201
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Varadwaj A, Varadwaj PR, Jin BY. Can an entirely negative fluorine in a molecule, viz. perfluorobenzene, interact attractively with the entirely negative site(s) on another molecule(s)? Like liking like! RSC Adv 2016. [DOI: 10.1039/c5ra27039a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The study presents the possibility for the formation of attractive intermolecular interactions between various entirely negative Lewis bases, leading to the formation of the thirteen isolated binary complexes examined.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan 10617
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering
- School of Engineering
- The University of Tokyo
- Japan 113-8656
| | - Bih-Yaw Jin
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan 10617
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202
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Nemec V, Cinčić D. Uncommon halogen bond motifs in cocrystals of aromatic amines and 1,4-diiodotetrafluorobenzene. CrystEngComm 2016. [DOI: 10.1039/c6ce01703g] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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203
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Silla JM, Freitas MP. A halogen bond does not dictate the conformational preferences of cis-1,3-disubstituted cyclohexanes. Org Biomol Chem 2016; 14:8610-8614. [DOI: 10.1039/c6ob01635a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A halogen bond is unlikely to control the conformation of cis-1,3-disubstituted cyclohexanes. In addition, polarization rather than the σ-hole effect describes this weak interaction more appropriately.
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Affiliation(s)
- Josué M. Silla
- Department of Chemistry
- Federal University of Lavras
- Lavras
- Brazil
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204
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Cooperative effects between halogen bonds and pnicogen bonds in XBr∙∙∙OFH2P∙∙∙NH3 (X = F, Cl, CN, NC, OH, and NO2) complexes. J Mol Model 2015; 22:5. [DOI: 10.1007/s00894-015-2872-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/22/2015] [Indexed: 12/16/2022]
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205
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Glavatskikh M, Madzhidov T, Solov'ev V, Marcou G, Horvath D, Graton J, Le Questel JY, Varnek A. Predictive Models for Halogen-bond Basicity of Binding Sites of Polyfunctional Molecules. Mol Inform 2015; 35:70-80. [PMID: 27491792 DOI: 10.1002/minf.201500116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 10/31/2015] [Indexed: 11/08/2022]
Abstract
Halogen bonding (XB) strength assesses the ability of an electron-enriched group to be involved in complexes with polarizable electrophilic halogenated or diatomic halogen molecules. Here, we report QSPR models of XB of particular relevance for an efficient screening of large sets of compounds. The basicity is described by pKBI2 , the decimal logarithm of the experimental 1 : 1 (B : I2 ) complexation constant K of organic compounds (B) with diiodine (I2 ) as a reference halogen-bond donor in alkanes at 298 K. Modeling involved ISIDA fragment descriptors, using SVM and MLR methods on a set of 598 organic compounds. Developed models were then challenged to make predictions for an external test set of 11 polyfunctional compounds for which unambiguous assignment of the measured effective complexation constant to specific groups out of the putative acceptor sites is not granted. At this stage, developed models were used to predict pKBI2 of all putative acceptor sites, followed by an estimation of the predicted effective complexation constant using the ChemEqui program. The best consensus models perform well both in cross-validation (root mean squared error RMSE=0.39-0.47 logKBI2 units) and external predictions (RMSE=0.49). The SVM models are implemented on our website (http://infochim.u-strasbg.fr/webserv/VSEngine.html) together with the estimation of their applicability domain and an automatic detection of potential halogen-bond acceptor atoms.
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Affiliation(s)
- Marta Glavatskikh
- Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, 1, rue Blaise Pascal, 67000 Strasbourg, France phone: + 33368851560.,Laboratory of Chemoinformatics and Molecular Modeling, Butlierov Institut of Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan, Russia
| | - Timur Madzhidov
- Laboratory of Chemoinformatics and Molecular Modeling, Butlierov Institut of Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan, Russia
| | - Vitaly Solov'ev
- Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskiy prospect, 31, 119071, Moscow, Russia
| | - Gilles Marcou
- Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, 1, rue Blaise Pascal, 67000 Strasbourg, France phone: + 33368851560
| | - Dragos Horvath
- Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, 1, rue Blaise Pascal, 67000 Strasbourg, France phone: + 33368851560
| | - Jérôme Graton
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière - BP 92208, 44322 Nantes Cedex 3 (France)
| | - Jean-Yves Le Questel
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière - BP 92208, 44322 Nantes Cedex 3 (France)
| | - Alexandre Varnek
- Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, 1, rue Blaise Pascal, 67000 Strasbourg, France phone: + 33368851560. .,Laboratory of Chemoinformatics and Molecular Modeling, Butlierov Institut of Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan, Russia.
