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Hall A, Chatzopoulou M, Frost J. Bioisoteres for carboxylic acids: From ionized isosteres to novel unionized replacements. Bioorg Med Chem 2024; 104:117653. [PMID: 38579492 DOI: 10.1016/j.bmc.2024.117653] [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: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 04/07/2024]
Abstract
Carboxylic acids are key pharmacophoric elements in many molecules. They can be seen as a problem by some, due to perceived permeability challenges, potential for high plasma protein binding and the risk of forming reactive metabolites due to acyl-glucuronidation. By others they are viewed more favorably as they can decrease lipophilicity by adding an ionizable center which can be beneficial for solubility, and can add enthalpic interactions with the target protein. However, there are many instances where the replacement of a carboxylic acid with a bioisosteric group is required. This has led to the development of a number of ionizable groups which sufficiently mimic the carboxylic acid functionality whilst improving, for example, the metabolic profile of the molecule in question. An alternative strategy involves replacement of the carboxylate by neutral functional groups. This review initially details carefully selected examples whereby tetrazoles, acyl sulfonamides or isoxazolols have been beneficially utilized as carboxylic acid bioisosteres altering physicohemical properties, interactions with the target and metabolism and/or pharmacokinetics, before delving further into the binding mode of carboxylic acid derivatives with their target proteins. This analysis highlights new ways to consider the replacement of carboxylic acids by neutral bioisosteric groups which either rely on hydrogen bonds or cation-π interactions. It should serve as a useful guide for scientists working in drug discovery.
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Affiliation(s)
- Adrian Hall
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK.
| | - Maria Chatzopoulou
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
| | - James Frost
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
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2
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Berlin CB, Sharma E, Kozlowski MC. Quantification of Hydrogen-Bond-Donating Ability of Biologically Relevant Compounds. J Org Chem 2024; 89:4684-4690. [PMID: 38483838 DOI: 10.1021/acs.joc.3c02939] [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] [Indexed: 04/06/2024]
Abstract
Hydrogen bonding is a key factor in the design of ligands for biological binding, including drug targets. Our group previously developed a method for experimentally assessing the hydrogen-bond-donating ability of an analyte using UV-vis titrations with a colorimetric sensor. Using this method, 79 new titrations were performed on weak hydrogen-bond donors, with a focus on heterocycles and pharmaceutically relevant motifs. The hydrogen-bond donating abilities of drug compounds and the substructures of drug compounds were also measured. These titrations will be used to build a database of hydrogen-bond donors.
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Affiliation(s)
- Cameron B Berlin
- Department of Chemistry, Roy and Diana Vagelos Laboratories, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Eesha Sharma
- Department of Chemistry, Roy and Diana Vagelos Laboratories, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Marisa C Kozlowski
- Department of Chemistry, Roy and Diana Vagelos Laboratories, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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3
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Yu Q, Yang J, Zhang HR, Liang PY, Gao G, Yuan Y, Dou W, Zhou PP. Investigations of the reaction mechanism of sodium with hydrogen fluoride to form sodium fluoride and the adsorption of hydrogen fluoride on sodium fluoride monomer and tetramer. J Mol Model 2024; 30:26. [PMID: 38191945 DOI: 10.1007/s00894-023-05821-z] [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: 10/13/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024]
Abstract
CONTEXT The reaction between Na and HF is a typical harpooning reaction which is of great interest due to its significance in understanding the elementary chemical reaction kinetics. This work aims to investigate the detailed reaction mechanisms of sodium with hydrogen fluoride and the adsorption of HF on the resultant NaF as well as the (NaF)4 tetramer. The results suggest that the reaction between Na and HF leads to the formation of sodium fluoride salt NaF and hydrogen gas. Na interacts with HF to form a complex HF···Na, and then the approaching of F atom of HF to Na results in a transition state H···F···Na. Accompanied by the broken of H-F bond, the bond forms between F and Na atoms as NaF, then the product NaF is yielded due to the removal of H atom. The resultant NaF can further form (NaF)4 tetramer. The interaction of NaF with HF leads to the complex NaF···HF; the form I as well as II of (NaF)4 can interact with HF to produce two complexes (i.e., (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF), but the form III of (NaF)4 can interact with HF to produce only one complex (NaF)4(III)···HF. These complexes were explored in terms of noncovalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses. NCI analyses confirm the existences of attractive interactions in the complexes HF···Na, NaF···HF, (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF, and (NaF)4(III)···HF. QTAIM analyses suggest that the F···Na interaction forms in the HF···Na complex while the F···H hydrogen bonds form in NaF···HF, (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF, and (NaF)4(III)···HF complexes. Natural bond orbital (NBO) analyses were also applied to analyze the intermolecular donor-acceptor orbital interactions in these complexes. These results would provide valuable insight into the chemical reaction of Na and HF and the adsorption interaction between sodium fluoride salt and HF. METHODS The calculations were carried out at the M06-L/6-311++G(2d,2p) level of theory which were performed using the Gaussian16 program. Intrinsic reaction coordinate (IRC) calculations were carried out at the same level of theory to confirm that the obtained transition state was true. The molecular surface electrostatic potential (MSEP) was employed to understand how the complex forms. Quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI) analysis was used to know the topology parameters at bond critical points (BCPs) and intermolecular interactions in the complex and intermediate. The topology parameters and the BCP plots were obtained by the Multiwfn software.
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Affiliation(s)
- Qinwei Yu
- State Key Laboratory of Fluorine & Nitrogen Chemicals, Xi'an Modern Chemistry Research Institute, Xi'an, 710065, People's Republic of China.
| | - Jianming Yang
- State Key Laboratory of Fluorine & Nitrogen Chemicals, Xi'an Modern Chemistry Research Institute, Xi'an, 710065, People's Republic of China.
| | - Hai-Rong Zhang
- Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, People's Republic of China
| | - Peng-Yu Liang
- Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, People's Republic of China
| | - Ge Gao
- Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, People's Republic of China
| | - Yongna Yuan
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, 730000, People's Republic of China
| | - Wei Dou
- Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, People's Republic of China
| | - Pan-Pan Zhou
- Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, People's Republic of China.
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4
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Yu J, Li Z, Chen G, Kong X, Hu J, Wang D, Cao D, Li Y, Huo R, Wang G, Liu X, Jiang H, Li X, Luo X, Zheng M. Computing the relative binding affinity of ligands based on a pairwise binding comparison network. NATURE COMPUTATIONAL SCIENCE 2023; 3:860-872. [PMID: 38177766 PMCID: PMC10766524 DOI: 10.1038/s43588-023-00529-9] [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: 05/05/2023] [Accepted: 09/05/2023] [Indexed: 01/06/2024]
Abstract
Structure-based lead optimization is an open challenge in drug discovery, which is still largely driven by hypotheses and depends on the experience of medicinal chemists. Here we propose a pairwise binding comparison network (PBCNet) based on a physics-informed graph attention mechanism, specifically tailored for ranking the relative binding affinity among congeneric ligands. Benchmarking on two held-out sets (provided by Schrödinger and Merck) containing over 460 ligands and 16 targets, PBCNet demonstrated substantial advantages in terms of both prediction accuracy and computational efficiency. Equipped with a fine-tuning operation, the performance of PBCNet reaches that of Schrödinger's FEP+, which is much more computationally intensive and requires substantial expert intervention. A further simulation-based experiment showed that active learning-optimized PBCNet may accelerate lead optimization campaigns by 473%. Finally, for the convenience of users, a web service for PBCNet is established to facilitate complex relative binding affinity prediction through an easy-to-operate graphical interface.
