Yang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Boyang Li
- College of Chemistry & Pharmacy, Northwest A&F University, Xian Yang Shi, Yangling, 712100, China
| | - Ji Wang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Yanchao Wang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Yu Kong
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Zihan Zhou
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Wei Zhao
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Xiao-Juan Yang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Juan Tang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Biao Wu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
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2
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Guo D, Zhang Z, Sun J, Zhao H, Hou W, Du N. A Fusion-Growth Protocell Model Based on Vesicle Interactions with Pyrite Particles. Molecules 2024; 29:2664. [PMID: 38893538 PMCID: PMC11173516 DOI: 10.3390/molecules29112664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Protocell models play a pivotal role in the exploration of the origin of life. Vesicles are one type of protocell model that have attracted much attention. Simple single-chain amphiphiles (SACs) and organic small molecules (OSMs) possess primitive relevance and were most likely the building blocks of protocells on the early Earth. OSM@SAC vesicles have been considered to be plausible protocell models. Pyrite (FeS2), a mineral with primitive relevance, is ubiquitous in nature and plays a crucial role in the exploration of the origin of life in the mineral-water interface scenario. "How do protocell models based on OSM@SAC vesicles interact with a mineral-water interface scenario that simulates a primitive Earth environment" remains an unresolved question. Hence, we select primitive relevant sodium monododecyl phosphate (SDP), isopentenol (IPN) and pyrite (FeS2) mineral particles to build a protocell model. The model investigates the basic physical and chemical properties of FeS2 particles and reveals the effects of the size, content and duration of interaction of FeS2 particles on IPN@SDP vesicles. This deepens the understanding of protocell growth mechanisms in scenarios of mineral-water interfaces in primitive Earth environments and provides new information for the exploration of the origin of life.
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Affiliation(s)
- Dong Guo
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Ziyue Zhang
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jichao Sun
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Hui Zhao
- National Engineering Technology Research Center for Colloidal Materials, Shandong University, Jinan 250100, China
| | - Wanguo Hou
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
- National Engineering Technology Research Center for Colloidal Materials, Shandong University, Jinan 250100, China
| | - Na Du
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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3
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Štěpánová S, Kašička V. Determination of physicochemical parameters of (bio)molecules and (bio)particles by capillary electromigration methods. J Sep Sci 2024; 47:e2400174. [PMID: 38867483 DOI: 10.1002/jssc.202400174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 06/14/2024]
Abstract
The review provides an overview of recent developments and applications of capillary electromigration (CE) methods for the determination of important physicochemical parameters of various (bio)molecules and (bio)particles. These parameters include actual and limiting (absolute) ionic mobilities, effective electrophoretic mobilities, effective charges, isoelectric points, electrokinetic potentials, hydrodynamic radii, diffusion coefficients, relative molecular masses, acidity (ionization) constants, binding constants and stoichiometry of (bio)molecular complexes, changes of Gibbs free energy, enthalpy and entropy and rate constants of chemical reactions and interactions, retention factors and partition and distribution coefficients. For the determination of these parameters, the following CE methods are employed: zone electrophoresis in a free solution or in sieving media, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography. In the individual sections, the procedures for the determination of the above parameters by the particular CE methods are described.
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Affiliation(s)
- Sille Štěpánová
- Electromigration methods, Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Kašička
- Electromigration methods, Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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4
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Rodrigues CC, Harayashiki CAY, S Pereira E, Rodrigues GLS, Neves BJ, Rocha TL. How do microplastics alter molluscicidal activity? Effects of weathered microplastics and niclosamide in developing freshwater snails. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171165. [PMID: 38395171 DOI: 10.1016/j.scitotenv.2024.171165] [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: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Despite the wide distribution and persistence of microplastics (MPs), their interactive effects with molluscicides are unknown. Schistosomiasis, a neglected tropical disease, affects 236.6 million people worldwide. Niclosamide (NCL) is the only molluscicide recommended by the World Health Organization (WHO) and it is used to control the population of Schistosoma spp.'s intermediate host. Thus, this study aimed to evaluate of the interaction between polyethylene (PE) MPs and NCL, and their associated toxicity in the freshwater snail Biomphalaria glabrata (Say 1818). Weathered PE MPs were characterized and theoretical analysis of NCL-MP adsorption nature was made using quantum mechanical calculations. The toxicity of NCL isolated (0.0265 to 0.0809 mg L-1) and under interaction with PE MPs (3400 μg L-1) in B. glabrata embryos and newly hatched snails was analyzed. In silico analysis confirmed the adsorption mechanisms of NCL into PE MPs. PE MPs decreased the NCL toxicity to both B. glabrata developmental stages, increasing their survival and NCL lethal concentrations, indicating concerns regarding NCL use as molluscicide in aquatic environments polluted by MPs. In conclusion, MPs may change the efficiency of chemicals used in snail control programs.
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Affiliation(s)
- Cândido C Rodrigues
- Laboratory of Environmental Biotechnology and Ecotoxicology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Cyntia A Y Harayashiki
- Laboratory of Environmental Biotechnology and Ecotoxicology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Eufrásia S Pereira
- Laboratory of Cheminformatics, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Gabriel L S Rodrigues
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Bruno J Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Thiago L Rocha
- Laboratory of Environmental Biotechnology and Ecotoxicology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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5
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Mehta MJ, Kim HJ, Lim SB, Naito M, Miyata K. Recent Progress in the Endosomal Escape Mechanism and Chemical Structures of Polycations for Nucleic Acid Delivery. Macromol Biosci 2024; 24:e2300366. [PMID: 38226723 DOI: 10.1002/mabi.202300366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/22/2023] [Indexed: 01/17/2024]
Abstract
Nucleic acid-based therapies are seeing a spiralling surge. Stimuli-responsive polymers, especially pH-responsive ones, are gaining widespread attention because of their ability to efficiently deliver nucleic acids. These polymers can be synthesized and modified according to target requirements, such as delivery sites and the nature of nucleic acids. In this regard, the endosomal escape mechanism of polymer-nucleic acid complexes (polyplexes) remains a topic of considerable interest owing to various plausible escape mechanisms. This review describes current progress in the endosomal escape mechanism of polyplexes and state-of-the-art chemical designs for pH-responsive polymers. The importance is also discussed of the acid dissociation constant (i.e., pKa) in designing the new generation of pH-responsive polymers, along with assays to monitor and quantify the endosomal escape behavior. Further, the use of machine learning is addressed in pKa prediction and polymer design to find novel chemical structures for pH responsiveness. This review will facilitate the design of new pH-responsive polymers for advanced and efficient nucleic acid delivery.
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Affiliation(s)
- Mohit J Mehta
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
- Department of Biological Engineering, College of Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Sung Been Lim
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Mitsuru Naito
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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6
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Štěpánová S, Andris E, Gutten O, Buděšínský M, Dejmek M, Břehová P, Rulíšek L, Kašička V. Acidity constants and protonation sites of cyclic dinucleotides determined by capillary electrophoresis, quantum chemical calculations, and NMR spectroscopy. Electrophoresis 2024; 45:687-705. [PMID: 38059733 DOI: 10.1002/elps.202300232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/11/2023] [Accepted: 11/18/2023] [Indexed: 12/08/2023]
Abstract
Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite for understanding their biological functions. Herein, we examine acid-base and electromigration properties of selected CDNs employing capillary electrophoresis (CE), density functional theory (DFT), and nuclear magnetic resonance (NMR) spectroscopy to provide benchmark pKa values, as well as to unambiguously determine the protonation sites. Acidity constants (pKa) of the NH+ moieties of adenine and guanine bases and actual and limiting ionic mobilities of CDNs were determined by nonlinear regression analysis of the pH dependence of their effective electrophoretic mobilities measured by CE in aqueous background electrolytes in a wide pH range (0.98-11.48), at constant temperature (25°C), and constant ionic strength (25 mM). The thermodynamic pKa values were found to be in the range 3.31-4.56 for adenine and 2.28-3.61 for guanine bases, whereas the pKa of enol group of guanine base was in the range 10.21-10.40. Except for systematic shifts of ∼2 pKa, the pKa values calculated by the DFT-D3//COSMO-RS composite protocol that included large-scale conformational sampling and "cross-morphing" were in a relatively good agreement with the pKas determined by CE and predict N1 atom of adenine and N7 atom of guanine as the protonation sites. The protonation of the N1 atom of adenine and N7 atom of guanine in acidic background electrolytes (BGEs) and the dissociation of the enol group of guanine in alkaline BGEs was confirmed also by NMR spectroscopy.