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206
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Parsy CC, Alexandre FR, Bidau V, Bonnaterre F, Brandt G, Caillet C, Cappelle S, Chaves D, Convard T, Derock M, Gloux D, Griffon Y, Lallos LB, Leroy F, Liuzzi M, Loi AG, Moulat L, Chiara M, Rahali H, Roques V, Rosinovsky E, Savin S, Seifer M, Standring D, Surleraux D. Discovery and structural diversity of the hepatitis C virus NS3/4A serine protease inhibitor series leading to clinical candidate IDX320. Bioorg Med Chem Lett 2015; 25:5427-36. [DOI: 10.1016/j.bmcl.2015.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
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207
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Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
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208
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209
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Effects of substituents and charge on the RCHO⋯X–Y {X = Cl, Br, I; Y = –CF3, –CF2H, –CFH2, –CN, –CCH, –CCCN; R = –OH, –OCH3, –NH2, –O−} halogen-bonded complexes. Struct Chem 2015. [DOI: 10.1007/s11224-015-0680-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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210
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Liu M, Cai M, Li Q, Li W, Cheng J. Synergistic and diminutive effects between halogen bond and lithium bond in complexes involving aromatic compounds. J Mol Model 2015; 21:257. [PMID: 26369917 DOI: 10.1007/s00894-015-2809-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/30/2015] [Indexed: 11/25/2022]
Abstract
Quantum chemical calculations have been performed to study the interplay between halogen bond and lithium bond in the ternary systems FX-C6H5CN-LiF, FLi-C6H5CN-XF, and FLi-C6H5X-NH3 (X = Cl, Br, and I) involving aromatic compounds. This effect was studied in terms of interaction energy, electron density, charge transfer, and orbital interaction. The results showed that both FX-C6H5CN-LiF and FLi-C6H5CN-XF exhibit diminutive effects with the weakening of halogen bond and lithium bond, while FLi-C6H5X-NH3 displays synergistic effects with the strengthening of halogen bond and lithium bond. The nature of halogen bond and lithium bond in the corresponding binary complexes has been unveiled by the quantum theory of atoms in molecules methodology and energy decomposition analysis.
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Affiliation(s)
- Mingxiu Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, People's Republic of China
| | - Mengyang Cai
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, People's Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, People's Republic of China.
| | - Wenzuo Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, People's Republic of China
| | - Jianbo Cheng
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, People's Republic of China
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211
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Alexandre FR, Brandt G, Caillet C, Chaves D, Convard T, Derock M, Gloux D, Griffon Y, Lallos L, Leroy F, Liuzzi M, Loi AG, Moulat L, Musiu C, Parsy C, Rahali H, Roques V, Seifer M, Standring D, Surleraux D. Synthesis and antiviral evaluation of a novel series of homoserine-based inhibitors of the hepatitis C virus NS3/4A serine protease. Bioorg Med Chem Lett 2015; 25:3984-91. [DOI: 10.1016/j.bmcl.2015.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 01/01/2023]
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212
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El Hage K, Piquemal JP, Hobaika Z, Maroun RG, Gresh N. Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.07.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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213
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Göker H, Karaaslan C, Püsküllü MO, Yildiz S, Duydu Y, Üstündağ A, Yalcin CÖ. Synthesis and In Vitro Activity of Polyhalogenated 2-phenylbenzimidazoles as a New Class of anti-MRSA and Anti-VRE Agents. Chem Biol Drug Des 2015. [PMID: 26221778 DOI: 10.1111/cbdd.12623] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A series of novel polyhalogenated 2-phenylbenzimidazoles have been synthesized and evaluated for in vitro antistaphylococcal activity against drug-resistant bacterial strains (methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococcus faecium. Certain compounds inhibit bacterial growth perfectly. 11 was active than vancomycin (0.78 μg/mL) with the lowest MIC values with 0.19 μg/mL against methicillin-resistant Staphylococcus aureus, 8 and 35 exhibited best inhibitory activity against vancomycin-resistant Enterococcus faecium (1.56 μg/mL). The mechanism of action for this class of compounds appears to be different than clinically used antibiotics. These polyhalogenated benzimidazoles have potential for further investigation as a new class of potent anti-methicillin-resistant Staphylococcus aureus and anti-vancomycin-resistant Enterococcus faecium agents.
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Affiliation(s)
- Hakan Göker
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Dogol Str, 06100 Ankara, Turkey
| | - Cigdem Karaaslan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Dogol Str, 06100 Ankara, Turkey
| | - Mustafa Orhan Püsküllü
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
| | - Sulhiye Yildiz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Ankara University, Dogol Str, 06100 Ankara, Turkey
| | - Yalcin Duydu
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Ankara University, Dogol Str, 06100 Ankara, Turkey
| | - Aylin Üstündağ
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Ankara University, Dogol Str, 06100 Ankara, Turkey
| | - Can Özgür Yalcin
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Ankara University, Dogol Str, 06100 Ankara, Turkey
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214
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Yang Y, Xu Z, Zhang Z, Yang Z, Liu Y, Wang J, Cai T, Li S, Chen K, Shi J, Zhu W. Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design? J Phys Chem B 2015; 119:11988-97. [DOI: 10.1021/acs.jpcb.5b04130] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yang Yang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- State
