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El-Wakil MH, El-Dershaby HA, Ghazallah RA, El-Yazbi AF, Abd El-Razik HA, Soliman FSG. Identification of new 5-(2,6-dichlorophenyl)-3-oxo-2,3-dihydro-5H-thiazolo[3,2-a]pyrimidine-7-carboxylic acids as p38α MAPK inhibitors: Design, synthesis, antitumor evaluation, molecular docking and in silico studies. Bioorg Chem 2024; 145:107226. [PMID: 38377818 DOI: 10.1016/j.bioorg.2024.107226] [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: 12/10/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
In pursuit of discovering novel scaffolds that demonstrate potential inhibitory activity against p38α MAPK and possess strong antitumor effects, we herein report the design and synthesis of new series of 17 final target 5-(2,6-dichlorophenyl)-3-oxo-2,3-dihydro-5H-thiazolo[3,2-a]pyrimidine-7-carboxylic acids (4-20). Chemical characterization of the compounds was performed using FT-IR, NMR, elemental analyses and mass spectra of some representative examples. With many compounds showing potential inhibitory activity against p38α MAPK, two derivatives, 8 and 9, demonstrated the highest activity (>70 % inhibition) among the series. Derivative 9 displayed IC50 value nearly 2.5 folds more potent than 8. As anticipated, they both showed explicit interactions inside the kinase active site with the key binding amino acid residues. Screening both compounds for cytotoxic effects, they exhibited strong antitumor activities against lung (A549), breast (MCF-7 and MDA MB-231), colon (HCT-116) and liver (Hep-G2) cancers more potent than reference 5-FU. Their noticeable strong antitumor activity pointed out to the possibility of an augmented DNA binding mechanism of antitumor action besides their kinase inhibition. Both 8 and 9 exhibited strong ctDNA damaging effects in nanomolar range. Further mechanistic antitumor studies revealed ability of compounds 8 and 9 to arrest cell cycle in MCF-7 cells at S phase, while in HCT-116 treated cells at G0-G1 and G2/M phases. They also displayed apoptotic induction effects in both MCF-7 and HCT-116 with total cell deaths more than control untreated cells in reference to 5-FU. Finally, the compounds were tested for their anti-migratory potential utilizing wound healing assay. They induced a significant decrease in wound closure percentage after 24 h treatment in the examined cancer cells when compared to untreated control MCF-7 and HCT-116 cells better than 5-FU. In silico computation of physicochemical parameters revealed the drug-like properties of 8 and 9 with no violation to Lipinski's rule of five as well as their tolerable ADMET parameters, thus suggesting their utilization as potential future drug leads amenable for further optimization and development.
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Affiliation(s)
- Marwa H El-Wakil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt.
| | - Hadeel A El-Dershaby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Rasha A Ghazallah
- Department of Medical Biochemistry, Faculty of Medicine, Alexandria University, Alexandria 21521, Egypt
| | - Amira F El-Yazbi
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Heba A Abd El-Razik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Farid S G Soliman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
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Herrington NB, Stein D, Li YC, Pandey G, Schlessinger A. Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555779. [PMID: 37693436 PMCID: PMC10491245 DOI: 10.1101/2023.08.31.555779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Protein kinase function and interactions with drugs are controlled in part by the movement of the DFG and ɑC-Helix motifs, which enable kinases to adopt various conformational states. Small molecule ligands elicit therapeutic effects with distinct selectivity profiles and residence times that often depend on the kinase conformation(s) they bind. However, the limited availability of experimentally determined structural data for kinases in inactive states restricts drug discovery efforts for this major protein family. Modern AI-based structural modeling methods hold potential for exploring the previously experimentally uncharted druggable conformational space for kinases. Here, we first evaluated the currently explored conformational space of kinases in the PDB and models generated by AlphaFold2 (AF2) (1) and ESMFold (2), two prominent AI-based structure prediction methods. We then investigated AF2's ability to predict kinase structures in different conformations at various multiple sequence alignment (MSA) depths, based on this parameter's ability to explore conformational diversity. Our results showed a bias within the PDB and predicted structural models generated by AF2 and ESMFold toward structures of kinases in the active state over alternative conformations, particularly those conformations controlled by the DFG motif. Finally, we demonstrate that predicting kinase structures using AF2 at lower MSA depths allows the exploration of the space of these alternative conformations, including identifying previously unobserved conformations for 398 kinases. The results of our analysis of structural modeling by AF2 create a new avenue for the pursuit of new therapeutic agents against a notoriously difficult-to-target family of proteins. Significance Statement Greater abundance of kinase structural data in inactive conformations, currently lacking in structural databases, would improve our understanding of how protein kinases function and expand drug discovery and development for this family of therapeutic targets. Modern approaches utilizing artificial intelligence and machine learning have potential for efficiently capturing novel protein conformations. We provide evidence for a bias within AlphaFold2 and ESMFold to predict structures of kinases in their active states, similar to their overrepresentation in the PDB. We show that lowering the AlphaFold2 algorithm's multiple sequence alignment depth can help explore kinase conformational space more broadly. It can also enable the prediction of hundreds of kinase structures in novel conformations, many of whose models are likely viable for drug discovery.