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Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Břehová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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7
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Putko P, Romero JA, Kazimierczuk K. A pH-enhanced resolution in benchtop NMR spectroscopy. Analyst 2024; 149:1998-2003. [PMID: 38421293 DOI: 10.1039/d3an02000b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
NMR spectroscopy is one of the most potent methods in analytical chemistry. NMR titration experiments are particularly useful since they measure molecular binding affinities and other concentration-dependent effects. These experiments, however, require a long series of measurements. An alternative to these serial measurements has recently been presented, exploiting a pH (or generally - a concentration) gradient along the NMR tube. The proposed experiment, although efficient, was based on the sensitivity- and hardware-demanding chemical shift imaging (CSI) method. Thus, it is practically limited to high-resolution NMR spectrometers. This paper proposes modifying and adapting the approach to the popular and cost-efficient benchtop NMR machines. Instead of CSI, we use a device that shifts the NMR tube vertically to measure the spectra of different sample volumes, which have different pH values due to the established gradient along the tube. We demonstrate the potential of the method on the test samples of L-tyrosine and 2,6-lutidine, and two real samples from the food industry - an infant formula and an energy drink. The proposed method boosts spectral resolution and allows for the sampling of a broader range of pH values when compared to the original approach.
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Affiliation(s)
- Paulina Putko
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland.
| | - Javier A Romero
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland.
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8
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Roh EH, Sullivan MO, Epps TH. Which Lipid Nanoparticle (LNP) Designs Work? A Simple Kinetic Model Linking LNP Chemical Structure to In Vivo Delivery Performance. ACS APPLIED MATERIALS & INTERFACES 2024; 16:13399-13410. [PMID: 38466900 DOI: 10.1021/acsami.3c15424] [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: 03/13/2024]
Abstract
Although lipid nanoparticles (LNPs) are the predominant nanocarriers for short-interfering RNA (siRNA) delivery, most therapies use nearly identical formulations that have taken 30 years to design but lack the diverse property ranges necessary for versatile application. This dearth in variety and the extended timeline for implementation are attributed to a limited understanding of how LNP properties facilitate overcoming biological barriers. Herein, a simple kinetic model was developed by using major rate-limiting steps for siRNA delivery, and this model enabled the identification of a critical parameter to predict LNP efficacy without extensive experimental testing. A volume-averaged log D, the "solubility" of charged molecules as a function of pH weighted by component volume fractions, resulted in a good correlation between LNP composition and siRNA delivery. Both the effects of modifying the structures of ionizable lipids and LNP composition on gene silencing were easily captured in the model predictions. Thus, this approach provides a robust LNP structure-activity relationship to dramatically accelerate the realization of effective LNP formulations.
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Affiliation(s)
- Esther H Roh
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Thomas H Epps
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- Center for Research in Soft matter and Polymers (CRiSP), University of Delaware, Newark Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
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9
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Wilson C, Karttunen M, de Groot BL, Gapsys V. Accurately Predicting Protein p Ka Values Using Nonequilibrium Alchemy. J Chem Theory Comput 2023; 19:7833-7845. [PMID: 37820376 PMCID: PMC10653114 DOI: 10.1021/acs.jctc.3c00721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 10/13/2023]
Abstract
The stability, solubility, and function of a protein depend on both its net charge and the protonation states of its individual residues. pKa is a measure of the tendency for a given residue to (de)protonate at a specific pH. Although pKa values can be resolved experimentally, theory and computation provide a compelling alternative. To this end, we assess the applicability of a nonequilibrium (NEQ) alchemical free energy method to the problem of pKa prediction. On a data set of 144 residues that span 13 proteins, we report an average unsigned error of 0.77 ± 0.09, 0.69 ± 0.09, and 0.52 ± 0.04 pK for aspartate, glutamate, and lysine, respectively. This is comparable to current state-of-the-art predictors and the accuracy recently reached using free energy perturbation methods (e.g., FEP+). Moreover, we demonstrate that our open-source, pmx-based approach can accurately resolve the pKa values of coupled residues and observe a substantial performance disparity associated with the lysine partial charges in Amber14SB/Amber99SB*-ILDN, for which an underused fix already exists.
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Affiliation(s)
- Carter
J. Wilson
- Department
of Mathematics, The University of Western
Ontario, N6A 5B7 London, Canada
- Centre
for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, N6A 5B7 London, Canada
| | - Mikko Karttunen
- Centre
for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, N6A 5B7 London, Canada
- Department
of Physics & Astronomy, The University
of Western Ontario, N6A
5B7 London, Canada
- Department
of Chemistry, The University of Western
Ontario, N6A 5B7 London, Canada
| | - Bert L. de Groot
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, 37077 Göttingen, Germany
| | - Vytautas Gapsys
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, 37077 Göttingen, Germany
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
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10
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Cárdenas G, Ledentu V, Huix-Rotllant M, Olivucci M, Ferré N. Automatic Rhodopsin Modeling with Multiple Protonation Microstates. J Phys Chem A 2023; 127:9365-9380. [PMID: 37877699 DOI: 10.1021/acs.jpca.3c05413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.
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Affiliation(s)
| | | | | | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
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11
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Pereira RW, Ramabhadran RO. Accurate Computation of Aqueous p Kas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box p K-Yay Method. J Phys Chem A 2023; 127:9121-9138. [PMID: 37862610 DOI: 10.1021/acs.jpca.3c02977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.
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Affiliation(s)
- Roshni W Pereira
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
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12
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Guo J, Albesa A, Wexler C. Advantages of Multidimensional Biasing in Accelerated Dynamics: Application to the Calculation of the Acid p Ka for Acetic Acid. J Phys Chem B 2023; 127:8446-8455. [PMID: 37738501 DOI: 10.1021/acs.jpcb.3c03795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
The use of accelerated sampling methods such as metadynamics has shown a significant advantage in calculations that involve infrequent events, which would otherwise require sampling a prohibitive number of configurations to determine the difference in free energies between two or more chemically distinct states such as in the calculation of acid dissociation constants Ka. In this case, the most common method is to bias the system via a single collective variable (CV) representing the coordination number of the proton donor group, which yields results in reasonable agreement with experiments. Here we study the deprotonation of acetic acid using the reactive force field ReaxFF and observe a significant dependence of Ka on the simulation box size when biasing only the coordination number CV, which is due to incomplete sampling of the deprotonated state for small simulation systems and inefficient sampling for larger ones. Incorporating a second CV representing the distance between the H3O+ cation and the acetate anion results in substantially more efficient sampling, both accelerating the dynamics and virtually eliminating the computational box size dependence.
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Affiliation(s)
- Jiasen Guo
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Alberto Albesa
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
- INIFTA, Universidad Nacional de La Plata, B1900 La Plata, Argentina
| | - Carlos Wexler
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
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13
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Berga M, Logviss K, Lauberte L, Paulausks A, Mohylyuk V. Flavonoids in the Spotlight: Bridging the Gap between Physicochemical Properties and Formulation Strategies. Pharmaceuticals (Basel) 2023; 16:1407. [PMID: 37895878 PMCID: PMC10610233 DOI: 10.3390/ph16101407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Flavonoids are hydroxylated polyphenols that are widely distributed in plants with diverse health benefits. Despite their popularity, the bioavailability of flavonoids is often overlooked, impacting their efficacy and the comparison of products. The study discusses the bioavailability-related physicochemical properties of flavonoids, with a focus on the poorly soluble compounds commonly found in dietary supplements and herbal products. This review sums up the values of pKa, log P, solubility, permeability, and melting temperature of flavonoids. Experimental and calculated data were compiled for various flavonoid subclasses, revealing variations in their physicochemical properties. The investigation highlights the challenges posed by poorly soluble flavonoids and underscores the need for enabling formulation approaches to enhance their bioavailability and therapeutic potential. Compared to aglycones, flavonoid glycosides (with sugar moieties) tend to be more hydrophilic. Most of the reviewed aglycones and glycosides exhibit relatively low log P and high melting points, making them "brick dust" candidates. To improve solubility and absorption, strategies like size reduction, the potential use of solid dispersions and carriers, as well as lipid-based formulations have been discussed.
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Affiliation(s)
| | | | | | | | - Valentyn Mohylyuk
- Laboratory of Finished Dosage Forms, Faculty of Pharmacy, Riga Stradiņš University, LV-1007 Riga, Latvia
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14
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Alcázar JJ, Misad Saide AC, Campodónico PR. Reliable and accurate prediction of basic pK[Formula: see text] values in nitrogen compounds: the pK[Formula: see text] shift in supramolecular systems as a case study. J Cheminform 2023; 15:90. [PMID: 37770903 PMCID: PMC10540475 DOI: 10.1186/s13321-023-00763-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
This article presents a quantitative structure-activity relationship (QSAR) approach for predicting the acid dissociation constant (pK[Formula: see text]) of nitrogenous compounds, including those within supramolecular complexes based on cucurbiturils. The model combines low-cost quantum mechanical calculations with QSAR methodology and linear regressions to achieve accurate predictions for a broad range of nitrogen-containing compounds. The model was developed using a diverse dataset of 130 nitrogenous compounds and exhibits excellent predictive performance, with a high coefficient of determination (R[Formula: see text]) of 0.9905, low standard error (s) of 0.3066, and high Fisher statistic (F) of 2142. The model outperforms existing methods, such as Chemaxon software and previous studies, in terms of accuracy and its ability to handle heterogeneous datasets. External validation on pharmaceutical ingredients, dyes, and supramolecular complexes based on cucurbiturils confirms the reliability of the model. To enhance usability, a script-like tool has been developed, providing a streamlined process for users to access the model. This study represents a significant advancement in pK[Formula: see text] prediction, offering valuable insights for drug design and supramolecular system optimization.