Key Laboratory of Medicinal Chemical Biology, Nankai University, 94
Weijin Road, Nankai District, Tianjin300071, China
| | - Zhengyan Zhang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- College
of Chemistry, Chemical Engineering and Materials Science of Soochow
University, Soochow University, Suzhou, Jiangsu 215123, China
| | - Zhuo Yang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yingtao Liu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jinan Wang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tingting Cai
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shujin Li
- College
of Chemistry, Chemical Engineering and Materials Science of Soochow
University, Soochow University, Suzhou, Jiangsu 215123, China
| | - Kaixian Chen
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiye Shi
- Informatics
Department, UCB Pharma, 216 Bath Road, Slough SL1 4EN, United Kingdom
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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215
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Peng L, Zhu P, Meng X, Zhang C. Bromine Bonding Induced Selective Recognition of Different Guests for Hexaphenylbenzene Bromides in the Solid State. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201500293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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216
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Gilday LC, Robinson SW, Barendt TA, Langton MJ, Mullaney BR, Beer PD. Halogen Bonding in Supramolecular Chemistry. Chem Rev 2015; 115:7118-95. [DOI: 10.1021/cr500674c] [Citation(s) in RCA: 913] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lydia C. Gilday
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sean W. Robinson
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Timothy A. Barendt
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Matthew J. Langton
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin R. Mullaney
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Paul D. Beer
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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217
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Solimannejad M, Orojloo M, Amani S. Effect of cooperativity in lithium bonding on the strength of halogen bonding and tetrel bonding: (LiCN)n···ClYF3 and (LiCN)n···YF3Cl (Y = C, Si and n = 1-5) complexes as a working model. J Mol Model 2015; 21:183. [PMID: 26134217 DOI: 10.1007/s00894-015-2722-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 06/01/2015] [Indexed: 10/23/2022]
Abstract
This paper reports results of cooperativity in lithium bonding on the strength of halogen bonding and tetrel bonding in complexes pairing CF3Cl and SiF3Cl with (LiCN)n complexes, where n varies from 1 to 5. Molecular geometries and stabilization energies of title complexes are calculated at the MP2 level with 6-311++G(d,p) basis set. Cooperative effects are found in terms of structural and energetic properties when lithium, halogen, and tetrel bonds are present in these complexes simultaneously. Our results reveal that strength of halogen and tetrel bondings are enhanced due to cooperativity of Li···N interactions in lithium bonded complexes. Good linear correlations between cooperativity parameters and electronic properties of complexes were established in the present study.
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Affiliation(s)
- Mohammad Solimannejad
- Department of Chemistry, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran,
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218
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Novel benzidine and diaminofluorene prolinamide derivatives as potent hepatitis C virus NS5A inhibitors. Eur J Med Chem 2015; 101:163-78. [PMID: 26134551 DOI: 10.1016/j.ejmech.2015.06.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/14/2015] [Accepted: 06/15/2015] [Indexed: 12/21/2022]
Abstract
Our study describes the discovery of a series of highly potent hepatitis C virus (HCV) NS5A inhibitors based on symmetrical prolinamide derivatives of benzidine and diaminofluorene. Through modification of benzidine, l-proline, and diaminofluorene derivatives, we developed novel inhibitor structures, which allowed us to establish a library of potent HCV NS5A inhibitors. After optimizing the benzidine prolinamide backbone, we identified inhibitors embedding meta-substituted benzidine core structures that exhibited the most potent anti-HCV activities. Furthermore, through a battery of studies including hERG ligand binding assay, CYP450 binding assay, rat plasma stability test, human liver microsomal stability test, and pharmacokinetic studies, the identified compounds 24, 26, 27, 42, and 43 are found to be nontoxic, and are expected to be effective therapeutic anti-HCV agents.
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219
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Uses of 3-(2-Bromoacetyl)-2H-chromen-2-one in the Synthesis of Heterocyclic Compounds Incorporating Coumarin: Synthesis, Characterization and Cytotoxicity. Molecules 2015; 20:11535-53. [PMID: 26111181 PMCID: PMC6272230 DOI: 10.3390/molecules200611535] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 12/12/2022] Open
Abstract
In this work, 3-bromoacetylcoumarin was used as the key starting material for the synthesis of pyran, pyridine, thiophene, thiazole and pyrazole derivatives through its reaction with different reagents. The structures of the newly synthesized compounds were confirmed on the basis of their spectral data and elemental analyses. All of the synthesized compounds were screened for their in vitro anticancer activity against six human cancer cell lines, namely: human gastric cancer (NUGC), human colon cancer (DLD1), human liver cancer (HA22T and HEPG2), nasopharyngeal carcinoma (HONE1), human breast cancer (MCF) and normal fibroblast cells (WI38). The IC50 values (the sample concentration that produces 50% reduction in cell growth) in nanomolars (nM)) showed most of the compounds exhibited significant cytotoxic effect. Among these derivatives, compound 6d showed almost equipotent cytotoxic activity against NUGC (IC50 = 29 nM) compared to the standard CHS 828 (IC50 = 25 nM).