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Affiliation(s)
- Jie Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Information Science and Technology, Shanghai Tech University, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Zhaojun Li
- College of Computer and Information Engineering, Dezhou University, Dezhou City, China
- Development Department, Suzhou Alphama Biotechnology Co., Ltd, Suzhou City, China
| | - Geng Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Xiangtai Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Hu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Dingyan Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Duanhua Cao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yanbei Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Ruifeng Huo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Gang Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Liu
- Development Department, Suzhou Alphama Biotechnology Co., Ltd, Suzhou City, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, China.
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5
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Hawash M, Jaradat N, Sabobeh R, Abualhasan M, Qaoud MT. New Thiazole Carboxamide Derivatives as COX Inhibitors: Design, Synthesis, Anticancer Screening, In Silico Molecular Docking, and ADME Profile Studies. ACS OMEGA 2023; 8:29512-29526. [PMID: 37599929 PMCID: PMC10433355 DOI: 10.1021/acsomega.3c03256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023]
Abstract
The goal of this work was to create and test a new series of thiazole carboxamide derivatives for their cyclooxygenase (COX) suppressor and anticancer effects. The compounds were characterized using 1H, 13C NMR, and HRMS spectrum analysis, and their selectivity toward COX-1 and COX-2 was assessed using an in vitro COX inhibition assay kit. Cytotoxicity was assessed using an MTS assay against a panel of cancer and normal cell lines. The docking studies were aided by the Prime MM-GBSA method for estimating binding affinities. The density functional theory (DFT) analysis was performed to assess compound chemical reactivity, which was calculated by computing the border orbital energy of both HOMO and LUMO orbitals, as well as the HOMO-LUMO energy gap. For ADME-T analysis, the QiKProp module was employed. Furthermore, using human X-ray crystal structures, molecular docking studies were carried out to discover the probable binding patterns of these drugs within both COX-1 and COX-2 isozymes. The results demonstrated that the most effective compound against the COX-1 enzyme was 2b with an IC50 of 0.239 μM. It also showed potent activity against COX-2 with an IC50 value of 0.191 μM and a selectivity ratio of 1.251. The highest selectivity ratio was 2.766 for compound 2a against COX-2 with an IC50 dose of 0.958 μM relating to the celecoxib ratio of 23.8 and its IC50 against COX-2 of 0.002 μM. Compound 2j also showed good selectivity toward COX-2 (1.507) with an IC50 value of 0.957 μM. All compounds showed negligible cytotoxic activity against the evaluated normal cell lines, and the IC50 values were more than 300 μM, except for compound 2b, whose IC50 values were 203.71 ± 1.89 and 116.96 ± 2.05 μM against LX-2 and Hek293t cell lines, respectively. Moreover, compound 2b showed moderate anticancer activity against COLO205 and B16F1 cancer cell lines with IC50 values of 30.79 and 74.15 μM, respectively.
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Affiliation(s)
- Mohammed Hawash
- Department
of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 400, Palestine
| | - Nidal Jaradat
- Department
of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 400, Palestine
| | - Rozan Sabobeh
- Department
of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 400, Palestine
| | - Murad Abualhasan
- Department
of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 400, Palestine
| | - Mohammed T. Qaoud
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, 06330 Ankara, Turkey
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6
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Roenfanz HF, Paniak TJ, Berlin CB, Tran V, Francisco KR, Lassalas P, Devas A, Landes O, Rosenberger A, Rotella ME, Ballatore C, Kozlowski MC. Hydrogen Bonding Parameters by Rapid Colorimetric Assessment: Evaluation of Structural Components Found in Biological Ligands and Organocatalysts. Chemistry 2023; 29:e202300696. [PMID: 36917701 PMCID: PMC10363249 DOI: 10.1002/chem.202300696] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023]
Abstract
Hydrogen bonding is a key molecular interaction in biological processes, drug delivery, and catalysis. This report describes a high throughput UV-Vis spectroscopic method to measure hydrogen bonding capacity using a pyrazinone sensor. This colormetric sensor reversibly binds to a hydrogen bond donor, resulting in a blue shift as additional equivalents of donor are added. Titration with excess equivalents of donor is used to determine the binding coefficient, ln(Keq ). Over 100 titrations were performed for a variety of biologically relevant compounds. This data enabled development a multiple linear regression model that is capable of predicting 95 % of ln(Keq ) values within 1 unit, allowing for the estimation of hydrogen bonding affinity from a single measurement. To show the effectiveness of the single point measurements, hydrogen bond strengths were obtained for a set of carboxylic acid bioisosteres. The values from the single point measurements were validated with full titrations.
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Affiliation(s)
- Hanna F Roenfanz
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Thomas J Paniak
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Cameron B Berlin
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Van Tran
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Karol R Francisco
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Pierrik Lassalas
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Anisha Devas
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Olivia Landes
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Avalon Rosenberger
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Madeline E Rotella
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Carlo Ballatore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Marisa C Kozlowski
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
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7
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Vincze A, Dékány G, Bicsak R, Formanek A, Moreau Y, Koplányi G, Takács G, Katona G, Balogh-Weiser D, Arany Á, Balogh GT. Natural Lipid Extracts as an Artificial Membrane for Drug Permeability Assay: In Vitro and In Silico Characterization. Pharmaceutics 2023; 15:pharmaceutics15030899. [PMID: 36986760 PMCID: PMC10053807 DOI: 10.3390/pharmaceutics15030899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
In vitro non-cellular permeability models such as the parallel artificial membrane permeability assay (PAMPA) are widely applied tools for early-phase drug candidate screening. In addition to the commonly used porcine brain polar lipid extract for modeling the blood–brain barrier’s permeability, the total and polar fractions of bovine heart and liver lipid extracts were investigated in the PAMPA model by measuring the permeability of 32 diverse drugs. The zeta potential of the lipid extracts and the net charge of their glycerophospholipid components were also determined. Physicochemical parameters of the 32 compounds were calculated using three independent forms of software (Marvin Sketch, RDKit, and ACD/Percepta). The relationship between the lipid-specific permeabilities and the physicochemical descriptors of the compounds was investigated using linear correlation, Spearman correlation, and PCA analysis. While the results showed only subtle differences between total and polar lipids, permeability through liver lipids highly differed from that of the heart or brain lipid-based models. Correlations between the in silico descriptors (e.g., number of amide bonds, heteroatoms, and aromatic heterocycles, accessible surface area, and H-bond acceptor–donor balance) of drug molecules and permeability values were also found, which provides support for understanding tissue-specific permeability.