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Affiliation(s)
- Jackson J. Alcázar
- Centro de Química Médica, Universidad del Desarrollo, Av.Plaza 680, 7780272 Santiago, RM Chile
| | | | - Paola R. Campodónico
- Centro de Química Médica, Universidad del Desarrollo, Av.Plaza 680, 7780272 Santiago, RM Chile
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15
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Gadzuk-Shea MM, Hubbard EE, Gozzo TA, Bush MF. Sample pH Can Drift during Native Mass Spectrometry Experiments: Results from Ratiometric Fluorescence Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1675-1684. [PMID: 37405934 PMCID: PMC10563179 DOI: 10.1021/jasms.3c00147] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The ability of nanoelectrospray ionization (nanoESI) to generate a continuous flow of charged droplets relies on the electrolytic nature of the process. This electrochemistry can lead to the accumulation of redox products in the sample solution. This consequence can have significant implications for native mass spectrometry (MS), which aims to probe the structures and interactions of biomolecules in solution. Here, ratiometric fluorescence imaging and a pH-sensitive, fluorescent probe are used to quantify changes in solution pH during nanoESI under conditions relevant to native MS. Results show that the extent and rate of change in sample pH depends on several experimental parameters. There is a strong correlation between the extent and rate of change in solution pH and the magnitude of both the nanoESI current and electrolyte concentration. Smaller changes in solution pH are observed during experiments when a negative potential is applied than for those when a positive potential is applied. Finally, we make specific recommendations for designing native MS experiments that control for these effects.
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Affiliation(s)
- Meagan M. Gadzuk-Shea
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
- Current Affiliation: Discovery Biology, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Waltham, MA 02451
| | - Evan E. Hubbard
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
- Current Affiliation: Current Affiliation: Department of Chemistry, University of California, Riverside, California 92521
| | - Theresa A. Gozzo
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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16
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Antoniw JM, Hallman MT, Kiriakou MV, Morse T, Cranston ED. Colloidal Stability Window for Carboxylated Cellulose Nanocrystals: Considerations for Handling, Characterization, and Formulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:10321-10334. [PMID: 37459396 DOI: 10.1021/acs.langmuir.3c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
The scale of production of cellulose nanocrystals (CNCs) has increased dramatically to meet the growing demand for sustainably sourced materials. This work defines the colloidal stability window for commercially produced carboxylated CNCs (DextraCel) compared to the more traditional sulfated CNCs. Phase diagrams showing the stable, reversibly agglomerated, irreversibly aggregated/sedimented, and colloidal glass "zones" as a function of suspension pH, ionic strength, CNC surface charge content, counterion, and concentration are presented. The pKa of carboxylated CNCs was measured to be 5.1, and suspensions of carboxylated CNCs (0.5-1.5 wt %) were visually stable from pH 3 to 11 (without salt). Carboxylated CNCs were highly sensitive to ionic strength, demonstrating some agglomeration with as little as 5 mM NaCl, supporting that weak acid surface groups and lower charge contents make CNCs more sensitive to solution conditions. Surface charge content had the greatest influence on colloidal stability followed by the counterion; carboxylated CNCs were more stable in the "as-received" sodium form, whereas sulfated CNCs had improved stability in acid form after ion exchange. The stability of carboxylated CNCs with industrially relevant additives (ionic and nonionic surfactants and initiators) was also investigated. Less concentrated suspensions were more colloidally stable, emphasizing that characterization and processing of CNCs favor dilute conditions. If carboxylated CNCs are subjected to conditions outside of their colloidal stability window, simple dilution or pH adjustment does not return them to colloidally stable discrete nanoparticles; however, ultrasonication can redisperse agglomerates. This study offers guidelines for handling carboxylated CNCs to broaden the range of products that can be improved by their incorporation.
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Affiliation(s)
- Julia M Antoniw
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Madeleine T Hallman
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | | | | | - Emily D Cranston
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- Department of Wood Science, University of British Columbia, Vancouver, British Columbia, CanadaV6T 1Z3
- UBC Bioproducts Institute, 2385 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
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17
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Walton-Raaby M, Floen T, García-Díez G, Mora-Diez N. Calculating the Aqueous pK a of Phenols: Predictions for Antioxidants and Cannabinoids. Antioxidants (Basel) 2023; 12:1420. [PMID: 37507958 PMCID: PMC10376140 DOI: 10.3390/antiox12071420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
We aim to develop a theoretical methodology for the accurate aqueous pKa prediction of structurally complex phenolic antioxidants and cannabinoids. In this study, five functionals (M06-2X, B3LYP, BHandHLYP, PBE0, and TPSS) and two solvent models (SMD and PCM) were combined with the 6-311++G(d,p) basis set to predict pKa values for twenty structurally simple phenols. None of the direct calculations produced good results. However, the correlations between the calculated Gibbs energy difference of each acid and its conjugate base, ΔGaq(BA)°=ΔGaqA-°-ΔGaq(HA)°, and the experimental aqueous pKa values had superior predictive accuracy, which was also tested relative to an independent set of ten molecules of which six were structurally complex phenols. New correlations were built with twenty-seven phenols (including the phenols with experimental pKa values from the test set), which were used to make predictions. The best correlation equations used the PCM method and produced mean absolute errors of 0.26-0.27 pKa units and R2 values of 0.957-0.960. The average range of predictions for the potential antioxidants (cannabinoids) was 0.15 (0.25) pKa units, which indicates good agreement between our methodologies. The new correlation equations could be used to make pKa predictions for other phenols in water and potentially in other solvents where they might be more soluble.
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Affiliation(s)
- Max Walton-Raaby
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Tyler Floen
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
| | | | - Nelaine Mora-Diez
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
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18
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Kashyap A, Nishil B, Thatikonda S. Experimental and numerical elucidation of the fate and transport of antibiotics in aquatic environment: A review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:942. [PMID: 37436551 DOI: 10.1007/s10661-023-11482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/08/2023] [Indexed: 07/13/2023]
Abstract
This review highlights various experimental and mathematical modeling strategies to investigate the fate and transport of antibiotics that elucidate antimicrobial selective pressure in aquatic environments. Globally, the residual antibiotic concentrations in effluents from bulk drug manufacturing industries were 30- and 1500-fold greater than values reported in municipal and hospital effluents, respectively. The antibiotic concentration from different effluents enters the waterbodies that usually get diluted as they go downstream and undergo various abiotic and biotic reactive processes. In aquatic systems, photolysis is the predominant process for antibiotic reduction in the water matrix, while hydrolysis and sorption are frequently reported in the sediment compartment. The rate of antibiotic reduction varies widely with influencing factors such as the chemical properties of the antibiotics and hydrodynamic conditions of river streams. Among all, tetracycline was found to more unstable (log Kow = - 0.62 to - 1.12) that can readily undergo photolysis and hydrolysis; whereas macrolides were more stable (log Kow = 3.06 to 4.02) that are prone to biodegradation. The processes like photolysis, hydrolysis, and biodegradation followed first-order reaction kinetics while the sorption followed a second-order kinetics for most antibiotic classes with reaction rates occurring in the decreasing order of Fluoroquinolones and Sulphonamides. The reports from various experiments on abiotic and biotic processes serve as input parameters for an integrated mathematical modeling to predict the fate of the antibiotics in the aquatic environment. Various mathematical models viz. Fugacity level IV, RSEMM, OTIS, GREAT-ER, SWAT, QWASI, and STREAM-EU are discussed for their potential capabilities. However, these models do not account for microscale interactions of the antibiotics and microbial community under real-field conditions. Also, the seasonal variations for contaminant concentrations that exert selective pressure for antimicrobial resistance has not been accounted. Addressing these aspects collectively is the key to exploring the emergence of antimicrobial resistance. Therefore, a comprehensive model involving antimicrobial resistance parameters like fitness cost, bacterial population dynamics, conjugation transfer efficiency, etc. is required to predict the fate of antibiotics.
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Affiliation(s)
- Arun Kashyap
- Environmental Engineering Division, Department of Civil Engineering, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Benita Nishil
- Environmental Engineering Division, Department of Civil Engineering, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Shashidhar Thatikonda
- Environmental Engineering Division, Department of Civil Engineering, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502285, India.