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Chen L, Zhang X, Ou Y, Liu M, Yu D, Song Z, Niu L, Zhang L, Shi J. Advances in RIPK1 kinase inhibitors. Front Pharmacol 2022; 13:976435. [PMID: 36249746 PMCID: PMC9554302 DOI: 10.3389/fphar.2022.976435] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 01/27/2023] Open
Abstract
Programmed necrosis is a new modulated cell death mode with necrotizing morphological characteristics. Receptor interacting protein 1 (RIPK1) is a critical mediator of the programmed necrosis pathway that is involved in stroke, myocardial infarction, fatal systemic inflammatory response syndrome, Alzheimer's disease, and malignancy. At present, the reported inhibitors are divided into four categories. The first category is the type I ATP-competitive kinase inhibitors that targets the area occupied by the ATP adenylate ring; The second category is type Ⅱ ATP competitive kinase inhibitors targeting the DLG-out conformation of RIPK1; The third category is type Ⅲ kinase inhibitors that compete for binding to allosteric sites near ATP pockets; The last category is others. This paper reviews the structure, biological function, and recent research progress of receptor interaction protein-1 kinase inhibitors.
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Affiliation(s)
- Lu Chen
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoqin Zhang
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Affiliated Hospital of University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yaqing Ou
- Department of Pharmacy, The Affiliated Chengdu 363 Hospital of Southwest Medical University, Chengdu, Sichuan, China
| | - Maoyu Liu
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Dongke Yu
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhiheng Song
- Suzhou University of Science and Technology, Suzhou, Jiangsu, China
| | - Lihong Niu
- Institute of Laboratory Animal Sciences, Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, Sichuan, China,*Correspondence: Lihong Niu, ; Lijuan Zhang, ; Jianyou Shi,
| | - Lijuan Zhang
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,*Correspondence: Lihong Niu, ; Lijuan Zhang, ; Jianyou Shi,
| | - Jianyou Shi
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,*Correspondence: Lihong Niu, ; Lijuan Zhang, ; Jianyou Shi,
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Santos C, Pimentel L, Canzian H, Oliveira A, Junior F, Dantas R, Hoelz L, Marinho D, Cunha A, Bastos M, Boechat N. Hybrids of Imatinib with Quinoline: Synthesis, Antimyeloproliferative Activity Evaluation, and Molecular Docking. Pharmaceuticals (Basel) 2022; 15:ph15030309. [PMID: 35337107 PMCID: PMC8950477 DOI: 10.3390/ph15030309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 02/01/2023] Open
Abstract
Imatinib (IMT) is the first-in-class BCR-ABL commercial tyrosine kinase inhibitor (TKI). However, the resistance and toxicity associated with the use of IMT highlight the importance of the search for new TKIs. In this context, heterocyclic systems, such as quinoline, which is present as a pharmacophore in the structure of the TKI inhibitor bosutinib (BST), have been widely applied. Thus, this work aimed to obtain new hybrids of imatinib containing quinoline moieties and evaluate them against K562 cells. The compounds were synthesized with a high purity degree. Among the produced molecules, the inhibitor 4-methyl-N3-(4-(pyridin-3-yl)pyrimidin-2-yl)-N1-(quinolin-4-yl)benzene-1,3-diamine (2g) showed a suitable reduction in cell viability, with a CC50 value of 0.9 µM (IMT, CC50 = 0.08 µM). Molecular docking results suggest that the interaction between the most active inhibitor 2g and the BCR-ABL1 enzyme occurs at the bosutinib binding site through a competitive inhibition mechanism. Despite being less potent and selective than IMT, 2g is a suitable prototype for use in the search for new drugs against chronic myeloid leukemia (CML), especially in patients with acquired resistance to IMT.