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220
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Millett AJ, Habtemariam A, Romero-Canelón I, Clarkson GJ, Sadler PJ. Contrasting Anticancer Activity of Half-Sandwich Iridium(III) Complexes Bearing Functionally Diverse 2-Phenylpyridine Ligands. Organometallics 2015; 34:2683-2694. [PMID: 26146437 PMCID: PMC4482135 DOI: 10.1021/acs.organomet.5b00097] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 12/30/2022]
Abstract
We report the synthesis, characterization, and antiproliferative activity of 15 iridium(III) half-sandwich complexes of the type [(η5-Cp*)Ir(2-(R'-phenyl)-R-pyridine)Cl] bearing either an electron-donating (-OH, -CH2OH, -CH3) or electron-withdrawing (-F, -CHO, -NO2) group at various positions on the 2-phenylpyridine (2-PhPy) chelating ligand giving rise to six sets of structural isomers. The X-ray crystal structures of [(η5-Cp*)Ir(2-(2'-fluorophenyl)pyridine)Cl] (1) and [(η5-Cp*)Ir(2-(4'-fluorophenyl)pyridine)Cl] (2) exhibit the expected "piano-stool" configuration. DFT calculations showed that substituents caused only localized effects on the electrostatic potential surface of the chelating 2-PhPy ligand of the complexes. Hydrolysis of all complexes is rapid, but readily reversed by addition of NaCl. The complexes show preferential binding to 9-ethylguanine over 9-methyladenine and are active catalysts for the oxidation of NADH to NAD+. Antiproliferative activity experiments in A2780 ovarian, MCF-7 breast, A549 lung, and HCT116 colon cancer cell lines showed IC50 values ranging from 1 to 89 μM, with the most potent complex, [(η5-Cp*)Ir(2-(2'-methylphenyl)pyridine)Cl] (13) (A2780 IC50 = 1.18 μM), being 10× more active than the parent, [(η5-Cp*)Ir(2-phenylpyridine)Cl], and 2× more active than [(η5-CpxPh)Ir(2-phenylpyridine)Cl]. Intriguingly, contrasting biological activities are observed between structural isomers despite exhibiting similar chemical reactivity. For pairs of structural isomers both the nature and position of the functional group can affect the hydrophobicity of the complex. An increase in hydrophobicity resulted in enhanced cellular-iridium accumulation in A2780 ovarian cells, which generally gave rise to an increase in potency. The structural isomers [(η5-Cp*)Ir(2-(4'-fluorophenyl)pyridine)Cl] (2) and [(η5-Cp*)Ir(2-phenyl-5-fluoropyridine)Cl] (4) preferentially localized in the cytosol > membrane and particulate > nucleus > cytoskeleton. This work highlights the strong dependence of biological behavior on the nature and position of the substituent on the chelating ligand and shows how this class of organometallic anticancer complexes can be fine-tuned to increase their potency without using extended cyclopentadienyl systems.
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Affiliation(s)
- Adam J. Millett
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K.
| | - Abraha Habtemariam
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K.
| | - Isolda Romero-Canelón
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K.
| | - Guy J. Clarkson
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K.
| | - Peter J. Sadler
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K.
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221
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Agniswamy J, Louis JM, Shen CH, Yashchuk S, Ghosh AK, Weber IT. Substituted Bis-THF Protease Inhibitors with Improved Potency against Highly Resistant Mature HIV-1 Protease PR20. J Med Chem 2015; 58:5088-95. [PMID: 26010498 DOI: 10.1021/acs.jmedchem.5b00474] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An extremely drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with two potent antiviral investigational inhibitors. GRL-5010A and GRL-4410A were designed to introduce hydrogen bond interactions with the flexible flaps of the PR by incorporating gem-difluorines and alkoxy, respectively, at the C4 position of the bis-THF of darunavir. PR20 provides an excellent model for high level resistance, since clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme. GRL-5010A and GRL-4410A show inhibition constants of 4.3 ± 7.0 and 1.7 ± 1.8 nM, respectively, for PR20, compared to the binding affinity of 41 ± 1 nM measured for darunavir. Crystal structures of PR20 in complexes with the two inhibitors confirmed the new hydrogen bond interactions with Gly 48 in the flap of the enzyme. The two new compounds are more effective than darunavir in inhibiting mature PR20 and show promise for further development of antiviral agents targeting highly resistant PR mutants.
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Affiliation(s)
- Johnson Agniswamy
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
| | - John M Louis
- ‡Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Chen-Hsiang Shen
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sofiya Yashchuk
- §Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Arun K Ghosh
- §Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Irene T Weber
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
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Wang C, Guan L, Danovich D, Shaik S, Mo Y. The origins of the directionality of noncovalent intermolecular interactions#. J Comput Chem 2015; 37:34-45. [DOI: 10.1002/jcc.23946] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Changwei Wang
- Department of Chemistry; School of Science; China University of Petroleum (East China); Changjiangxi Road 66 266580 Tsingtao China
| | - Liangyu Guan
- Department of Chemistry; Western Michigan University; Kalamazoo Michigan 49008
| | - David Danovich
- Institute of Chemistry and Lise Meitner Minerva Center for Computational Quantum Chemistry; the Hebrew University; Jerusalem 91904 Israel
| | - Sason Shaik
- Institute of Chemistry and Lise Meitner Minerva Center for Computational Quantum Chemistry; the Hebrew University; Jerusalem 91904 Israel
| | - Yirong Mo
- Department of Chemistry; Western Michigan University; Kalamazoo Michigan 49008
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223
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Li W, Zeng Y, Zhang X, Zheng S, Meng L. The enhancing effects of group V σ-hole interactions on the F···O halogen bond. Phys Chem Chem Phys 2015; 16:19282-9. [PMID: 25099757 DOI: 10.1039/c4cp02430c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The σ-hole interaction, which occurs between the covalent IV-VII atoms and nucleophilic substances, has become a hot issue of weak interaction. In this work, NCF···O=PX3···(NCF)n (X = F, Cl, Br, H, CH3·; n = 0, 1, 2) complexes were constructed and studied based on the second-order Møller-Plesset perturbation theory (MP2) calculations to investigate the enhancing effects of group V σ-hole interactions on the F···O halogen bond. With increasing n, the FO halogen bond becomes stronger, indicating that the group V σ-hole interactions could enhance the F···O halogen bond. As the capacity of donating electrons of X increases, the most negative electrostatic potentials outside the oxygen atom of O=PX3···(NCF)n (n = 0, 1, 2) become more negative, resulting in a stronger F···O halogen bond. In the formation of a F···O halogen bond, along the sequence of X = F, Cl, Br, H, CH3 of the negative sites O=PX3, the electric field of the lone pair of oxygen becomes greater and causes a larger decrease in electron density outside the fluorine atom. On the other hand, with increasing n from 0 to 2, the group V σ-hole interactions also increase the electric field of lone pair of oxygen and results in a larger decrease in electron density outside the fluorine atom.