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19
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Fondeur F, White TL, Coleman CJ, Diprete DP, Nash CA, Looney BB. Proton nuclear magnetic resonance (1H NMR) of flammable organic chemicals in radioactive high-level supernatant waste at the Savannah River Site (SRS). MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:407-417. [PMID: 36967631 DOI: 10.1002/mrc.5349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 06/09/2023]
Abstract
The Savannah River Site stores approximately 36 million gallons of radioactive and hazardous waste that contains approximately 245 million curies. The waste is sent through various chemical processes to reduce its volume and to separate various components. The facility plans to replace formic acid (a chemical used to reduce soluble mercury) with glycolic acid. Recycle solution with glycolate may flow back to the tank farm, where the glycolate can generate hydrogen gas by thermal and radiolytic mechanisms. The current analytical method for detecting glycolate (ion chromatography) in supernatant requires a large dilution to reduce interference from the nitrate anions. Hydrogen nuclear magnetic resonance is an analytical method that requires less sample dilution. It takes advantage of the CH2 group in glycolate. Liquid samples were spiked with four different levels of glycolate to build a calibration line, as it is recommended in the standard addition method. The detection and quantitation limits determined were 1 and 5 ppm, respectively, for 32 scans, which is well below the process limit of 10 ppm. In one test, 800 scans of a supernatant spiked with 1 ppm glycolate resulted in a -CH2 peak with a signal-to-noise ratio of 36.
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Affiliation(s)
| | - Thomas L White
- Savannah River National Laboratory, Aiken, SC, 29841, USA
| | | | | | - Charles A Nash
- Savannah River National Laboratory, Aiken, SC, 29841, USA
| | - Brian B Looney
- Savannah River National Laboratory, Aiken, SC, 29841, USA
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20
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Safronov NE, Kostova IP, Palafox MA, Belskaya NP. Combined NMR Spectroscopy and Quantum-Chemical Calculations in Fluorescent 1,2,3-Triazole-4-carboxylic Acids Fine Structures Analysis. Int J Mol Sci 2023; 24:ijms24108947. [PMID: 37240293 DOI: 10.3390/ijms24108947] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
The peculiarities of the optical properties of 2-aryl-1,2,3-triazole acids and their sodium salts were investigated in different solvents (1,4-dioxane, dimethyl sulfoxide DMSO, methanol MeOH) and in mixtures with water. The results were discussed in terms of the molecular structure formed by inter- and intramolecular noncovalent interactions (NCIs) and their ability to ionize in anions. Theoretical calculations using the Time-Dependent Density Functional Theory (TDDFT) were carried out in different solvents to support the results. In polar and nonpolar solvents (DMSO, 1,4-dioxane), fluorescence was provided by strong neutral associates. Protic MeOH can weaken the acid molecules' association, forming other fluorescent species. The fluorescent species in water exhibited similar optical characteristics to those of triazole salts; therefore, their anionic character can be assumed. Experimental 1H and 13C-NMR spectra were compared to their corresponding calculated spectra using the Gauge-Independent Atomic Orbital (GIAO) method and several relationships were established. All these findings showed that the obtained photophysical properties of the 2-aryl-1,2,3-triazole acids noticeably depend on the environment and, therefore, are good candidates as sensors for the identification of analytes with labile protons.
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Affiliation(s)
- Nikita E Safronov
- Department of Technology for Organic Synthesis, Ural Federal University, 19 Mira Str., Yekaterinburg 620002, Russia
| | - Irena P Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University-Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Mauricio Alcolea Palafox
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Nataliya P Belskaya
- Department of Technology for Organic Synthesis, Ural Federal University, 19 Mira Str., Yekaterinburg 620002, Russia
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21
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Li G, Wang Y, Sun C, Liu F. Determination of the microscopic acid dissociation constant of piperacillin and identification of dissociated molecular forms. Front Chem 2023; 11:1177128. [PMID: 37179774 PMCID: PMC10169600 DOI: 10.3389/fchem.2023.1177128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023] Open
Abstract
For amphoteric ß-lactam antibiotics, the acid dissociation constant (pK a) is a fundamental parameter to characterize physicochemical and biochemical properties of antibiotics and to predict persistence and removal of drugs. pK a of piperacillin (PIP) is determined by potentiometric titration with a glass electrode. Electrospray ionization mass spectrometry (ESI-MS) is creatively applied to verify the reasonable pK a value at every dissociation step. Two microscopic pK a values (3.37 ± 0.06 and 8.96 ± 0.10) are identified and attributed to the direct dissociation of the carboxylic acid functional group and one secondary amide group, respectively. Different from other ß-lactam antibiotics, PIP presents a dissociation pattern where direct dissociation is involved instead of protonation dissociation. Moreover, the degradation tendency of PIP in an alkaline solution may alter the dissociation pattern or dismiss the corresponding pK a of the amphoteric ß-lactam antibiotics. This work offers a reliable determination of the acid dissociation constant of PIP and a clear interpretation of the effect of stability of antibiotics on the dissociation process.
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Affiliation(s)
- Guoao Li
- Beijing Key Laboratory of Water Resources and Environmental Engineering, School of water resource and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Yaling Wang
- Beijing Municipal Research Institute of Eco-Environmental Protection, Beijing, China
- National Engineering Research Center for Urban Environmental Pollution Control, Beijing, China
| | - Chengyi Sun
- Beijing Municipal Research Institute of Eco-Environmental Protection, Beijing, China
- National Engineering Research Center for Urban Environmental Pollution Control, Beijing, China
| | - Fei Liu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, School of water resource and Environment, China University of Geosciences (Beijing), Beijing, China
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22
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Awoonor-Williams E, Golosov AA, Hornak V. Benchmarking In Silico Tools for Cysteine p Ka Prediction. J Chem Inf Model 2023; 63:2170-2180. [PMID: 36996330 DOI: 10.1021/acs.jcim.3c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Accurate estimation of the pKa's of cysteine residues in proteins could inform targeted approaches in hit discovery. The pKa of a targetable cysteine residue in a disease-related protein is an important physiochemical parameter in covalent drug discovery, as it influences the fraction of nucleophilic thiolate amenable to chemical protein modification. Traditional structure-based in silico tools are limited in their predictive accuracy of cysteine pKa's relative to other titratable residues. Additionally, there are limited comprehensive benchmark assessments for cysteine pKa predictive tools. This raises the need for extensive assessment and evaluation of methods for cysteine pKa prediction. Here, we report the performance of several computational pKa methods, including single-structure and ensemble-based approaches, on a diverse test set of experimental cysteine pKa's retrieved from the PKAD database. The dataset consisted of 16 wildtype and 10 mutant proteins with experimentally measured cysteine pKa values. Our results highlight that these methods are varied in their overall predictive accuracies. Among the test set of wildtype proteins evaluated, the best method (MOE) yielded a mean absolute error of 2.3 pK units, highlighting the need for improvement of existing pKa methods for accurate cysteine pKa estimation. Given the limited accuracy of these methods, further development is needed before these approaches can be routinely employed to drive design decisions in early drug discovery efforts.
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Affiliation(s)
- Ernest Awoonor-Williams
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrei A Golosov
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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23
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Schulz JA, Stresser DM, Kalvass JC. Plasma Protein-Mediated Uptake and Contradictions to the Free Drug Hypothesis: A Critical Review. Drug Metab Rev 2023:1-34. [PMID: 36971325 DOI: 10.1080/03602532.2023.2195133] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
According to the free drug hypothesis (FDH), only free, unbound drug is available to interact with biological targets. This hypothesis is the fundamental principle that continues to explain the vast majority of all pharmacokinetic and pharmacodynamic processes. Under the FDH, the free drug concentration at the target site is considered the driver of pharmacodynamic activity and pharmacokinetic processes. However, deviations from the FDH are observed in hepatic uptake and clearance predictions, where observed unbound intrinsic hepatic clearance (CLint,u) is larger than expected. Such deviations are commonly observed when plasma proteins are present and form the basis of the so-called plasma protein-mediated uptake effect (PMUE). This review will discuss the basis of plasma protein binding as it pertains to hepatic clearance based on the FDH, as well as several hypotheses that may explain the underlying mechanisms of PMUE. Notably, some, but not all, potential mechanisms remained aligned with the FDH. Finally, we will outline possible experimental strategies to elucidate PMUE mechanisms. Understanding the mechanisms of PMUE and its potential contribution to clearance underprediction is vital to improving the drug development process.
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24
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Han GE, Priefer R. A systematic review of various pK a determination techniques. Int J Pharm 2023; 635:122783. [PMID: 36858133 DOI: 10.1016/j.ijpharm.2023.122783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023]
Abstract
The pKa values of functional groups is crucial in determining the pharmacokinetic properties of a drug, affecting its absorption and thus bioavailability. This physicochemical property is also vital for the designing of drug excipients and vehicles. There are currently 13 known methods of determining a pKa value, namely: potentiometric titration, spectrometry, fluorometry, NMR, HPLC, conductometry, electrophoresis, voltammetry, solubility, partition coefficient, calorimetry, computational, and surface tension. Some of these techniques are more widely utilized and well-established compared to others, with each having their inherent advantages and disadvantages. This review discusses each of the aforementioned techniques with emphasis on their pros and cons.