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Affiliation(s)
- Anna Vincze
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Gergely Dékány
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Richárd Bicsak
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - András Formanek
- ESAT-STADIUS KU LEUVEN, 3001 Leuven, Belgium
- Department of Measurement and Information Systems, Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Yves Moreau
- ESAT-STADIUS KU LEUVEN, 3001 Leuven, Belgium
| | - Gábor Koplányi
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Gergely Takács
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Mcule.com Kft, Bartók Béla út 105-113, H-1115 Budapest, Hungary
| | - Gábor Katona
- Institute of Pharmaceutical Technology and Regulatory Affairs, Faculty of Pharmacy, University of Szeged, Eötvös Str. 6, H-6720 Szeged, Hungary
| | - Diána Balogh-Weiser
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Ádám Arany
- ESAT-STADIUS KU LEUVEN, 3001 Leuven, Belgium
| | - György T. Balogh
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös u. 6, H-6720 Szeged, Hungary
- Correspondence:
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8
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Candito DA, Simov V, Gulati A, Kattar S, Chau RW, Lapointe BT, Methot JL, DeMong DE, Graham TH, Kurukulasuriya R, Keylor MH, Tong L, Morriello GJ, Acton JJ, Pio B, Liu W, Scott JD, Ardolino MJ, Martinot TA, Maddess ML, Yan X, Gunaydin H, Palte RL, McMinn SE, Nogle L, Yu H, Minnihan EC, Lesburg CA, Liu P, Su J, Hegde LG, Moy LY, Woodhouse JD, Faltus R, Xiong T, Ciaccio P, Piesvaux JA, Otte KM, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Neelamkavil S, Wood HB, Fuller PH, Ellis JM. Discovery and Optimization of Potent, Selective, and Brain-Penetrant 1-Heteroaryl-1 H-Indazole LRRK2 Kinase Inhibitors for the Treatment of Parkinson's Disease. J Med Chem 2022; 65:16801-16817. [PMID: 36475697 DOI: 10.1021/acs.jmedchem.2c01605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inhibition of leucine-rich repeat kinase 2 (LRRK2) kinase activity represents a genetically supported, chemically tractable, and potentially disease-modifying mechanism to treat Parkinson's disease. Herein, we describe the optimization of a novel series of potent, selective, central nervous system (CNS)-penetrant 1-heteroaryl-1H-indazole type I (ATP competitive) LRRK2 inhibitors. Type I ATP-competitive kinase physicochemical properties were integrated with CNS drug-like properties through a combination of structure-based drug design and parallel medicinal chemistry enabled by sp3-sp2 cross-coupling technologies. This resulted in the discovery of a unique sp3-rich spirocarbonitrile motif that imparted extraordinary potency, pharmacokinetics, and favorable CNS drug-like properties. The lead compound, 25, demonstrated exceptional on-target potency in human peripheral blood mononuclear cells, excellent off-target kinase selectivity, and good brain exposure in rat, culminating in a low projected human dose and a pre-clinical safety profile that warranted advancement toward pre-clinical candidate enabling studies.
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Affiliation(s)
- David A Candito
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Solomon Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ryan W Chau
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Blair T Lapointe
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Joey L Methot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Duane E DeMong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Thomas H Graham
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ravi Kurukulasuriya
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ling Tong
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - John J Acton
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Barbara Pio
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Weiguo Liu
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Jack D Scott
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Michael J Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Theodore A Martinot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew L Maddess
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Hakan Gunaydin
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Hongshi Yu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ellen C Minnihan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Charles A Lesburg
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Jing Su
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Paul Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Jennifer A Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Santhosh Neelamkavil
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Harold B Wood
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - J Michael Ellis
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
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9
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Hawash M, Qaoud MT, Jaradat N, Abdallah S, Issa S, Adnan N, Hoshya M, Sobuh S, Hawash Z. Anticancer Activity of Thiophene Carboxamide Derivatives as CA-4 Biomimetics: Synthesis, Biological Potency, 3D Spheroid Model, and Molecular Dynamics Simulation. Biomimetics (Basel) 2022; 7:247. [PMID: 36546947 PMCID: PMC9775471 DOI: 10.3390/biomimetics7040247] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The present study aimed to synthesize thiophene carboxamide derivatives, which are considered biomimetics of the anticancer medication Combretastatin A-4 (CA-4), and compare the similarity in the polar surface area (PSA) between the novel series and CA-4. Our results showed that the PSA of the most synthesized structures was biomimetic to CA-4, and similar chemical and biological properties were observed against Hep3B cancer cell line. Among the synthesized series 2b and 2e compounds were the most active molecules on Hep3B (IC50 = 5.46 and 12.58 µM, respectively). The 3D results revealed that both 2b and 2e structures confuse the surface of Hep3B cancer cell lines' spheroid formation and force these cells to aggregate into a globular-shaped spheroid. The 2b and 2e showed a comparable interaction pattern to that observed for CA-4 and colchicine within the tubulin-colchicine-binding pocket. The thiophene ring, due to holding a high aromaticity character, participated critically in that observed interaction profile and showed additional advanced interactions over CA-4. The 2b and 2e tubulin complexes showed optimal dynamics trajectories within a time scale of 100 ns at 300 K temperature, which asserts their high stability and compactness. Together, these findings revealed the biomimetic role of 2b and 2e compounds in CA-4 in preventing cancer progression.
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Affiliation(s)
- Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine
| | - Mohammed T. Qaoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, 06330 Ankara, Turkey
| | - Nidal Jaradat
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine
| | - Samer Abdallah
- Department of Biology & Biotechnology, Faculty of Science, An-Najah National University, Nablus 00970, Palestine
| | - Shahd Issa
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine
| | - Nawal Adnan
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine
| | - Marah Hoshya
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine
| | - Shorooq Sobuh
- Department of Biomedical Sciences, Physiology, Pharmacology & Toxicology Division, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine
| | - Zafer Hawash
- Department of Physics, Faculty of Science, Birzeit University, Birzeit, Ramallah 71939, Palestine
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10
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Storer MC, Hunter CA. The surface site interaction point approach to non-covalent interactions. Chem Soc Rev 2022; 51:10064-10082. [PMID: 36412990 DOI: 10.1039/d2cs00701k] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The functional properties of molecular systems are generally determined by the sum of many weak non-covalent interactions, and therefore methods for predicting the relative magnitudes of these interactions is fundamental to understanding the relationship between function and structure in chemistry, biology and materials science. This review focuses on the Surface Site Interaction Point (SSIP) approach which describes molecules as a set of points that capture the properties of all possible non-covalent interactions that the molecule might make with another molecule. The first half of the review focuses on the empirical non-covalent interaction parameters, α and β, and provides simple rules of thumb to estimate free energy changes for interactions between different types of functional group. These parameters have been used to have been used to establish a quantitative understanding of the role of solvent in solution phase equilibria, and to describe non-covalent interactions at the interface between macroscopic surfaces as well as in the solid state. The second half of the review focuses on a computational approach for obtaining SSIPs and applications in multi-component systems where many different interactions compete. Ab initio calculation of the Molecular Electrostatic Potential (MEP) surface is used to derive an SSIP description of a molecule, where each SSIP is assigned a value equivalent to the corresponding empirical parameter, α or β. By considering the free energies of all possible pairing interactions between all SSIPs in a molecular ensemble, it is possible to calculate the speciation of all intermolecular interactions and hence predict thermodynamic properties using the SSIMPLE algorithm. SSIPs have been used to describe both the solution phase and the solid state and provide accurate predictions of partition coefficients, solvent effects on association constants for formation of intermolecular complexes, and the probability of cocrystal formation. SSIPs represent a simple and intuitive tool for describing the relationship between chemical structure and non-covalent interactions with sufficient accuracy to understand and predict the properties of complex molecular ensembles without the need for computationally expensive simulations.