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Affiliation(s)
- Carine Santos
- Laboratório de Sintese de Farmacos-LASFAR, Instituto de Tecnologia em Farmacos-Farmanguinhos, FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, Brazil; (C.S.); (L.P.); (H.C.); (A.O.); (L.H.); (D.M.); (M.B.)
- Programa de Pós-graduação em Farmacologia e Química Medicinal do Instituto de Ciências Biomédicas–ICB-UFRJ, Centro de Ciências da Saúde-CCS, Bloco J, Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Luiz Pimentel
- Laboratório de Sintese de Farmacos-LASFAR, Instituto de Tecnologia em Farmacos-Farmanguinhos, FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, Brazil; (C.S.); (L.P.); (H.C.); (A.O.); (L.H.); (D.M.); (M.B.)
| | - Henayle Canzian
- Laboratório de Sintese de Farmacos-LASFAR, Instituto de Tecnologia em Farmacos-Farmanguinhos, FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, Brazil; (C.S.); (L.P.); (H.C.); (A.O.); (L.H.); (D.M.); (M.B.)
| | - Andressa Oliveira
- Laboratório de Sintese de Farmacos-LASFAR, Instituto de Tecnologia em Farmacos-Farmanguinhos, FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, Brazil; (C.S.); (L.P.); (H.C.); (A.O.); (L.H.); (D.M.); (M.B.)
- Programa de Pós-graduação em Farmacologia e Química Medicinal do Instituto de Ciências Biomédicas–ICB-UFRJ, Centro de Ciências da Saúde-CCS, Bloco J, Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Floriano Junior
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz FIOCRUZ, Av. Brasil 4365, Manguinhos, Rio de Janeiro 21040-360, Brazil; (F.J.); (R.D.)
| | - Rafael Dantas
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz FIOCRUZ, Av. Brasil 4365, Manguinhos, Rio de Janeiro 21040-360, Brazil; (F.J.); (R.D.)
| | - Lucas Hoelz
- Laboratório de Sintese de Farmacos-LASFAR, Instituto de Tecnologia em Farmacos-Farmanguinhos, FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, Brazil; (C.S.); (L.P.); (H.C.); (A.O.); (L.H.); (D.M.); (M.B.)
| | - Debora Marinho
- Laboratório de Sintese de Farmacos-LASFAR, Instituto de Tecnologia em Farmacos-Farmanguinhos, FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, Brazil; (C.S.); (L.P.); (H.C.); (A.O.); (L.H.); (D.M.); (M.B.)
| | - Anna Cunha
- Departamento de Química Orgânica, Campus do Valonguinho, Universidade Federal Fluminense–UFF, Niterói 24020-150, Brazil;
| | - Monica Bastos
- Laboratório de Sintese de Farmacos-LASFAR, Instituto de Tecnologia em Farmacos-Farmanguinhos, FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, Brazil; (C.S.); (L.P.); (H.C.); (A.O.); (L.H.); (D.M.); (M.B.)
- Programa de Pós-graduação em Farmacologia e Química Medicinal do Instituto de Ciências Biomédicas–ICB-UFRJ, Centro de Ciências da Saúde-CCS, Bloco J, Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Nubia Boechat
- Laboratório de Sintese de Farmacos-LASFAR, Instituto de Tecnologia em Farmacos-Farmanguinhos, FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, Brazil; (C.S.); (L.P.); (H.C.); (A.O.); (L.H.); (D.M.); (M.B.)
