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Steinebach C, Bricelj A, Murgai A, Sosič I, Bischof L, Ng YLD, Heim C, Maiwald S, Proj M, Voget R, Feller F, Košmrlj J, Sapozhnikova V, Schmidt A, Zuleeg MR, Lemnitzer P, Mertins P, Hansen FK, Gütschow M, Krönke J, Hartmann MD. Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs. J Med Chem 2023; 66:14513-14543. [PMID: 37902300 PMCID: PMC10641816 DOI: 10.1021/acs.jmedchem.3c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/11/2023] [Accepted: 10/05/2023] [Indexed: 10/31/2023]
Abstract
Immunomodulatory imide drugs (IMiDs) such as thalidomide, pomalidomide, and lenalidomide are the most common cereblon (CRBN) recruiters in proteolysis-targeting chimera (PROTAC) design. However, these CRBN ligands induce the degradation of IMiD neosubstrates and are inherently unstable, degrading hydrolytically under moderate conditions. In this work, we simultaneously optimized physiochemical properties, stability, on-target affinity, and off-target neosubstrate modulation features to develop novel nonphthalimide CRBN binders. These efforts led to the discovery of conformationally locked benzamide-type derivatives that replicate the interactions of the natural CRBN degron, exhibit enhanced chemical stability, and display a favorable selectivity profile in terms of neosubstrate recruitment. The utility of the most potent ligands was demonstrated by their transformation into potent degraders of BRD4 and HDAC6 that outperform previously described reference PROTACs. Together with their significantly decreased neomorphic ligase activity on IKZF1/3 and SALL4, these ligands provide opportunities for the design of highly selective and potent chemically inert proximity-inducing compounds.
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Affiliation(s)
| | - Aleša Bricelj
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Arunima Murgai
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Izidor Sosič
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Luca Bischof
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Yuen Lam Dora Ng
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Christopher Heim
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Samuel Maiwald
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Matic Proj
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Rabea Voget
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Felix Feller
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Janez Košmrlj
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, SI 1000 Ljubljana, Slovenia
| | - Valeriia Sapozhnikova
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
- Max
Delbrück
Center for Molecular Medicine, D-13125 Berlin, Germany
- German
Cancer Consortium (DKTK), Partner Site Berlin, DKFZ, D-69120 Heidelberg, Germany
| | - Annika Schmidt
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Maximilian Rudolf Zuleeg
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Patricia Lemnitzer
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Philipp Mertins
- Max
Delbrück
Center for Molecular Medicine, D-13125 Berlin, Germany
- Berlin
Institute of Health, D-10178 Berlin, Germany
| | - Finn K. Hansen
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Jan Krönke
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
- German
Cancer Consortium (DKTK), Partner Site Berlin, DKFZ, D-69120 Heidelberg, Germany
| | - Marcus D. Hartmann
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
- Interfaculty
Institute of Biochemistry, University of
Tübingen, D-72076 Tübingen, Germany
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Hybrid Molecules as Potential Drugs for the Treatment of HIV: Design and Applications. Pharmaceuticals (Basel) 2022; 15:ph15091092. [PMID: 36145313 PMCID: PMC9502546 DOI: 10.3390/ph15091092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection is a major problem for humanity because HIV is constantly changing and developing resistance to current drugs. This necessitates the development of new anti-HIV drugs that take new approaches to combat an ever-evolving virus. One of the promising alternatives to combination antiretroviral therapy (cART) is the molecular hybrid strategy, in which two or more pharmacophore units of bioactive scaffolds are combined into a single molecular structure. These hybrid structures have the potential to have higher efficacy and lower toxicity than their parent molecules. Given the potential advantages of the hybrid molecular approach, the development and synthesis of these compounds are of great importance in anti-HIV drug discovery. This review focuses on the recent development of hybrid compounds targeting integrase (IN), reverse transcriptase (RT), and protease (PR) proteins and provides a brief description of their chemical structures, structure–activity relationship, and binding mode.