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Affiliation(s)
- Gi Eun Han
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, United States
| | - Ronny Priefer
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, United States.
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25
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Determination of the Ionization Constant of the Hydroxyl Group of Glycolic Acid from 5 to 45 °C by Raman Spectroscopy. J SOLUTION CHEM 2023. [DOI: 10.1007/s10953-022-01243-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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26
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Merkel A, Vavro M, Čopák L, Dvořák L, Ahrné L, Ruchti C. Lactose Mother Liquor Stream Valorisation Using an Effective Electrodialytic Process. MEMBRANES 2022; 13:29. [PMID: 36676836 PMCID: PMC9860800 DOI: 10.3390/membranes13010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
The integrated electrodialysis (ED) process supports valorisation of a lactose-rich side stream from the dairy industry, creating an important source of milk sugar used in various branches of the industry. This work focuses on the optimization of the downstream processes before the crystallization of lactose. The process line includes a pre-treatment and desalination by ED of the industrial waste solution of the lactose mother liquor (LML). The LML was diluted to 25% total solids to overcome hydraulic issues with the ED desalination process. Two different levels of electrical conductivity reduction (70% and 90%) of the LML solutions were applied to decrease the mineral components and organic acids of the LML samples. The ED performance parameters such as ash transfer rate (J), the specific capacity (CF) of the ED and specific electric energy consumption (E) were determined and the influence of the LML solution on the monopolar ion-exchange membranes has been investigated. A higher degree of desalination is associated with higher electric energy consumption (by 50%) and lower specific capacity (by 40%). A noticeable decrease (by 12.8%) in the resistance of the anion exchange membranes was measured after the trials whereas the resistance of the cation exchange membranes remained practically unchanged. Any deposition of the alkaline earth metals on the membrane surface was not observed.
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Affiliation(s)
- Arthur Merkel
- MemBrain s.r.o. (Membrane Innovation Centre), Pod Vinicí 87, 471 27 Stráž pod Ralskem, Czech Republic
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Matej Vavro
- MemBrain s.r.o. (Membrane Innovation Centre), Pod Vinicí 87, 471 27 Stráž pod Ralskem, Czech Republic
| | - Ladislav Čopák
- MemBrain s.r.o. (Membrane Innovation Centre), Pod Vinicí 87, 471 27 Stráž pod Ralskem, Czech Republic
| | - Lukáš Dvořák
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17 Liberec, Czech Republic
| | - Lilia Ahrné
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
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27
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Aksenova I, Pomogaev V. Stability of Dibromo-Dipyrromethene Complexes Coordinated with B, Zn, and Cd in Solutions of Various Acidities. Molecules 2022; 27:molecules27248815. [PMID: 36557945 PMCID: PMC9784619 DOI: 10.3390/molecules27248815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
The spectral luminescent properties of dipyrromethenates halogenated with bromine on both ends of the long axis and coordinated using boron fluoride, zinc, or cadmium in neutral ethanol and acidified with hydrochloric acid solutions were studied. The constants of the acid-base equilibrium of the complexes in the proton-donor solvents in the ground and excited states was determined. The mechanisms of complex protonation were discussed, depending on the structure of the compounds. The electronic structures of the neutral and protonated compounds were modeled and analyzed based on the quantum-chemical method. The structures and spectral-luminescence properties were calculated using the SMD model of ethanol solvent using the TD-DFT theory with the B3LYP functional and the composite def2-SVP/def2-TZVP/def2-TZVPP_ECP basis sets, depending on the atomic number of the elements.
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Udofia IA, Ekama T, Ogunbayo TB, Oloba-Whenu OA, Rhyman L, Isanbor C, Ramasami P. Experimental and theoretical calculation of pKa values of substituted-2,4,6-trinitrodiphenylamines. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Fully Symmetric Cyclodextrin Polycarboxylates: How to Determine Reliable Protonation Constants from NMR Titration Data. Int J Mol Sci 2022; 23:ijms232214448. [PMID: 36430926 PMCID: PMC9696085 DOI: 10.3390/ijms232214448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Acid-base properties of cyclodextrins (CDs), persubstituted at C-6 by 3-mercaptopropionic acid, sualphadex (Suα-CD), subetadex (Suβ-CD) and sugammadex (Suγ-CD, the antidote of neuromuscular blocking steroids) were studied by 1H NMR-pH titrations. For each CD, the severe overlap in protonation steps prevented the calculation of macroscopic pKa values using the standard data fitting model. Considering the full symmetry of polycarboxylate structures, we reduced the number of unknown NMR parameters in the "Q-fitting" or the novel "equidistant macroscopic" evaluation approaches. These models already provided pKa values, but some of them proved to be physically unrealistic, deceptively suggesting cooperativity in carboxylate protonations. The latter problem could be circumvented by adapting the microscopic site-binding (cluster expansion) model by Borkovec, which applies pairwise interactivity parameters to quantify the mutual basicity-decreasing effect of carboxylate protonations. Surprisingly, only a single averaged interactivity parameter could be calculated reliably besides the carboxylate 'core' microconstant for each CD derivative. The speciation of protonation isomers hence could not be resolved, but the optimized microscopic basicity parameters could be converted to the following sets of macroscopic pKa values: 3.84, 4.35, 4.81, 5.31, 5.78, 6.28 for Suα-CD; 3.82, 4.31, 4.73, 5.18, 5.64, 6.06, 6.54 for Suβ-CD and 3.83, 4.28, 4.65, 5.03, 5.43, 5.81, 6.18, 6.64 for Suγ-CD. The pH-dependent charge of these compounds can now be accurately calculated, in support of designing new analytical methods to exploit their charge-dependent molecular recognition such as in cyclodextrin-aided chiral capillary electrophoresis.
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Zuchniarz J, Liu Y, Li C, Voth GA. Accurate p Ka Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values. J Phys Chem B 2022; 126:7321-7330. [PMID: 36106487 PMCID: PMC9528908 DOI: 10.1021/acs.jpcb.2c04899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/28/2022] [Indexed: 11/29/2022]
Abstract
Classical molecular dynamics simulations are a versatile tool in the study of biomolecular systems, but they usually rely on a fixed bonding topology, precluding the explicit simulation of chemical reactivity. Certain modifications can permit the modeling of reactions. One such method, multiscale reactive molecular dynamics, makes use of a linear combination approach to describe condensed-phase free energy surfaces of reactive processes of biological interest. Before these simulations can be performed, models of the reactive moieties must first be parametrized using electronic structure data. A recent study demonstrated that gas-phase electronic structure data can be used to derive parameters for glutamate and lysine which reproduce experimental pKa values in both bulk water and the staphylococcal nuclease protein with remarkable accuracy and transferability between the water and protein environments. In this work, we first present a new model for aspartate derived in similar fashion and demonstrate that it too produces accurate pKa values in both bulk and protein contexts. We also describe a modification to the prior methodology, involving refitting some of the classical force field parameters to density functional theory calculations, which improves the transferability of the existing glutamate model. Finally and most importantly, this reactive molecular dynamics approach, based on rigorous statistical mechanics, allows one to specifically analyze the fundamental physical causes for the marked pKa shift of both aspartate and glutamate between bulk water and protein and also to demonstrate that local steric and electrostatic effects largely explain the observed differences.
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Affiliation(s)
- Joshua Zuchniarz
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United States
| | - Yu Liu
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United States
| | - Chenghan Li
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United States
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31
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Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry 2022; 61:2165-2176. [PMID: 36161872 PMCID: PMC9583617 DOI: 10.1021/acs.biochem.2c00349] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cysteine side chains
can exist in distinct oxidation
states depending
on the pH and redox potential of the environment, and cysteine oxidation
plays important yet complex regulatory roles. Compared with the effects
of post-translational modifications such as phosphorylation, the effects
of oxidation of cysteine to sulfenic, sulfinic, and sulfonic acid
on protein structure and function remain relatively poorly characterized.
We present an analysis of the role of cysteine reactivity as a regulatory
factor in proteins, emphasizing the interplay between electrostatics
and redox potential as key determinants of the resulting oxidation
state. A review of current computational approaches suggests underdeveloped
areas of research for studying cysteine reactivity through molecular
simulations.
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Affiliation(s)
- Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Emma L Gunderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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32
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Bischoff M, Kim NY, Joo JB, Marchioro A. Water Orientation at the Anatase TiO 2 Nanoparticle Interface: A Probe of Surface p Ka Values. J Phys Chem Lett 2022; 13:8677-8683. [PMID: 36094378 PMCID: PMC10226479 DOI: 10.1021/acs.jpclett.2c02453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 05/31/2023]
Abstract
The acid-base properties of surfaces significantly influence catalytic and (photo)electrochemical processes. Estimation of acid dissociation constants (pKa values) for colloids is commonly performed through electroanalytical techniques or spectroscopic methods employing label molecules. Here, we show that polarimetric angle-resolved second harmonic scattering (AR-SHS) can be used as an all-optical, label-free probe of colloid surface pKa values. We apply AR-SHS to dispersions of 100 nm anatase TiO2 particles to extract surface potential and surface susceptibility, a measure of interfacial water orientation, as a function of pH. The surface potential follows changes in surface charge density, while the interfacial water orientation inverts at pH ∼4.8, ∼6, and ∼7.6. As the variation in bulk pH modifies the populations of Ti-OH2+, Ti-OH, and Ti-O- interfacial groups, a change in water orientation reports on the ratio of protonated/deprotonated species. Such observation allows for pKa evaluation from plots of surface susceptibility versus pH. A Nerstian trend in the surface potential is additionally demonstrated.