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Affiliation(s)
- Wei Li
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang 050024, P. R. China.
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224
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Yang Z, Liu Y, Chen Z, Xu Z, Shi J, Chen K, Zhu W. A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions. J Mol Model 2015; 21:138. [DOI: 10.1007/s00894-015-2681-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/13/2015] [Indexed: 03/08/2023]
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226
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 760] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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227
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Blood–brain barrier permeable anticholinesterase aurones: Synthesis, structure–activity relationship, and drug-like properties. Eur J Med Chem 2015; 94:195-210. [DOI: 10.1016/j.ejmech.2015.02.055] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 11/29/2022]
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228
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Kawai S, Sadeghi A, Xu F, Peng L, Orita A, Otera J, Goedecker S, Meyer E. Extended halogen bonding between fully fluorinated aromatic molecules. ACS NANO 2015; 9:2574-2583. [PMID: 25716456 DOI: 10.1021/nn505876n] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Halogen bonding is a noncovalent interaction where an electrophilic cap on a halogen atom, the so-called σ-hole, attracts a nucleophilic site on an adjacent molecule. The polarizability of halogens relates to the strength of the σ-hole, and accordingly the halogen-halogen distance becomes shorter in the order of Cl, Br, and I. Fully fluoro-substituted aromatic molecules, on the contrary, are generally believed not to form halogen bonds due to the absence of a σ-hole. Here, we study atomic-scale in-plane F-F contacts with high-resolution force microscopy. Our ab initio calculations show that the attractive dispersion forces can overcome the electrostatic repulsion between the fluorine atoms, while the anisotropic distribution of the negative electrostatic potential leads the directional bond and even changes the gap. The coexistence of these two competing forces results in the formation of a "windmill" structure, containing three C-F···F bonds among neighboring molecules. While the σ-hole is absent, the scheme of the C-F···F bonding has a high similarity to halogen bonding.
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Affiliation(s)
- Shigeki Kawai
- †Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
- ‡PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Ali Sadeghi
- †Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
- §Department of Physics, Shahid Beheshti University, Evin, 19839 Tehran, Iran
| | - Feng Xu
- ⊥Department of Applied Chemistry, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Lifen Peng
- ⊥Department of Applied Chemistry, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Akihiro Orita
- ⊥Department of Applied Chemistry, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Junzo Otera
- ⊥Department of Applied Chemistry, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Stefan Goedecker
- †Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Ernst Meyer
- †Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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229
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Ai X, Shen S, Shen L, Lu S. An interaction map of small-molecule kinase inhibitors with anaplastic lymphoma kinase (ALK) mutants in ALK-positive non-small cell lung cancer. Biochimie 2015; 112:111-20. [PMID: 25769414 DOI: 10.1016/j.biochi.2015.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/02/2015] [Indexed: 12/16/2022]
Abstract
Human anaplastic lymphoma kinase (ALK) has become a well-established target for the treatment of ALK-positive non-small cell lung cancer (NSCLC). Here, we have profiled seven small-molecule inhibitors, including 2 that are approved drugs, against a panel of clinically relevant mutations in ALK tyrosine kinase (TK) domain, aiming at a comprehensive understanding of molecular mechanism and biological implication underlying inhibitor response to ALK TK mutation. We find that (i) the gatekeeper mutation L1196M causes crizotinib resistance by simultaneously increasing and decreasing the binding affinities of, respectively, ATP and inhibitor to ALK, whereas the secondary mutation C1156Y, which is located far away from the ATP-binding site of ALK TK domain, causes the resistance by inducing marked allosteric effect on the site, (ii) the 2nd and 3rd generation kinase inhibitors exhibit relatively high sensitivity towards ALK mutants as compared to 1st generation inhibitors, (iii) the pan-kinase inhibitor staurosporine is insensitive for most mutations due to its high structural compatibility, and (iv) ATP affinity to ALK is generally reduced upon most clinically relevant mutations. Furthermore, we also identify six novel mutation-inhibitor pairs that are potentially associated with drug resistance. In addition, the G1202R and C1156Y mutations are expected to generally cause resistance for many existing inhibitors, since they can address significant effect on the geometric shape and physicochemical property of ALK active pocket.
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Affiliation(s)
- Xinghao Ai
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shengping Shen
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lan Shen
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shun Lu
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China.