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Affiliation(s)
- Maria Chiara Storer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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11
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Uppadhayay RK, Kumar A, Teotia J, Singh A. Multifaceted Chemistry of Tetrazole. Synthesis, Uses, and Pharmaceutical Applications. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428022120090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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12
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Kenny PW. Hydrogen-Bond Donors in Drug Design. J Med Chem 2022; 65:14261-14275. [DOI: 10.1021/acs.jmedchem.2c01147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter W. Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
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13
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14
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Conformation and structural features of diuron and irgarol: insights from quantum chemistry calculations. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Storer MC, Hunter CA. Quantification of secondary electrostatic interactions in H-bonded complexes. Phys Chem Chem Phys 2022; 24:18124-18132. [PMID: 35852121 DOI: 10.1039/d2cp03004g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The H-bonding properties of compounds that contain multiple functional groups are difficult to predict, because there are through-bond polarisation effects and long-range secondary electrostatic interactions that have significant effects on the interactions with solvents and other molecules. Here we use experimental measurements of association constants for formation of 1 : 1 H-bonded complexes that contain a single well-defined H-bond and a single well-defined secondary electrostatic interaction to quantify the magnitude of this effect. The results were used to develop a computational method for calculating functional group H-bond parameters that accurately reproduce the magnitudes of both primary H-bonding interaction and secondary electrostatic interactions. The effects of secondary electrostatic interactions are observed in calculations of ab initio Molecular Electrostatic Potential (MEP) values, but at the van der Waals surface, the magnitude of the effect is highly overestimated. MEP values calculated on electron density isosurfaces that lie closer to the nuclei provide a more accurate description of the experimental observations. H-bond parameters calculated using this approach successfully account for the properties of arrays of multiple H-bond donor and acceptor groups in different configurations. The results provide insight into the factors that govern the interaction properties of molecules that contain multiple functional groups and provide an accurate method for prediction of solution phase complexation free energies based on gas phase calculations of individual molecules.
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Affiliation(s)
- Maria Chiara Storer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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16
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Vulpetti A, Lingel A, Dalvit C, Schiering N, Oberer L, Henry C, Lu Y. Efficient Screening of Target-Specific Selected Compounds in Mixtures by 19F NMR Binding Assay with Predicted 19F NMR Chemical Shifts. ChemMedChem 2022; 17:e202200163. [PMID: 35475323 DOI: 10.1002/cmdc.202200163] [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: 03/28/2022] [Revised: 04/26/2022] [Indexed: 11/06/2022]
Abstract
Ligand-based 19 F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental 19 F NMR chemical shifts. Here, we introduce a complementary knowledge-based 19 F NMR screening approach, named 19 Focused screening, enabling the efficient screening of putative active molecules selected by computational hit finding methodologies, in mixtures assembled and on-the-fly deconvoluted based on predicted 19 F NMR chemical shifts. In this study, we developed a novel approach, named LEFshift , for 19 F NMR chemical shift prediction using rooted topological fluorine torsion fingerprints in combination with a random forest machine learning method. A demonstration of this approach to a real test case is reported.
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Affiliation(s)
- Anna Vulpetti
- Novartis Pharma AG, Global Discovery Chemistry, Novartis Campus, 4002, Basel, SWITZERLAND
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Claudio Dalvit
- Novartis Institutes for BioMedical Research Basel, Protease Platform, SWITZERLAND
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research Basel, Protease Platform, SWITZERLAND
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Chrystelle Henry
- Novartis Institutes for BioMedical Research Basel, Protein Science, SWITZERLAND
| | - Yipin Lu
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
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17
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Gholivand K, Mohammadpanah F, Pooyan M, Roohzadeh R. Evaluating anti-coronavirus activity of some phosphoramides and their influencing inhibitory factors using molecular docking, DFT, QSAR, and NCI-RDG studies. J Mol Struct 2022; 1248:131481. [PMID: 34538931 PMCID: PMC8435241 DOI: 10.1016/j.molstruc.2021.131481] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022]
Abstract
The recent prevalence of coronavirus disease in 2019 (COVID-19) has triggered widespread global health concerns.Antiviral drugs based on phosphoramides have significant inhibitory activity against the main protease (Mpro) of the virus and prevent transcription and viral replication. Hence, in order to design and introduce a group of inhibitors affecting the coronavirus, 35 phosphoramide compounds based on phospho-guanine and phospho-pyrazine derivatives were selected for molecular docking study. The results showed that most phosphoguanides containing the amino benzimidazole have a high interaction tendency with COVID-19. Among them, compound 19 was identified as the strongest inhibitor with the -9.570 kcal/mol binding energy whereas, the binding energy of Remdesivir is -6.75 kcal/mol. The quantitative structure-activity relationship (QSAR) results demonstrated that the number of aromatic rings, amide's nitrogens and their ability in π-staking, and hydrogen interactions with Mpro active sites are major factors contributing to the inhibitory activity of these compounds.Also, the NCI-RDG and DFT results were in good accordance with those of QSAR and molecular docking. The findings of this investigation can be underlying the synthesis of effective and efficient drugs against COVID-19.
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Affiliation(s)
- Khodayar Gholivand
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Fahimeh Mohammadpanah
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Mahsa Pooyan
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Roohollah Roohzadeh
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
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18
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Verma S, Pathak RK. Discovery and optimization of lead molecules in drug designing. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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19
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Tortorella S, Carosati E, Sorbi G, Bocci G, Cross S, Cruciani G, Storchi L. Combining machine learning and quantum mechanics yields more chemically aware molecular descriptors for medicinal chemistry applications. J Comput Chem 2021; 42:2068-2078. [PMID: 34410004 PMCID: PMC9291213 DOI: 10.1002/jcc.26737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 11/24/2022]
Abstract
Molecular interaction fields (MIFs), describing molecules in terms of their ability to interact with any chemical entity, are one of the most established and versatile concepts in drug discovery. Improvement of this molecular description is highly desirable for in silico drug discovery and medicinal chemistry applications. In this work, we revised a well‐established molecular mechanics' force field and applied a hybrid quantum mechanics and machine learning approach to parametrize the hydrogen‐bonding (HB) potentials of small molecules, improving this aspect of the molecular description. Approximately 66,000 molecules were chosen from available drug databases and subjected to density functional theory calculations (DFT). For each atom, the molecular electrostatic potential (EP) was extracted and used to derive new HB energy contributions; this was subsequently combined with a fingerprint‐based description of the structural environment via partial least squares modeling, enabling the new potentials to be used for molecules outside of the training set. We demonstrate that parameter prediction for molecules outside of the training set correlates with their DFT‐derived EP, and that there is correlation of the new potentials with hydrogen‐bond acidity and basicity scales. We show the newly derived MIFs vary in strength for various ring substitution in accordance with chemical intuition. Finally, we report that this derived parameter, when extended to non‐HB atoms, can also be used to estimate sites of reaction.