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Affiliation(s)
- Marie Bischoff
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI), Ecole polytechnique fédérale de Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Na Yeon Kim
- Department
of Chemical Engineering, Konkuk University, Seoul 05029, Korea
| | - Ji Bong Joo
- Department
of Chemical Engineering, Konkuk University, Seoul 05029, Korea
| | - Arianna Marchioro
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI), Ecole polytechnique fédérale de Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
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33
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Samzadeh A, Dehghani M, Baghapour MA, Azhdarpoor A, Derakhshan Z, Cvetnić M, Bolanča T, Giannakis S, Cao Y. Comparative photo-oxidative degradation of etodolac, febuxostat and imatinib mesylate by UV-C/H 2O 2 and UV-C/S 2O 82- processes: Modeling, treatment optimization and biodegradability enhancement. ENVIRONMENTAL RESEARCH 2022; 212:113385. [PMID: 35569533 DOI: 10.1016/j.envres.2022.113385] [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: 04/10/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The pharmaceutical contamination in aquatic environment has arisen increasing concern due to its potentially chronic toxicity. In recent years, HO° and SO4°- based advanced oxidation processes (AOPs) have been widely applied in water and wastewater treatments due to their highly efficiency on contaminant removal. Here, the response surface modeling (RSM) was used to investigate the degradation of three typical pharmaceuticals (i.e., etodolac (ETD), febuxostat (FBU) and imatinib mesylate (IMT)) by UV/H2O2 and UV/S2O82- processes. Based on the multiple regression analysis on full factorial design matrix and calculated reaction rate constants, the RSM was built. The experimental rate constants under optimal conditions were quite close to those obtained from the model, implying the good fit of the RSM. In addition, the RSM results indicated that UV/S2O82- process was less sensitive to pH in comparison to the UV/H2O2 process on target contaminant removal. Finally, it showed that UV/S2O82- process was superior to the UV/H2O2 process to on the enhancement of target contaminant biodegradability.
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Affiliation(s)
- Amin Samzadeh
- Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mansooreh Dehghani
- Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran; Research Center for Health Sciences, Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Mohammad Ali Baghapour
- Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abooalfazl Azhdarpoor
- Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Derakhshan
- Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran; Research Center for Health Sciences, Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Matija Cvetnić
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia
| | - Tomislav Bolanča
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia; University North, Trg Dr. Žarka Dolinara 1, Koprivnica, 48000, Croatia
| | - Stefanos Giannakis
- Universidad Politécnica de Madrid, E.T.S. Ingenieros de Caminos, Canales y Puertos, Departamento de Ingeniería Civil: Hidráulica, Energía y Medio Ambiente, Unidad docente Ingeniería Sanitaria, c/ Profesor Aranguren, s/n, ES-28040, Madrid, Spain
| | - Ying Cao
- Universidad Politécnica de Madrid, E.T.S. Ingenieros de Caminos, Canales y Puertos, Departamento de Ingeniería Civil: Hidráulica, Energía y Medio Ambiente, Unidad docente Ingeniería Sanitaria, c/ Profesor Aranguren, s/n, ES-28040, Madrid, Spain; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
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34
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Wang J, Li B, Tang J, Qiu L, Qiao X, Xu N, Yang H. Ionic Liquid Pilocarpine Analog as an Antiglaucoma Drug Candidate. ACS Pharmacol Transl Sci 2022; 5:752-760. [DOI: 10.1021/acsptsci.2c00024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Juan Wang
- College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Boxuan Li
- Tianjin Key Laboratory of Biomedical Materials, Key Laboratory of Biomaterials and Nanotechnology for Cancer Immunotherapy, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, China
| | - Jing Tang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Li Qiu
- College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xin Qiao
- College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Na Xu
- College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Hu Yang
- Linda and Bipin Doshi Department of Chemical and Biochemical Engineering, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
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35
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Zhang J, Feng Y, Bo Y, Chinnam AK, Singh J, Staples RJ, He X, Wang K, Zhang J, Shreeve JM. Synthesis of a high-energy-density material through rapid replacement of crystal water of hydrates. Chem 2022. [DOI: 10.1016/j.chempr.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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36
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O'Connell KC, Lawless NK, Stewart BM, Landers JP. Dielectric heating of highly corrosive and oxidizing reagents on a hybrid glass microfiber-polymer centrifugal microfluidic device. LAB ON A CHIP 2022; 22:2549-2565. [PMID: 35674228 DOI: 10.1039/d2lc00221c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many assays necessitate the use of highly concentrated acids, powerful oxidizing agents, or a combination of the two. Although microfluidic devices offer vast potential for rapid analytical interrogation at the point-of-need (PON), they cannot escape the fundamental requirement for reagent compatibility. Worse, many innovative protocols have been developed that would represent a significant improvement to current field-forward practices within their respective disciplines, but adoption falters due to chemical incompatibility with challenging reagents. Polymeric centrifugal microfluidic devices meet many of the needs for accommodating complex chemical or biochemical protocols in a multiplexed and automatable format. Yet, they also struggle to accommodate highly reactive chemical components long term. In this work, we report on a simple and inexpensive reagent storage strategy that bypasses the typical complexity involved with integration of liquid reagents on microfluidic devices. Moreover, we demonstrate microdevice compatibility and operation after six months of corrosive reagent storage as well as post dielectric heating. This new strategy allows for storage of multiple highly corrosive and oxidative reagents simultaneously, enhancing the possibilities for multistep assay integration at the PON for a diverse array of applications. Successful detection after one week of corrosive reagent storage of an illicit drug and neurotransmitter metabolite, for forensic and clinical applications, is demonstrated. Furthermore, environmental sample preparation via microwave-assisted wet acid digestion is performed on-disc and integrated with downstream detection. Quantitative detection of a heavy metal in soil is achieved by way of on-disc calibration and found to be accurate within 2.4% compared to a gold standard reference (ICP-OES).
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Affiliation(s)
- Killian C O'Connell
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA.
| | - Nicola K Lawless
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
- Department of Cognitive Science, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Brennan M Stewart
- Department of Biochemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA.
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, Virginia 22904, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, USA
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37
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Lesnicki D, Wank V, Cyran JD, Backus EHG, Sulpizi M. Lower degree of dissociation of pyruvic acid at water surfaces than in bulk. Phys Chem Chem Phys 2022; 24:13510-13513. [PMID: 35640627 DOI: 10.1039/d2cp01293f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the acid/base behavior of environmentally relevant organic acids is of key relevance for accurate climate modelling. Here we investigate the effect of pH on the (de)protonation state of pyruvic acid at the air-water interface and in bulk by using the analytical techniques surface-specific vibrational sum frequency generation and attenuated total reflection spectroscopy. To provide a molecular interpretation of the observed behavior, simulations are carried out using a free energy perturbation approach in combination with electronic structure-based molecular dynamics. In both the experimental and theoretical results we observe that the protonated form of pyruvic acid is preferred at the air-water interface. The increased proton affinity is the result of the specific microsolvation at the interface.
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Affiliation(s)
- Dominika Lesnicki
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz, Germany.
| | - Veronika Wank
- University of Vienna, Faculty of Chemistry, Institute of Physical Chemistry, Währinger Straße 42, 1090 Vienna, Austria. .,University of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Straße 42, 1090 Vienna, Austria
| | - Jenée D Cyran
- Department of Chemistry and Biochemistry, Baylor University, 76706 Waco, Texas, USA
| | - Ellen H G Backus
- University of Vienna, Faculty of Chemistry, Institute of Physical Chemistry, Währinger Straße 42, 1090 Vienna, Austria. .,University of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Straße 42, 1090 Vienna, Austria
| | - Marialore Sulpizi
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz, Germany. .,Department of Physics, Ruhr Universität Bochum, 44780 Bochum, Germany
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38
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Romero AH, Cerecetto HE. High CT-Fluorophore Featuring a Basic Moiety into D-A Chain as a p Ka Probe. J Org Chem 2022; 87:7618-7634. [PMID: 35671375 DOI: 10.1021/acs.joc.1c03104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The determination of acidity represents a significant challenge within fluorometry, and no effective strategy has been developed successfully yet. It is attributed to the fact that acidity tends to be enhanced upon excitation, giving, in general, an overestimation of the ionization constant, pKa. Herein, we developed a strategy for pKa estimation of Brønsted acids in solution through fluorometry by using a convenient pKa probe, N1-aryl-7-methoxy-2-(trifluoromethyl)benzo[b][1,8]naphthyridin-4(1H)-one. It allowed us to obtain a linear log KSV versus pKa correlation derived from the selective quenching response of the probe by an interaction with different Brønsted acids. The key points of N1-aryl-7-methoxy-2-(trifluoromethyl)benzo[b][1,8]naphthyridin-4(1H)-one as a pKa probe were (i) the location of a weak basic moiety in the donor-acceptor chain of the fluorophore, which favors a selective quenching of the intramolecular charge-transfer process according to the acidity of acid, and (ii) the high CT character upon excitation that promotes higher quenching magnitudes and favors a wider pKa range (19.5pKa) for the log KSV versus pKa correlation. Other key principles were to delimit the study to pure proton transfer and nonfluorescent acids, which allowed restricting the quenching response to a process dependent mainly on the acid-base equilibrium. All these findings open a new perspective as a proof of concept to design effective fluorescent pKa probes.