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230
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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231
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Zierkiewicz W, Bieńko DC, Michalska D, Zeegers-Huyskens T. Theoretical investigation of the halogen bonded complexes between carbonyl bases and molecular chlorine. J Comput Chem 2015; 36:821-32. [DOI: 10.1002/jcc.23860] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/23/2015] [Accepted: 01/25/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Wiktor Zierkiewicz
- Department of Chemistry; Wrocław University of Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Dariusz C. Bieńko
- Department of Chemistry; Wrocław University of Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Danuta Michalska
- Department of Chemistry; Wrocław University of Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
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232
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Brown DG, Gagnon MM, Boström J. Understanding Our Love Affair with p-Chlorophenyl: Present Day Implications from Historical Biases of Reagent Selection. J Med Chem 2015; 58:2390-405. [DOI: 10.1021/jm501894t] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dean G. Brown
- Infection Innovative Medicines, AstraZeneca R&D Boston, Waltham, Massachusetts 02451, United States
| | - Moriah M. Gagnon
- Infection Innovative Medicines, AstraZeneca R&D Boston, Waltham, Massachusetts 02451, United States
| | - Jonas Boström
- CVMD
Innovative Medicines, AstraZeneca, Mölndal SE-431
83, Sweden
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233
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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234
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Xu W, Lucke AJ, Fairlie DP. Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets. J Mol Graph Model 2015; 57:76-88. [PMID: 25682361 DOI: 10.1016/j.jmgm.2015.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 12/17/2022]
Abstract
Accurately predicting relative binding affinities and biological potencies for ligands that interact with proteins remains a significant challenge for computational chemists. Most evaluations of docking and scoring algorithms have focused on enhancing ligand affinity for a protein by optimizing docking poses and enrichment factors during virtual screening. However, there is still relatively limited information on the accuracy of commercially available docking and scoring software programs for correctly predicting binding affinities and biological activities of structurally related inhibitors of different enzyme classes. Presented here is a comparative evaluation of eight molecular docking programs (Autodock Vina, Fitted, FlexX, Fred, Glide, GOLD, LibDock, MolDock) using sixteen docking and scoring functions to predict the rank-order activity of different ligand series for six pharmacologically important protein and enzyme targets (Factor Xa, Cdk2 kinase, Aurora A kinase, COX-2, pla2g2a, β Estrogen receptor). Use of Fitted gave an excellent correlation (Pearson 0.86, Spearman 0.91) between predicted and experimental binding only for Cdk2 kinase inhibitors. FlexX and GOLDScore produced good correlations (Pearson>0.6) for hydrophilic targets such as Factor Xa, Cdk2 kinase and Aurora A kinase. By contrast, pla2g2a and COX-2 emerged as difficult targets for scoring functions to predict ligand activities. Although possessing a high hydrophobicity in its binding site, β Estrogen receptor produced reasonable correlations using LibDock (Pearson 0.75, Spearman 0.68). These findings can assist medicinal chemists to better match scoring functions with ligand-target systems for hit-to-lead optimization using computer-aided drug design approaches.
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Affiliation(s)
- Weijun Xu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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235
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Chauhan NPS, Mozafari M, Ameta R, Punjabi PB, Ameta SC. Spectral and thermal characterization of halogen-bonded novel crystalline oligo(p-bromoacetophenone formaldehyde). J Phys Chem B 2015; 119:3223-30. [PMID: 25594328 DOI: 10.1021/jp510320g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel oligomer p-bromoacetophenone-formaldehyde (OPBAF) was prepared by condensation polymerization in the presence of an acid as catalyst. It was characterized by FT-IR, NMR, pyrolysis GC/MS, XRD, GPC, and TG-DTG. The crystallographic parameters and space group for hexagonal OPBAF were a = b = 2.0810 Å and c = 9.2340 Å and P3̅m1, respectively. The degradation activation energy of the oligomer was studied by the Kissinger method. The kinetic parameters were also obtained. Halogen bonding interactions in the crystalline oligomers are identified between halogen···carbonyl and halogen···halogen. Little correlation was found in the halogen bonding motifs exhibited as a function of bromine present in this oligomer, and a unique bifurcated Br···Br/Br···O═C halogen bonding synthon was identified. This newly developed oligomer may be used as an interesting material for the development of 3D-designed structural products.
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Affiliation(s)
- Narendra Pal Singh Chauhan
- Department of Chemistry, Bhupal Nobles Post Graduate (B.N.P.G.) College , Udaipur 313001, Rajasthan, India
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236
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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237
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Mocelo-Castell R, Villanueva-Novelo C, Cáceres-Castillo D, Carballo RM, Quijano-Quiñones RF, Quesadas-Rojas M, Cantillo-Ciau Z, Cedillo-Rivera R, Moo-Puc RE, Moujir LM, Mena-Rejón GJ. 2-Amino-4-arylthiazole Derivatives as Anti-giardial Agents: Synthesis, Biological Evaluation and QSAR Studies. OPEN CHEM 2015. [DOI: 10.1515/chem-2015-0127] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractA series of seven 2-amino-4-arylthiazoles were prepared following Hantzsch’s modified method under microwave irradiation. A set of 50 derivatives was obtained and the in vitro activity against Giardia intestinalis was evaluated. The results on the biological activity revealed that, in general, the N-(5-bromo-4-aryl-thiazol-2-yl)-acetamide scaffold showed high bioactivity. In particular, compounds 6e (IC50 = 0.39 μM) and 6b (IC50 = 0.87 μM) were found to be more potent than the positive control metronidazole. Citoxicity and acute toxicity tests performed showed low toxicity and high selectivity of the most active compounds (6e SI = 139, 6b SI = 52.3). A QSAR analysis was applied to a data set of 37 obtained 2-amino-4-arylthiazoles derivatives and the best model described a strongly correlation between the anti-giardiasic activity and molecular descriptors as E2M, RDF115m, F10, MATS6v, and Hypnotic-80, with high statistical quality. This finding indicates that N-substituted aminothiazole scaffold should be investigated for the development of highly selective anti-giardial agent.