- Programa de Pós-graduação em Farmacologia e Química Medicinal do Instituto de Ciências Biomédicas–ICB-UFRJ, Centro de Ciências da Saúde-CCS, Bloco J, Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
- Correspondence: ; Tel.: +55-(21)-3977-2465
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Pimentel LCF, Hoelz LVB, Canzian HF, Branco FSC, de Oliveira AP, Campos VR, Júnior FPS, Dantas RF, Resende JALC, Cunha AC, Boechat N, Bastos MM. (Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia. Beilstein J Org Chem 2021; 17:2260-2269. [PMID: 34621389 PMCID: PMC8450943 DOI: 10.3762/bjoc.17.144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/19/2021] [Indexed: 11/23/2022] Open
Abstract
The enzyme tyrosine kinase BCR-Abl-1 is the main molecular target in the treatment of chronic myeloid leukemia and can be competitively inhibited by tyrosine kinase inhibitors such as imatinib. New potential competitive inhibitors were synthesized using the (phenylamino)pyrimidine-pyridine (PAPP) group as a pharmacophoric fragment, and these compounds were biologically evaluated. The synthesis of twelve new compounds was performed in three steps and assisted by microwave irradiation in a 1,3-dipolar cycloaddition to obtain 1,2,3-triazole derivatives substituted on carbon C-4 of the triazole nucleus. All compounds were evaluated for their inhibitory activities against a chronic myeloid leukemia cell line (K562) that expresses the enzyme tyrosine kinase BCR-Abl-1 and against healthy cells (WSS-1) to observe their selectivity. Three compounds showed promising results, with IC50 values between 1.0 and 7.3 μM, and were subjected to molecular docking studies. The results suggest that such compounds can interact at the same binding site as imatinib, probably sharing a competitive inhibition mechanism. One compound showed the greatest interaction affinity for BCR-Abl-1 in the docking studies.
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Affiliation(s)
- Luiz Claudio Ferreira Pimentel
- Laboratorio de Sintese de Farmacos - LASFAR, Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos -Manguinhos, CEP 21041-250, Rio de Janeiro, Brazil
| | - Lucas Villas Boas Hoelz
- Laboratorio de Sintese de Farmacos - LASFAR, Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos -Manguinhos, CEP 21041-250, Rio de Janeiro, Brazil
| | - Henayle Fernandes Canzian
- Laboratorio de Sintese de Farmacos - LASFAR, Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos -Manguinhos, CEP 21041-250, Rio de Janeiro, Brazil
| | - Frederico Silva Castelo Branco
- Laboratorio de Sintese de Farmacos - LASFAR, Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos -Manguinhos, CEP 21041-250, Rio de Janeiro, Brazil
| | - Andressa Paula de Oliveira
- Laboratorio de Sintese de Farmacos - LASFAR, Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos -Manguinhos, CEP 21041-250, Rio de Janeiro, Brazil
| | - Vinicius Rangel Campos
- Departamento de Química Orgânica, Universidade Federal Fluminense, Campus do Valonguinho, CEP 24020-150,Niterói, Brazil
| | - Floriano Paes Silva Júnior
- Laboratório de Bioquímica Experimental e Computacional de Farmacos, Fundaçao Oswaldo Cruz, Instituto Oswaldo Cruz, CEP 21040-900, Rio de Janeiro, Brazil
| | - Rafael Ferreira Dantas
- Laboratório de Bioquímica Experimental e Computacional de Farmacos, Fundaçao Oswaldo Cruz, Instituto Oswaldo Cruz, CEP 21040-900, Rio de Janeiro, Brazil
| | | | - Anna Claudia Cunha
- Departamento de Química Orgânica, Universidade Federal Fluminense, Campus do Valonguinho, CEP 24020-150,Niterói, Brazil
| | - Nubia Boechat
- Laboratorio de Sintese de Farmacos - LASFAR, Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos -Manguinhos, CEP 21041-250, Rio de Janeiro, Brazil
| | - Mônica Macedo Bastos
- Laboratorio de Sintese de Farmacos - LASFAR, Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos -Manguinhos, CEP 21041-250, Rio de Janeiro, Brazil
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Vásquez AF, Reyes Muñoz A, Duitama J, González Barrios A. Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products. J Biomol Struct Dyn 2020; 39:3285-3299. [DOI: 10.1080/07391102.2020.1763839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrés Felipe Vásquez
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Reyes Muñoz
- Grupo de Biología Computacional Ecología Microbiana (BCEM), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
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Foreword: Pacific Fragments. Molecules 2016; 21:molecules21070926. [PMID: 27438812 PMCID: PMC6273443 DOI: 10.3390/molecules21070926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 11/24/2022] Open
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