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Affiliation(s)
- Angel H Romero
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Hugo E Cerecetto
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.,Área de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay
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39
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Sülzner N, Haberhauer J, Hättig C, Hellweg A. Prediction of acid pK a values in the solvent acetone based on COSMO-RS. J Comput Chem 2022; 43:1011-1022. [PMID: 35460090 DOI: 10.1002/jcc.26864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 11/08/2022]
Abstract
In this contribution we extent the use of the conductor-like screening model for realistic solvation (COSMO-RS) to the prediction of pKa values in acetone, a commonly used dipolar aprotic solvent. For this, we calculated the Gibbs free energy of dissociation of 120 organic acids (nine acrylic acids, 87 benzoic acids, nine phenols, and 15 benzenesulfonamides) using COSMO-RS at the two levels BP-TZVP and BP-TZVPD-FINE and determined the parameters for a linear free energy relation for the p K a prediction by performing linear fits to experimental values. Our results suggest that the data set dissects into two groups, with the phenols being different from the other three subsets. The acrylic and benzoic acids and the sulfonamides can be treated together and yield an excellent linear correlation ( r 2 > 0.95 ) with an RMSD of only ~0.3. The slope is found to be significantly smaller than the theoretical value ( 1 / RT ln 10 ), only 45% of it, which is in accordance with findings in the literature. The phenols, however, while similarly well correlated in their own subset with an RMSD of 1.7-1.9, exhibit a slope larger than one. We discuss both a higher uncertainty in the reference values as well as physical origins as possible reasons.
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Affiliation(s)
- Niklas Sülzner
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum, 44780, Germany
| | - Julia Haberhauer
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum, 44780, Germany
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum, 44780, Germany
| | - Arnim Hellweg
- Dassault Systèmes Deutschland GmbH, Am Kabellager 11-15, Köln, 51063, Germany
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40
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Guerrini G, Magrì D, Gioria S, Medaglini D, Calzolai L. Characterization of nanoparticles-based vaccines for COVID-19. NATURE NANOTECHNOLOGY 2022; 17:570-576. [PMID: 35710950 DOI: 10.1038/s41565-022-01129-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Several vaccines against COVID-19 use nanoparticles to protect the antigen cargo (either proteins or nucleic acids), increase the immunogenicity and ultimately the efficacy. The characterization of these nanomedicines is challenging due to their intrinsic complexity and requires the use of multidisciplinary techniques and competencies. The accurate characterization of nanovaccines can be conceptualized as a combination of physicochemical, immunological and toxicological assays. This will help to address key challenges in the preclinical characterization, will guide the rapid development of safe and effective vaccines for current and future health crises, and will streamline the regulatory process.
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Affiliation(s)
| | - Davide Magrì
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Sabrina Gioria
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy.
| | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
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41
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de Andrade LM, Paternoster C, Chevallier P, Gambaro S, Mengucci P, Mantovani D. Surface processing for iron-based degradable alloys: A preliminary study on the importance of acid pickling. Bioact Mater 2022; 11:166-180. [PMID: 34938921 PMCID: PMC8665346 DOI: 10.1016/j.bioactmat.2021.09.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 09/04/2021] [Accepted: 09/20/2021] [Indexed: 01/01/2023] Open
Abstract
The formation of a heterogeneous oxidized layer, also called scale, on metallic surfaces is widely recognized as a rapid manufacturing event for metals and their alloys. Partial or total removal of the scale represents a mandatory integrated step for the industrial fabrication processes of medical devices. For biodegradable metals, acid pickling has already been reported as a preliminary surface preparation given further processes, such as electropolishing. Unfortunately, biodegradable medical prototypes presented discrepancies concerning acid pickling studies based on samples with less complex geometry (e.g., non-uniform scale removal and rougher surface). Indeed, this translational knowledge lacks a detailed investigation on this process, deep characterization of treated surfaces properties, as well as a comprehensive discussion of the involved mechanisms. In this study, the effects of different acidic media (HCl, HNO3, H3PO4, CH3COOH, H2SO4 and HF), maintained at different temperatures (21 and 60 °C) for various exposition time (15-240 s), on the chemical composition and surface properties of a Fe-13Mn-1.2C biodegradable alloy were investigated. Changes in mass loss, morphology and wettability evidenced the combined effect of temperature and time for all conditions. Pickling in HCl and HF solutions favor mass loss (0.03-0.1 g/cm2) and effectively remove the initial scale.
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Affiliation(s)
- Letícia Marin de Andrade
- Laboratory for Biomaterials and Bioengineering, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Department of Min-Met-Materials Engineering, Research Center of CHU de Quebec, Division of Regenerative Medicine, Laval University, Quebec City, QC, G1V 0A6, Canada
| | - Carlo Paternoster
- Laboratory for Biomaterials and Bioengineering, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Department of Min-Met-Materials Engineering, Research Center of CHU de Quebec, Division of Regenerative Medicine, Laval University, Quebec City, QC, G1V 0A6, Canada
| | - Pascale Chevallier
- Laboratory for Biomaterials and Bioengineering, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Department of Min-Met-Materials Engineering, Research Center of CHU de Quebec, Division of Regenerative Medicine, Laval University, Quebec City, QC, G1V 0A6, Canada
| | - Sofia Gambaro
- Laboratory for Biomaterials and Bioengineering, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Department of Min-Met-Materials Engineering, Research Center of CHU de Quebec, Division of Regenerative Medicine, Laval University, Quebec City, QC, G1V 0A6, Canada
- National Research Council, Institute of Condensed Matter Chemistry and Technologies for Energy CNR-ICMATE, Genoa, 16149, Italy
| | | | - Diego Mantovani
- Laboratory for Biomaterials and Bioengineering, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Department of Min-Met-Materials Engineering, Research Center of CHU de Quebec, Division of Regenerative Medicine, Laval University, Quebec City, QC, G1V 0A6, Canada
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42
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Sůra R, Antalík M. Determination of proton dissociation constants (pK a) of hydroxyl groups of 2,5-dihydroxy-1,4-benzoquinone (DHBQ) by UV-Vis, fluorescence and ATR-FTIR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120863. [PMID: 35077982 DOI: 10.1016/j.saa.2022.120863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
The dissociation constant is an important physicochemical parameter of amolecule. The protonation state of a molecule reflects its reactivity, solubility or ability to chemically interact with other molecules. In the present study, dissociation constants (pKa) values of 2,5-dihydroxy-1,4-benzoquinone (DHBQ) were determined by UV-Vis, fluorescence and ATR-FTIR spectroscopy at 25 °C. The resulting pKa values for DHBQ were 2.95 and 5.25. We have also experimentally found out that the monoanionic form (HBQ-) provides weak fluorescence in the pH range of about 3-6. This allowed us to determine not only the pKa in the ground but also the excited state of the molecule (pKa1* = 4.38 andpKa2* = 5.27).
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Affiliation(s)
- Roland Sůra
- Department of Biochemistry, Faculty of Natural Sciences, Pavol Jozef Šafárik University, Šrobárová 2, 041 54 Košice, Slovakia.
| | - Marián Antalík
- Department of Biochemistry, Faculty of Natural Sciences, Pavol Jozef Šafárik University, Šrobárová 2, 041 54 Košice, Slovakia
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43
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Liang SP, Masquelier E, Morse DE, Gordon MJ, Sepunaru L. Low Voltage Voltammetry Probes Proton Dissociation Equilibria of Amino Acids and Peptides. Anal Chem 2022; 94:4948-4953. [PMID: 35290024 DOI: 10.1021/acs.analchem.1c03371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Platinum-catalyzed electrochemical reduction of dissociable protons at low potentials was used to investigate proton dissociation equilibria of freely diffusing and peptide-incorporated charged amino acids. We first demonstrate with five charged essential amino acids and their analogs that the electrochemically induced deprotonation of each amino acid occurs at distinct formal reduction potential. Moreover, the observed direct reduction for all the charged species, excluding arginine, occurs at low potentials suitable for investigation under aqueous conditions (-0.4 to -0.9 V vs Ag/AgCl). The direct proton reduction was resolved via deconvolution of the observed differential pulse voltammogram (DPV) from background hydronium reduction and water electrolysis. A linear correlation was found between the formal reduction potentials and the pKa values of the dissociable protons hosted by various molecular moieties in the amino acids and their analogs and further verified with tripeptides. DPV of poly(l-lysine) decamer (Lys10) distinctively resolved the pKa values of the amino groups in the side chains and N-terminus, at a resolution not possible by conventional acid-base titration. This work demonstrates selective electrochemical titration of dissociable protons in charged amino acids in the free state and as residues in biomolecules, as well as the utility of DPV to indirectly interrogate local electrostatic environments that are essential to the stability and function of biomolecules.