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Affiliation(s)
- Sara Tortorella
- Molecular Horizon srl, via Montelino 30, Bettona (Perugia), 06084, Italy
| | - Emanuele Carosati
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Giulia Sorbi
- Molecular Horizon srl, via Montelino 30, Bettona (Perugia), 06084, Italy
| | - Giovanni Bocci
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | | | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Loriano Storchi
- Dipartimento di Farmacia, Università G. D'Annunzio, Chieti, Italy.,Molecular Discovery Ltd, Hertfordshire, UK
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20
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Vulpetti A, Dalvit C. Hydrogen Bond Acceptor Propensity of Different Fluorine Atom Types: An Analysis of Experimentally and Computationally Derived Parameters. Chemistry 2021; 27:8764-8773. [PMID: 33949737 DOI: 10.1002/chem.202100301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/29/2022]
Abstract
The propensity of organic fluorine acting as a weak hydrogen bond acceptor (HBA) in intermolecular and intramolecular interactions has been the subject of many experimental and theoretical studies often reaching different conclusions. Over the last few years, new and stronger evidences have emerged for the direct involvement of fluorine in weak hydrogen bond (HB) formation. However, not all the fluorine atom types can act as weak HBA. In this work, the differential HBA propensity of various types of fluorine atoms was analyzed with a particular emphasis for the different types of alkyl fluorides. This was carried out by evaluating ab initio computed parameters, experimental 19 F NMR chemical shifts and small molecule crystallographic structures (extracted from the CSD database). According to this analysis, shielded (with reference to the 19 F NMR chemical shift) alkyl mono-fluorinated motifs display the highest HBA propensity in agreement with solution studies. Although much weaker than other well-characterized HB complexes, the fragile HBs formed by these fluorinated motifs have important implications for the chemical-physical and structural properties of the molecules, chemical reactions, and protein-ligand recognition.
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Affiliation(s)
- Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
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21
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Aydın F, Arslan NB. Synthesis, spectral properties, crystal structure and theoretical calculations of a new geminal diamine: 2,2,2-Trichloro-N,N׳-bis(2-nitrophenyl)-ethane-1,1-diamine. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Wang Y, Guo Y, Wu Z, Zhang H, Wang C, Zhao G. Conformational torsion, intramolecular hydrogen bonding and solvent effects in intersystem crossing of singlet-triplet excited states for heavy-atom-free organic long persistent luminescence. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Almutlaq N, Al-Hossainy A, Zoromba M. Combined experimental and theoretical study, characterization, and nonlinear optical properties of doped-poly (p-nitroaniline -co- o-aminophenol) thin films. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129712] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM. A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. J Med Chem 2020; 63:14626-14646. [PMID: 33215924 DOI: 10.1021/acs.jmedchem.0c01174] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
STK17B is a member of the death-associated protein kinase family and has been genetically linked to the development of diverse diseases. However, the role of STK17B in normal and disease pathology is poorly defined. Here, we present the discovery of thieno[3,2-d] pyrimidine SGC-STK17B-1 (11s), a high-quality chemical probe for this understudied "dark" kinase. 11s is an ATP-competitive inhibitor that showed remarkable selectivity over other kinases including the closely related STK17A. X-ray crystallography of 11s and related thieno[3,2-d]pyrimidines bound to STK17B revealed a unique P-loop conformation characterized by a salt bridge between R41 and the carboxylic acid of the inhibitor. Molecular dynamic simulations of STK17B revealed the flexibility of the P-loop and a wide range of R41 conformations available to the apo-protein. The isomeric thieno[2,3-d]pyrimidine SGC-STK17B-1N (19g) was identified as a negative control compound. The >100-fold lower activity of 19g on STK17B was attributed to the reduced basicity of its pyrimidine N1.
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Affiliation(s)
- Alfredo Picado
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Julie E Pickett
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Frank E Kwarcinski
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Parvathi Sinha
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Chandi S de Silva
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Reena Zutshi
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany.,German Translational Cancer Network (DKTK) site Frankfurt/Mainz, Frankfurt am Main 60596, Germany.,Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, Frankfurt am Main 60596, Germany
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
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25
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Li F, Zheng Z, Xia S, Yu L. Synthesis, co-crystal structure, and DFT calculations of a multicomponent co-crystal constructed from 1H-benzotriazole and tetrafluoroterephthalic acid. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128480] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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26
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Discovery of Novel Imidazopyridine GSK-3β Inhibitors Supported by Computational Approaches. Molecules 2020; 25:molecules25092163. [PMID: 32380735 PMCID: PMC7248956 DOI: 10.3390/molecules25092163] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 11/17/2022] Open
Abstract
The interest of research groups and pharmaceutical companies to discover novel GSK-3β inhibitors has increased over the years considering the involvement of this enzyme in many pathophysiological processes and diseases. Along this line, we recently reported on 1H-indazole-3-carboxamide (INDZ) derivatives 1-6, showing good GSK-3β inhibition activity. However, they suffered from generally poor central nervous system (CNS) permeability. Here, we describe the design, synthesis, and in vitro characterization of novel imidazo[1,5-a]pyridine-1-carboxamide (IMID 1) and imidazo[1,5-a]pyridine-3-carboxamide (IMID 2) compounds (7-18) to overcome such liability. In detail, structure-based approaches and fine-tuning of physicochemical properties guided the design of derivatives 7-18 resulting in ameliorated absorption, distribution, metabolism, and excretion (ADME) properties. A crystal structure of 16 in complex with GSK-3β enzyme (PDB entry 6Y9S) confirmed the in silico models. Despite the nanomolar inhibition activity, the new core compounds showed a reduction in potency with respect to INDZ derivatives 1-6. In this context, Molecular Dynamics (MD) and Quantum Mechanics (QM) based approaches along with NMR investigation helped to rationalize the observed structure activity relationship (SAR). With these findings, the key role of the acidic hydrogen of the central core for a tight interaction within the ATP pocket of the enzyme reflecting in good GSK-3β affinity was demonstrated.
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27
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Chen Y, Piao Y, Feng X, Yu X, Jin X, Zhao G. Excited state intramolecular proton transfer (ESIPT) luminescence mechanism for 4-N,N-diethylamino-3-hydroxyflavone in propylene carbonate, acetonitrile and the mixed solvents. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 224:117416. [PMID: 31394389 DOI: 10.1016/j.saa.2019.117416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/15/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
In this work, density functional theory (DFT) and time density functional theory (TDDFT) methods were employed to investigate the nature of the double fluorescence emission of DEAHF in these three solvents. We analyzed the geometric structures, vibrational frequencies, frontier molecular orbitals (MOs), molecular electrostatic potential surface (MEPS), calculated absorption and fluorescence spectra and the potential-energy curves for DEAHF. All the results show that the intramolecular hydrogen bond of DEAHF is strengthened from S0 to S1 and the electron density redistribution occurs between the proton acceptor and donor, which can facilitate ESIPT. Moreover, the geometric structures, absorption and emission spectra, MEPS and potential-energy curve of DEAHF are identical. It reveals theoretically that ACN and PC can maintain the polarity of the solvent with 1:1 mixing, which is consistent with the experimental results.