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238
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Xu HY, Wang W, Zou JW, Xu XL. Theoretical calculations of π-type pnicogen bonds in the triad intermolecular complexes. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633614500680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The pnicogen bonding interactions of PCl3and π-electron systems (acetylene, ethylene, benzene) were calculated by using MP2/aug-cc-pVDZ method and the effect of hydrogen bond on pnicogen bond systems were investigated. It has been indicated that the hydrogen bonding and the pnicogen bonding interactions have influence on each other and the positively cooperative effect has been detected. The interaction energies of pnicogen bonded supramolecular system were also calculated by using DFT method (M06-2X) and some simple comparisons with those by using MP2 method were made. It has been disclosed from natural bond orbitals (NBO) analysis that more the amount of charge transfer of pnicogen bonding interaction, the greater the stability of the corresponding complex. Through AIM topological analysis, it has been revealed that the electron density of pnicogen bond BCP point is positively correlated with the stability of trimeric complex. Electron localization function (ELF) was also adopted to analyze the nature of pnicogen bonding interactions. Furthermore, density difference function (DDF) method was adopted to analyze the variation of electron density of pnicogen bond system because of hydrogen bond.
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Affiliation(s)
- Hui-Ying Xu
- College of Biology and Environment Engineering, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang Province, P. R. China
| | - Wei Wang
- Zhejiang Surveying Institute of Estuary and Coast, Hangzhou, 310008, Zhejiang Province, P. R. China
| | - Jian-Wei Zou
- College of Biology and Environment Engineering, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang Province, P. R. China
- Ningbo Institute of Technology, Zhejiang University, Ningbo, 315200, Zhejiang Province, P. R. China
| | - Xiao-Lu Xu
- College of Biology and Environment Engineering, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang Province, P. R. China
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239
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Carter KP, Cahill CL. Combining coordination and supramolecular chemistry to explore uranyl assembly in the solid state. Inorg Chem Front 2015. [DOI: 10.1039/c4qi00183d] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Supramolecular assembly of uranyl species via halogen–oxo and halogen–halogen interactions is explored in the solid state.
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Affiliation(s)
- Korey P. Carter
- Department of Chemistry
- The George Washington University
- Washington
- USA
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240
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Xu R, Lord SA, Peterson RM, Fergason-Cantrell EA, Lever JR, Lever SZ. Ether modifications to 1-[2-(3,4-dimethoxyphenyl)ethyl]-4-(3-phenylpropyl)piperazine (SA4503): effects on binding affinity and selectivity for sigma receptors and monoamine transporters. Bioorg Med Chem 2015; 23:222-30. [PMID: 25468036 PMCID: PMC4274187 DOI: 10.1016/j.bmc.2014.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/25/2014] [Accepted: 11/04/2014] [Indexed: 11/22/2022]
Abstract
Two series of novel ether analogs of the sigma (σ) receptor ligand 1-[2-(3,4-dimethoxyphenyl)ethyl]-4-(3-phenylpropyl)piperazine (SA4503) have been prepared. In one series, the alkyl portion of the 4-methoxy group was replaced with allyl, propyl, bromoethyl, benzyl, phenethyl, and phenylpropyl moieties. In the second series, the 3,4-dimethoxy was replaced with cyclic methylenedioxy, ethylenedioxy and propylenedioxy groups. These ligands, along with 4-O-des-methyl SA4503, were evaluated for σ1 and σ2 receptor affinity, and compared to SA4503 and several known ether analogs. SA4503 and a subset of ether analogs were also evaluated for dopamine transporter (DAT) and serotonin transporter (SERT) affinity. The highest σ1 receptor affinities, Ki values of 1.75-4.63 nM, were observed for 4-O-des-methyl SA4503, SA4503 and the methylenedioxy analog. As steric bulk increased, σ1 receptor affinity decreased, but only to a point. Allyl, propyl and bromoethyl substitutions gave σ1 receptor Ki values in the 20-30 nM range, while bulkier analogs having phenylalkyl, and Z- and E-iodoallyl, ether substitutions showed higher σ1 affinities, with Ki values in the 13-21 nM range. Most ligands studied exhibited comparable σ1 and σ2 affinities, resulting in little to no subtype selectivity. SA4503, the fluoroethyl analog and the methylenedioxy congener showed modest six- to fourteen-fold selectivity for σ1 sites. DAT and SERT interactions proved much more sensitive than σ receptor interactions to these structural modifications. For example, the benzyl congener (σ1Ki=20.8 nM; σ2Ki=16.4 nM) showed over 100-fold higher DAT affinity (Ki=121 nM) and 6-fold higher SERT affinity (Ki=128nM) than the parent SA4503 (DAT Ki=12650 nM; SERT Ki=760 nM). Thus, ether modifications to the SA4503 scaffold can provide polyfunctional ligands having a broader spectrum of possible pharmacological actions.