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Affiliation(s)
- Sheng-Ping Liang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Eloise Masquelier
- Materials Department, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Daniel E Morse
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Institute of Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael J Gordon
- Institute of Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Lior Sepunaru
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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44
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Jones EL, Mlotkowski AJ, Hebert SP, Schlegel HB, Chow CS. Calculations of p Ka Values for a Series of Naturally Occurring Modified Nucleobases. J Phys Chem A 2022; 126:1518-1529. [PMID: 35201779 DOI: 10.1021/acs.jpca.1c10905] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Modified nucleobases are found in functionally important regions of RNA and are often responsible for essential structural roles. Many of these nucleobase modifications are dynamically regulated in nature, with each modification having a different biological role in RNA. Despite the high abundance of modifications, many of their characteristics are still poorly understood. One important property of a nucleobase is its pKa value, which has been widely studied for unmodified nucleobases, but not for the modified versions. In this study, the pKa values of modified nucleobases were determined by performing ab initio quantum mechanical calculations using a B3LYP density functional with the 6-31+G(d,p) basis set and a combination of implicit-explicit solvation systems. This method, which was previously employed to determine the pKa values of unmodified nucleobases, is applicable to a variety of modified nucleobases. Comparisons of the pKa values of modified nucleobases give insight into their structural and energetic impacts within nucleic acids.
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Affiliation(s)
- Evan L Jones
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Alan J Mlotkowski
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Sebastien P Hebert
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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45
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Hofsommer DT, Liang Y, Uttarwar SS, Gautam M, Pishgar S, Gulati S, Grapperhaus CA, Spurgeon JM. The pH and Potential Dependence of Pb-Catalyzed Electrochemical CO 2 Reduction to Methyl Formate in a Dual Methanol/Water Electrolyte. CHEMSUSCHEM 2022; 15:e202102289. [PMID: 34979055 DOI: 10.1002/cssc.202102289] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/13/2021] [Indexed: 06/14/2023]
Abstract
The conversion of waste CO2 to value-added chemicals through electrochemical reduction is a promising technology for mitigating climate change while simultaneously providing economic opportunities. The use of non-aqueous solvents like methanol allows for higher CO2 availability and novel products. In this work, the electrochemistry of CO2 reduction in acidic methanol catholyte at a Pb working electrode was investigated while using a separate aqueous anolyte to promote a sustainable water oxidation half-reaction. The selectivity among methyl formate (a product unique to reduction of CO2 in methanol), formic acid, and formate was critically dependent on the catholyte pH, with higher pH conditions leading to formate and low pH favoring methyl formate. The potential dependence of the product distribution in acidic catholyte was also investigated, with a faradaic efficiency for methyl formate as high as 75 % measured at -2.0 V vs. Ag/AgCl.
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Affiliation(s)
- Dillon T Hofsommer
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky, 40292, USA
| | - Ying Liang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, P. R. China
- Conn Center for Renewable Energy Research, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Sandesh S Uttarwar
- Conn Center for Renewable Energy Research, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Manu Gautam
- Conn Center for Renewable Energy Research, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Sahar Pishgar
- Conn Center for Renewable Energy Research, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Saumya Gulati
- Conn Center for Renewable Energy Research, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Craig A Grapperhaus
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky, 40292, USA
| | - Joshua M Spurgeon
- Conn Center for Renewable Energy Research, University of Louisville, Louisville, Kentucky, 40292, USA
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46
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Graf HG, Biebl SM, Müller L, Breitenstein C, Huhn C. Capillary electrophoresis applied for the determination of acidity constants and limiting electrophoretic mobilities of ionizable herbicides including glyphosate and its metabolites and for their simultaneous separation. J Sep Sci 2022; 45:1128-1139. [PMID: 34984811 DOI: 10.1002/jssc.202100952] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 11/11/2022]
Abstract
Thermodynamic acidity constants and limiting ionic mobilities were determined for polyprotic non-chromophore analytes using capillary electrophoresis with capacitively coupled contactless conductivity detection. It was not necessary to work with buffers of identical ionic strength as ionic strength effects on effective electrophoretic mobilities were corrected by modeling during data evaluation (software AnglerFish). The mobility data from capillary electrophoresis coupled to conductivity detection were determined in the pH range from 1.25 to 12.02 with a high resolution (36 pH steps). With this strategy, thermodynamic acidity constants and limiting ionic mobilities for various acidic herbicides were determined, sometimes for the first time. The model analytes included glyphosate, its metabolites, and its acetylated derivates (aminomethyl phosphonic acid, glyoxylic acid, sarcosine, glycine, N-acetyl glyphosate, N-acetyl aminomethyl phosphonic acid, hydroxymethyl phosphonic acid). The obtained data were used in simulations to optimize separations by capillary electrophoresis. Simulations correlated very well to experimental results. With the new method, the separation of glyphosate from interfering components like phosphate in beer samples was possible.
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Affiliation(s)
- Hannes Georg Graf
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Sonja Maria Biebl
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Linda Müller
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Christina Breitenstein
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Carolin Huhn
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
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47
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A physiologically based pharmacokinetic (PBPK) model exploring the blood-milk barrier in lactating species - A case study with oxytetracycline administered to dairy cows and goats. Food Chem Toxicol 2022; 161:112848. [DOI: 10.1016/j.fct.2022.112848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022]
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48
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Teng J, Pang J, Sun Y, Wang J. A New Approach to the Determination of pKa and pKb of Brønsted–Lowry Weak Acid and Weak Base in Aprotic Solvent. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116172] [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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49
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Sahoo AK, Schreiber F, Netz RR, Maiti PK. Role of entropy in determining the phase behavior of protein solutions induced by multivalent ions. SOFT MATTER 2022; 18:592-601. [PMID: 34928291 DOI: 10.1039/d1sm00730k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex hydration effects that result in a net entropy gain upon phase separation. To decipher the underlying molecular mechanism, we use all-atom molecular dynamics simulations along with the two-phase thermodynamic method for entropy calculation. Based on simulations of a single BSA protein in various salt solutions (NaCl, CaCl2, MgCl2, and YCl3) at temperatures (T) ranging 283-323 K, we find that the cation-protein binding affinity increases with T, reflecting its thermodynamic driving force to be entropic in origin. We show that in the cation binding process, many tightly bound water molecules from the solvation shells of a cation and the protein are released to the bulk, resulting in entropy gain. To rationalize the LCST behavior, we calculate the ζ-potential that shows charge inversion of the protein for solutions containing multivalent ions. The ζ-potential increases with T. Performing simulations of two BSA proteins, we demonstrate that the protein-protein binding is mediated by multiple cation bridges and involves similar dehydration effects that cause a large entropy gain which more than compensates for rotational and translational entropy losses of the proteins. Thus, the LCST behavior is entropy-driven, but the associated solvation effects are markedly different from hydrophobic hydration. Our findings have direct implications for tuning the phase behavior of biological and soft-matter systems, e.g., protein condensation and crystallization.
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Affiliation(s)
- Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore-560012, India.
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Frank Schreiber
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Department of Physics, Indian Institute of Science, Bangalore-560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore-560012, India.
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50
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Han S, Ding B, Xiong H, Zuo B, Ye Y, Li H, Song X. Chlorination-induced p Ka decrease: an improved strategy to design ratiometric hypochlorite fluorescent probes with ideally high selectivity. Analyst 2022; 147:5300-5305. [DOI: 10.1039/d2an01476a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Based on the ClO−-triggered chlorination reaction and the subsequent pKa decrease, a two-photon ratiometric ClO− fluorescent probe was designed.
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Affiliation(s)
- Shaohui Han
- College of Chemistry & Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Binghui Ding
- College of Chemistry & Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Haiqing Xiong
- College of Chemistry & Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Bojun Zuo
- Shandong Academy of Pesticide Sciences, Jinan, Shandong 250033, China
| | - Yong Ye
- College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Haipu Li
- College of Chemistry & Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Xiangzhi Song
- College of Chemistry & Chemical Engineering, Central South University, Changsha, Hunan 410083, China
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