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Affiliation(s)
- Yan Chen
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China; Tianjin Key Laboratory of Molecular Optoelectronic Sciences, National Demonstration Center for Experimental Chemistry & Chemical Engineering Education, National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical engineering Education, Department of Chemistry, School of Science, Tianjin University, Tianjin 300354, China
| | - Yongzhe Piao
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China; College of Life Sciences, Dalian Nationalities University, Dalian 116600, China.
| | - Xia Feng
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, National Demonstration Center for Experimental Chemistry & Chemical Engineering Education, National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical engineering Education, Department of Chemistry, School of Science, Tianjin University, Tianjin 300354, China
| | - Xi Yu
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, National Demonstration Center for Experimental Chemistry & Chemical Engineering Education, National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical engineering Education, Department of Chemistry, School of Science, Tianjin University, Tianjin 300354, China
| | - Xiaoning Jin
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, National Demonstration Center for Experimental Chemistry & Chemical Engineering Education, National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical engineering Education, Department of Chemistry, School of Science, Tianjin University, Tianjin 300354, China
| | - Guangjiu Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, National Demonstration Center for Experimental Chemistry & Chemical Engineering Education, National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical engineering Education, Department of Chemistry, School of Science, Tianjin University, Tianjin 300354, China.
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Yang J, Yu Q, Yang FL, Lu K, Yan CX, Dou W, Yang L, Zhou PP. Competition and cooperativity of hydrogen-bonding and tetrel-bonding interactions involving triethylene diamine (DABCO), H2O and CO2in air. NEW J CHEM 2020. [DOI: 10.1039/c9nj06036g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triethylene diamine (DABCO) can interact with H2O and CO2in air to form dimeric and trimeric complexesviahydrogen bond, tetrel bond as well as van der Waals interactions.
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Affiliation(s)
- Jianming Yang
- Xi’an Modern Chemistry Research Institute
- Xi’an 710065
- P. R. China
| | - Qinwei Yu
- Xi’an Modern Chemistry Research Institute
- Xi’an 710065
- P. R. China
| | - Fang-Ling Yang
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Ka Lu
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Chao-Xian Yan
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Wei Dou
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Lizi Yang
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Pan-Pan Zhou
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
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Singh V, Ibnusaud I, Gadre SR, Deshmukh MM. Fragmentation method reveals a wide spectrum of intramolecular hydrogen bond energies in antioxidant natural products. NEW J CHEM 2020. [DOI: 10.1039/d0nj00304b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Very strong and weak IHBs in curcumin.
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Affiliation(s)
- Vijay Singh
- Department of Chemistry
- Dr. Harisingh Gour Vishwavidyalaya (A Central University)
- Sagar
- India
| | - Ibrahim Ibnusaud
- Institute for Intensive Research in Basic Sciences
- Mahatma Gandhi University Campus
- P.O. Kottayam
- India
| | - Shridhar R. Gadre
- Interdisciplinary School of Scientific Computing and Department of Chemistry
- Savitribai Phule Pune University
- Pune 411 007
- India
| | - Milind M. Deshmukh
- Department of Chemistry
- Dr. Harisingh Gour Vishwavidyalaya (A Central University)
- Sagar
- India
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30
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Diarylthiazole and diarylimidazole selective COX-1 inhibitor analysis through pharmacophore modeling, virtual screening, and DFT-based approaches. Struct Chem 2019. [DOI: 10.1007/s11224-019-01414-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Bauer CA. How to Model Inter- and Intramolecular Hydrogen Bond Strengths with Quantum Chemistry. J Chem Inf Model 2019; 59:3735-3743. [DOI: 10.1021/acs.jcim.9b00132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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33
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Gholivand K, Mohammadpanah F, Pooyan M, Valmoozi AAE, Sharifi M, Mani-Varnosfaderani A, Hosseini Z. Synthesis, crystal structure, insecticidal activities, molecular docking and QSAR studies of some new phospho guanidines and phospho pyrazines as cholinesterase inhibitors. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 157:122-137. [PMID: 31153459 DOI: 10.1016/j.pestbp.2019.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/10/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
Novel phospho guanidine and phospho pyrazine derivatives were synthesized and characterized by 31P, 13C, 1HNMR and IR spectroscopy to obtain novel and human-safe insecticides. Compound 35 [(C4H4N2NH)2P(O)(C6H6)] was investigated by X-ray crystallography. The inhibitory effects of synthesized compounds were evaluated on human and insect acetylcholinesterase (AChE) using in vitro Ellman method. A few of these compounds, which had low human toxicity, were selected for assessing the killing effects (in vivo) on the elm leaf beetle (X.luteola). The in vitro and in vivo results indicated that compounds bearing both phosphoryl groups and aromatic systems were found to possess a good selectivity for the inhibition of insect AChE over human AChE; up to 550-fold selectivity was achieved for compound 19. Docking studies were performed to explain reasons for the selective behavior of AChE inhibitors. Additionally, the quantitative structure-activity relationship (QSAR) and density functional theory (DFT) results of AChEs demonstrated that the size, shape, dipole moment, and ability to form hydrogen bond played the main role in both models. In addition, the aromatic π - π interactions and charge of the amide nitrogen had a major effect on insecticidal activity of the compounds. The present research can be helpful to gain a better understanding of the interactions between the insect AChE and its inhibitors and introduces compounds which are capable of becoming human-safe insecticides.
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Affiliation(s)
| | | | - Mahsa Pooyan
- Department of Chemistry, Tarbiat Modares University, Tehran, Iran
| | | | - Mahboobeh Sharifi
- Department of plant protection, Agricultural and Natural Resources Research Center, ARREO, Gorgan, Iran
| | | | - Zahra Hosseini
- Department of Chemistry, Tarbiat Modares University, Tehran, Iran
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34
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Ravi GRR, Biswal J, Kanagarajan S, Jeyakanthan J. Exploration of N5-CAIR Mutase Novel Inhibitors from Pyrococcus horikoshii OT3: A Computational Study. J Comput Biol 2019; 26:457-472. [PMID: 30785305 DOI: 10.1089/cmb.2018.0248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In bacterial and archaeal purine biosynthetic pathways, sixth step involves utilization of enzyme PurE, catalyzing the translation of aminoimidazole ribonucleotide to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) with carbon dioxide. The formation of CAIR takes place through an unstable intermediate N5-CAIR, played by two enzymes-N5-CAIR synthetase (PurK) and N5-CAIR mutase (PurE) that further catalyzes the reaction of N5-CAIR to CAIR. In this study, N5-CAIR mutase (PH0320) from Pyrococcus horikoshii OT3 (PurE) was considered. The three-dimensional structure of Pyrococcus horikoshii OT3 was modeled based on the structure of PurE from Escherichia coli. The modeled structure was subjected to molecular dynamics simulation up to 100 ns, and least energy structure from the simulation was subjected to virtual screening and induced fit docking to identify the best potent leads. A total of five best antagonists were identified based on their affinity and mode of binding leading with conserved residues Ser18, Ser20, Asp21, Ser45, Ala46, His47, Arg48, Ala72, Gly73, Ala75, and His77 promotes the activity of Ph-N5-CAIR mutase. In addition to molecular dynamics, absorption, digestion, metabolism, and excretion properties, binding free energy and density functional theory calculations of compounds were carried out. Based on analyses, compound from National Cancer Institute (NCI) database, NCI_826 was adjudged as the best potent lead molecule and could be suggested as the suitable inhibitor of N5-CAIR mutase.