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Affiliation(s)
- Rong Xu
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | - Sarah A Lord
- Department of Radiology, University of Missouri, Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Ryan M Peterson
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | - Emily A Fergason-Cantrell
- Department of Radiology, University of Missouri, Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - John R Lever
- Department of Radiology, University of Missouri, Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA.
| | - Susan Z Lever
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA; Department of MU Research Reactor Center, University of Missouri, Columbia, MO 65211, USA.
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241
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Alshahateet SF, Bhadbhade MM, Bishop R, Craig DC, Scudder ML. Halogen containing clusters N2Br2, N2Br4, S2Br4and S2Br6yield penannular inclusion compounds. CrystEngComm 2015. [DOI: 10.1039/c5ce01838b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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242
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Varadwaj PR, Varadwaj A, Jin BY. Unusual bonding modes of perfluorobenzene in its polymeric (dimeric, trimeric and tetrameric) forms: entirely negative fluorine interacting cooperatively with entirely negative fluorine. Phys Chem Chem Phys 2015; 17:31624-45. [DOI: 10.1039/c5cp03209a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Laplacian of the charge density plot for the tetramer of perfluorobenzene, displaying the attraction between entirely negative fluorine atoms, as well as the windmill type intermolecular topology between those atoms.
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Affiliation(s)
| | - Arpita Varadwaj
- Department of Chemistry
- National Taiwan University
- Taipei
- Republic of China
| | - Bih-Yaw Jin
- Department of Chemistry
- National Taiwan University
- Taipei
- Republic of China
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243
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Kratzer P, Ramming B, Römisch S, Maas G. The iodine–oxygen halogen bond: solid-state structures of 3-iodopropiolamides. CrystEngComm 2015. [DOI: 10.1039/c5ce00365b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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244
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245
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Bartashevich EV, Tsirelson VG. Interplay between non-covalent interactions in complexes and crystals with halogen bonds. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rcr4440] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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246
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Yang Z, Xu Z, Liu Y, Wang J, Shi J, Chen K, Zhu W. Unstable, metastable, or stable halogen bonding interaction involving negatively charged donors? A statistical and computational chemistry study. J Phys Chem B 2014; 118:14223-33. [PMID: 25390886 DOI: 10.1021/jp506291v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The noncovalent halogen bonding could be attributed to the attraction between the positively charged σ-hole and a nucleophile. Quantum mechanics (QM) calculation indicated that the negatively charged organohalogens have no positively charged σ-hole on their molecular surface, leading to a postulation of repulsion between negatively charged organohalogens and nucleophiles in vacuum. However, PDB survey revealed that 24% of the ligands with halogen bonding geometry could be negatively charged. Moreover, 36% of ionizable drugs in CMC (Comprehensive Medicinal Chemistry) are possibly negatively charged at pH 7.0. QM energy scan showed that the negatively charged halogen bonding is probably metastable in vacuum. However, the QM calculated bonding energy turned negative in various solvents, suggesting that halogen bonding with negatively charged donors should be stable in reality. Indeed, QM/MM calculation on three crystal structures with negatively charged ligands revealed that the negatively charged halogen bonding was stable. Hence, we concluded that halogen bonding with negatively charged donors is unstable or metastable in vacuum but stable in protein environment, and possesses similar geometric and energetic characteristics as conventional halogen bonding. Therefore, negatively charged organohalogens are still effective halogen bonding donors for medicinal chemistry and other applications.
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Affiliation(s)
- Zhuo Yang
- Drug Discovery and Design Center, Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, 201203, China
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247
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Angelina E, Andujar S, Moreno L, Garibotto F, Párraga J, Peruchena N, Cabedo N, Villecco M, Cortes D, Enriz RD. 3-Chlorotyramine Acting as Ligand of the D2
Dopamine Receptor. Molecular Modeling, Synthesis and D2
Receptor Affinity. Mol Inform 2014; 34:28-43. [DOI: 10.1002/minf.201400093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/04/2014] [Indexed: 12/12/2022]
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248
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El Hage K, Piquemal JP, Hobaika Z, Maroun RG, Gresh N. Could the “Janus-like” properties of the halobenzene CX bond (XCl, Br) be leveraged to enhance molecular recognition? J Comput Chem 2014; 36:210-21. [DOI: 10.1002/jcc.23786] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/21/2014] [Accepted: 10/27/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Krystel El Hage
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomédicale; Paris France
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; B.P. 11-514 Riad El Solh Beirut 1107 2050 Lebanon
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS; Paris France
| | - Zeina Hobaika
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; B.P. 11-514 Riad El Solh Beirut 1107 2050 Lebanon
| | - Richard G. Maroun
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; B.P. 11-514 Riad El Solh Beirut 1107 2050 Lebanon
| | - Nohad Gresh
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomédicale; Paris France
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249
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SAR analysis and biological studies of synthesized podophyllum derivates obtained by N linkage modification at C-4 position. Bioorg Med Chem 2014; 22:6183-92. [DOI: 10.1016/j.bmc.2014.08.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 11/21/2022]
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250
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Celis-Barros C, Saavedra-Rivas L, Salgado JC, Cassels BK, Zapata-Torres G. Molecular dynamics simulation of halogen bonding mimics experimental data for cathepsin L inhibition. J Comput Aided Mol Des 2014; 29:37-46. [DOI: 10.1007/s10822-014-9802-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022]
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