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Affiliation(s)
- Guru Raj Rao Ravi
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jayashree Biswal
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Sureka Kanagarajan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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35
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Tang Z, Lu M, Liu K, Zhao Y, Qi Y, Wang Y, Zhang P, Zhou P. Solvation effect on the ESIPT mechanism of 2-(4′-amino-2′-hydroxyphenyl)-1H-imidazo-[4,5-c]pyridine. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.08.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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A series of cocrystals formed by 2,3-dimethylpyrazine bridging various aromatic acids through hydrogen bonds: Synthesis, structural characterization and synthon discussion. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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37
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Testa A, Lucas X, Castro GV, Chan KH, Wright JE, Runcie AC, Gadd MS, Harrison WTA, Ko EJ, Fletcher D, Ciulli A. 3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation. J Am Chem Soc 2018; 140:9299-9313. [PMID: 29949369 PMCID: PMC6430500 DOI: 10.1021/jacs.8b05807] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Indexed: 12/13/2022]
Abstract
Hydroxylation and fluorination of proline alters the pyrrolidine ring pucker and the trans:cis amide bond ratio in a stereochemistry-dependent fashion, affecting molecular recognition of proline-containing molecules by biological systems. While hydroxyprolines and fluoroprolines are common motifs in medicinal and biological chemistry, the synthesis and molecular properties of prolines containing both modifications, i.e., fluoro-hydroxyprolines, have not been described. Here we present a practical and facile synthesis of all four diastereoisomers of 3-fluoro-4-hydroxyprolines (F-Hyps), starting from readily available 4-oxo-l-proline derivatives. Small-molecule X-ray crystallography, NMR spectroscopy, and quantum mechanical calculations are consistent with fluorination at C3 having negligible effects on the hydrogen bond donor capacity of the C4 hydroxyl, but inverting the natural preference of Hyp from C4-exo to C4-endo pucker. In spite of this, F-Hyps still bind to the von Hippel-Lindau (VHL) E3 ligase, which naturally recognizes C4-exo Hyp in a stereoselective fashion. Co-crystal structures and electrostatic potential calculations support and rationalize the observed preferential recognition for (3 R,4 S)-F-Hyp over the corresponding (3 S,4 S) epimer by VHL. We show that (3 R,4 S)-F-Hyp provides bioisosteric Hyp substitution in both hypoxia-inducible factor 1 alpha (HIF-1α) substrate peptides and peptidomimetic ligands that form part of PROTAC (proteolysis targeting chimera) conjugates for targeted protein degradation. Despite a weakened affinity, Hyp substitution with (3 S,4 S)-F-Hyp within the PROTAC MZ1 led to Brd4-selective cellular degradation at concentrations >100-fold lower than the binary Kd for VHL. We anticipate that the disclosed chemistry of 3-fluoro-4-hydroxyprolines and their application as VHL ligands for targeted protein degradation will be of wide interest to medicinal organic chemists, chemical biologists, and drug discoverers alike.
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Affiliation(s)
- Andrea Testa
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Xavier Lucas
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Guilherme V. Castro
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Kwok-Ho Chan
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Jane E. Wright
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Andrew C. Runcie
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Morgan S. Gadd
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - William T. A. Harrison
- Department
of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K.
| | - Eun-Jung Ko
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Daniel Fletcher
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Alessio Ciulli
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
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38
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Matsui T, Yamamoto K, Fujita T, Morihashi K. Molecular Dynamics and Quantum Chemical Approach for the Estimation of an Intramolecular Hydrogen Bond Strength in Okadaic Acid. J Phys Chem B 2018; 122:7233-7242. [DOI: 10.1021/acs.jpcb.8b03272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Yang FL, Yang X, Wu RZ, Yan CX, Yang F, Ye W, Zhang LW, Zhou PP. Intermolecular interactions between σ- and π-holes of bromopentafluorobenzene and pyridine: computational and experimental investigations. Phys Chem Chem Phys 2018; 20:11386-11395. [PMID: 29645034 DOI: 10.1039/c8cp00420j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The characters of σ- and π-holes of bromopentafluorobenzene (C6F5Br) enable it to interact with an electron-rich atom or group like pyridine which possesses an electron lone-pair N atom and a π ring. Theoretical studies of intermolecular interactions between C6F5Br and C5H5N have been carried out at the M06-2X/aug-cc-pVDZ level without and with the counterpoise method, together with single point calculations at M06-2X/TZVP, wB97-XD/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels. The σ- and π-holes of C6F5Br exhibiting positive electrostatic potentials make these sites favorably interact with the N atom and the π ring of C5H5N with negative electrostatic potentials, leading to five different dimers connected by a σ-holen bond, a σ-holeπ bond or a π-holeπ bond. Their geometrical structures, characteristics, nature and spectroscopy behaviors were systematically investigated. EDA analyses reveal that the driving forces in these dimers are different. NCI, QTAIM and NBO analyses confirm the existence of intermolecular interactions formed via σ- and π-holes of C6F5Br and the N atom and the π ring of C5H5N. The experimental IR and Raman spectra gave us important information about the formation of molecular complexes between C6F5Br and C5H5N. We expect that the results could provide valuable insights into the investigation of intermolecular interactions involving σ- and π-holes.
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Affiliation(s)
- Fang-Ling Yang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, P. R. China.
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40
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Moreau RJ, Skepper CK, Appleton BA, Blechschmidt A, Balibar CJ, Benton BM, Drumm JE, Feng BY, Geng M, Li C, Lindvall MK, Lingel A, Lu Y, Mamo M, Mergo W, Polyakov V, Smith TM, Takeoka K, Uehara K, Wang L, Wei JR, Weiss AH, Xie L, Xu W, Zhang Q, de Vicente J. Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase from Gram-Negative Bacteria. J Med Chem 2018; 61:3309-3324. [DOI: 10.1021/acs.jmedchem.7b01691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Robert J. Moreau
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Colin K. Skepper
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brent A. Appleton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Anke Blechschmidt
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Carl J. Balibar
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Bret M. Benton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Joseph E. Drumm
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian Y. Feng
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mei Geng
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cindy Li
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mika K. Lindvall
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yipin Lu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mulugeta Mamo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Valery Polyakov
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Thomas M. Smith
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kenneth Takeoka
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kyoko Uehara
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lisha Wang
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jun-Rong Wei
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andrew H. Weiss
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lili Xie
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wenjian Xu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Qiong Zhang
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Javier de Vicente
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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41
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Synthesis, crystal structures, computational studies and antimicrobial activity of new designed bis((5-aryl-1,3,4-oxadiazol-2-yl)thio)alkanes. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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42
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Ferreira LA, Uversky VN, Zaslavsky BY. Effects of the Hofmeister series of sodium salts on the solvent properties of water. Phys Chem Chem Phys 2018; 19:5254-5261. [PMID: 28150000 DOI: 10.1039/c6cp08214a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvent features of water (solvent dipolarity/polarizability, π*, hydrogen bond donor acidity, α, and hydrogen bond acceptor basicity, β) were examined in aqueous solutions of Na2SO4, NaF, CH3COONa, NaCl, NaBr, NaI, and NaClO4 at concentrations of each salt from 0 to 1.0 M (up to 2.0 M for NaClO4). The solvent features of water in solutions of different concentrations for each salt were found to be linearly related as π* = z + aα + bβ. The coefficients of this relationship were suggested to represent the signature of the salt effect on the solvent features of water. The normalized distances for each salt were calculated using glucose as a reference compound. These distances may be used as the relative measures of the salt-water interactions. It is demonstrated that the distances for all salts examined are interrelated with structural water entropies and static polarizabilities of anions. It is shown that the distance may be used as a measure of the relative effects of salts on precipitation of ferric oxide, excessive chemical potential of propanol in salt solutions, surface tension, and viscosity. The distance represents the relative measure of the salt effect on the solvent features of water in a salt solution. The examples presented confirm that the approach used does enable us to characterize the differences between the effects of salts in the Hofmeister series on the properties of water.
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Affiliation(s)
- L A Ferreira
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, Ohio 44114, USA.
| | - V N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - B Y Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, Ohio 44114, USA.
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43
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Yang Y, Li D, Li C, Liu Y, Jiang K. Photoexcitation effect on the adsorption of hazardous gases on silica surface. JOURNAL OF HAZARDOUS MATERIALS 2018; 341:93-101. [PMID: 28772253 DOI: 10.1016/j.jhazmat.2017.07.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/11/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
There is very little scientific understanding of photoexcitation effect on the adsorption properties of adsorbent. The adsorption of four hazardous gases (SARIN (propan-2-ylmethylphospho-nofluoridate), methyl dichlorophosphate (MDCP), trimethyl phosphate (TMP) and hydrogen sulfide (H2S)) on silica surface is taken as target sample in this work. The adsorption energy order (MDCP<SARIN<TMP) in the ground state is consistent with the strength order of intermolecular hydrogen bond (inter-HB) between hydroxyl group of silica surface and hazardous gas, and the desorption order of the three gases in previous reports. However, with the adsorption energy increase of MDCP and the decrease of SARIN and TMP, this order changes remarkably to SARIN<TMP<MDCP after photoexcitation to excited state by absorbing shortwave ultraviolet irradiation. This change is opposite to the inter-HB weakening of MDCP in the first excited (S1) state and the strengthening of TMP and SARIN in the second excited (S2) state. This opposite change is caused by formation of intermolecular charge transfer state of MDCP and local excitation of SARIN and TMP. The H2S is dissociated after photoexcitation to the S1 state. This work presents photoexcitation as a new standard for the design and detection of adsorption properties of adsorbent for its striking effect on adsorption behaviors.
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Affiliation(s)
- Yonggang Yang
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Donglin Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Chaozheng Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Yufang Liu
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China.
| | - Kai Jiang
- School of Environment, Henan Normal University, Xinxiang 453007, China
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Andree SNL, Aakeröy CB. Molecular electrostatic potentials as a quantitative measure of hydrogen bonding preferences in solution. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1418876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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45
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Tang Z, Wang Y, Bao D, Lv M, Yang Y, Tian J, Dong L. Theoretical Investigation of an Excited-State Intramolecular Proton-Transfer Mechanism for an Asymmetric Structure of 3,7-Dihydroxy-4-oxo-2-phenyl-4H-chromene-8-carbaldehyde: Single or Double? J Phys Chem A 2017; 121:8807-8814. [DOI: 10.1021/acs.jpca.7b08266] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhe Tang
- School
of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yi Wang
- School
of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Dongshuai Bao
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Meiheng Lv
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yi Yang
- School of Light Industry & Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Jing Tian
- School
of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Liang Dong
- School
of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
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Padmaja R, Rej S, Chanda K. Environmentally friendly, microwave-assisted synthesis of 5-substituted 1 H-tetrazoles by recyclable CuO nanoparticles via (3+2) cycloaddition of nitriles and NaN3. CHINESE JOURNAL OF CATALYSIS 2017. [DOI: 10.1016/s1872-2067(17)62920-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Silva DG, Ribeiro JF, De Vita D, Cianni L, Franco CH, Freitas-Junior LH, Moraes CB, Rocha JR, Burtoloso AC, Kenny PW, Leitão A, Montanari CA. A comparative study of warheads for design of cysteine protease inhibitors. Bioorg Med Chem Lett 2017; 27:5031-5035. [DOI: 10.1016/j.bmcl.2017.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/28/2017] [Accepted: 10/01/2017] [Indexed: 02/07/2023]
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48
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Bohr HG, Shim I, Stein C, Ørum H, Hansen HF, Koch T. Electronic Structures of LNA Phosphorothioate Oligonucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:428-441. [PMID: 28918042 PMCID: PMC5537454 DOI: 10.1016/j.omtn.2017.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 01/08/2023]
Abstract
Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules.
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Affiliation(s)
- Henrik G Bohr
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Irene Shim
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Cy Stein
- Department of Medical Oncology and Experimental Therapeutics and Molecular and Cellular Biology, City of Hope Medical Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Henrik Ørum
- Anemonevej 4, Hareskov, 3500 Værløse, Denmark
| | - Henrik F Hansen
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Denmark
| | - Troels Koch
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Denmark
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49
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Lan RF, Yang YF, Ma YZ, Li YQ. The theoretical study of excited-state intramolecular proton transfer of 2,5-bis(benzoxazol-2-yl)thiophene-3,4-diol. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:37-44. [PMID: 28433832 DOI: 10.1016/j.saa.2017.04.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/12/2017] [Accepted: 04/15/2017] [Indexed: 06/07/2023]
Abstract
The symmetrical structures 2,5-bis(benzoxazol-2-yl)thiophene-3,4-diol (BBTD) can take shape two intramolecular hydrogen bonds in chloroform. In order to research the molecular dynamic behavior of BBTD upon photo-induced process, we utilize density functional theory (DFT) and time-dependent density functional theory (TDDFT) to complete theoretical calculation. Through the comparison of bond length, bond angle, IR spectra, and frontier molecular orbitals between ground state (S0) and first excited state (S1), it clearly indicates that photoexcitation have slightly influence for intensity of hydrogen bond. For the sake of understanding the mechanism of excited state intramolecular proton transfer (ESIPT) of BBTD in chloroform, potential energy surfaces have been scanned along with the orientation of O1-H2 and O4-H5 in S0 and S1 state, respectively. A intrigued hydrogen bond dynamic phenomenon has been found that ESIPT of BBTD is not a synergetic double proton transfer process, but a stepwise single proton transfer process BBTD→BBTD-S→BBTD-D. Moreover, the proton transfer process of BBTD-S→BBTD-D is easier to occur than that of BBTD→BBTD-S in S1 state.
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Affiliation(s)
- Rui-Fang Lan
- Department of Physics, Liaoning University, Shenyang 110036, PR China
| | - Yun-Fan Yang
- Department of Physics, Liaoning University, Shenyang 110036, PR China; State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yan-Zhen Ma
- Department of Physics, Liaoning University, Shenyang 110036, PR China
| | - Yong-Qing Li
- Department of Physics, Liaoning University, Shenyang 110036, PR China.
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50
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Padmaja RD, Meena DR, Maiti B, Chanda K. [Cu(phen)(PPh3)2]NO3-catalyzed microwave-assisted green synthesis of 5-substituted 1H-tetrazoles. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-3080-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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