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Díaz I, Salido S, Nogueras M, Cobo J. Design and Synthesis of New Pyrimidine-Quinolone Hybrids as Novel hLDHA Inhibitors. Pharmaceuticals (Basel) 2022; 15:ph15070792. [PMID: 35890090 PMCID: PMC9322123 DOI: 10.3390/ph15070792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 02/05/2023] Open
Abstract
A battery of novel pyrimidine-quinolone hybrids was designed by docking scaffold replacement as lactate dehydrogenase A (hLDHA) inhibitors. Structures with different linkers between the pyrimidine and quinolone scaffolds (10-21 and 24−31) were studied in silico, and those with the 2-aminophenylsulfide (U-shaped) and 4-aminophenylsulfide linkers (24−31) were finally selected. These new pyrimidine-quinolone hybrids (24−31)(a−c) were easily synthesized in good to excellent yields by a green catalyst-free microwave-assisted aromatic nucleophilic substitution reaction between 3-(((2/4-aminophenyl)thio)methyl)quinolin-2(1H)-ones 22/23(a−c) and 4-aryl-2-chloropyrimidines (1−4). The inhibitory activity against hLDHA of the synthesized hybrids was evaluated, resulting IC50 values of the U-shaped hybrids 24−27(a−c) much better than the ones of the 1,4-linked hybrids 28−31(a−c). From these results, a preliminary structure−activity relationship (SAR) was established, which enabled the design of novel 1,3-linked pyrimidine-quinolone hybrids (33−36)(a−c). Compounds 35(a−c), the most promising ones, were synthesized and evaluated, fitting the experimental results with the predictions from docking analysis. In this way, we obtained novel pyrimidine-quinolone hybrids (25a, 25b, and 35a) with good IC50 values (<20 μM) and developed a preliminary SAR.
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Sharma V, Das R, Kumar Mehta D, Gupta S, Venugopala KN, Mailavaram R, Nair AB, Shakya AK, Kishore Deb P. Recent insight into the biological activities and SAR of quinolone derivatives as multifunctional scaffold. Bioorg Med Chem 2022; 59:116674. [DOI: 10.1016/j.bmc.2022.116674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/07/2022] [Accepted: 02/13/2022] [Indexed: 01/09/2023]
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Mahboubi-Rabbani M, Abbasi M, Hajimahdi Z, Zarghi A. HIV-1 Reverse Transcriptase/Integrase Dual Inhibitors: A Review of Recent Advances and Structure-activity Relationship Studies. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:333-369. [PMID: 34567166 PMCID: PMC8457747 DOI: 10.22037/ijpr.2021.115446.15370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The significant threat to humanity is HIV infection, and it is uncertain whether a definitive treatment or a safe HIV vaccine is. HIV-1 is continually evolving and resistant to commonly used HIV-resistant medications, presenting significant obstacles to HIV infection management. The drug resistance adds to the need for new anti-HIV drugs; it chooses ingenious approaches to fight the emerging virus. Highly Active Antiretroviral Therapy (HAART), a multi-target approach for specific therapies, has proved effective in AIDS treatment. Therefore, it is a dynamic system with high prescription tension, increased risk of medication reactions, and adverse effects, leading to poor compliance with patients. In the HIV-1 lifecycle, two critical enzymes with high structural and functional analogies are reverse transcriptase (RT) and integrase (IN), which can be interpreted as druggable targets for modern dual-purpose inhibitors. Designed multifunctional ligand (DML) is a new technique that recruited many targets to be achieved by one chemical individual. A single chemical entity that acts for multiple purposes can be much more successful than a complex multidrug program. The production of these multifunctional ligands as antiretroviral drugs is valued with the advantage that the viral-replication process may end in two or more phases. This analysis will discuss the RT-IN dual-inhibitory scaffolds' developments documented so far.
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Affiliation(s)
- Mohammad Mahboubi-Rabbani
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abbasi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zahra Hajimahdi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Zarghi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Ding L, Zhuang C, Chen F. Druggability modification strategies of the diarylpyrimidine-type non-nucleoside reverse transcriptase inhibitors. Med Res Rev 2021; 41:1255-1290. [PMID: 33497504 DOI: 10.1002/med.21760] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022]
Abstract
Drug discovery of human immunodeficiency virus (HIV) is a hot field in medicinal chemistry community for many years. The diarylpyrimidines (DAPYs) are the second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting reverse transcriptase, playing a great irreplaceable role in HIV transcriptional therapy. However, fast-growing drug-resistant mutations as nonnegligible challenge are still unpredictably appeared in the clinical practice, leading to deactivate or reduce the existing drugs. In the last 20 years, more and more novel DAPY derivatives have developed with the purpose to counter the mutants. Nevertheless, most of them have dissatisfactory pharmacokinetics (PK) or poor antiviral activity toward resistant mutant strains. In this article, we will analyze the NNRTI derivatives with promising druggability, and summarize a series of druggability modification strategies to improve the antiviral activity, reduce toxicity and improve the PK properties in recent years. The prospects of DAPYs and the directions for future efforts will be discussed.
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Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Fener Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China.,Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou, China
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7
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Toan DN, Thanh ND, Truong MX, Van DT. Synthesis, Cytotoxicity, ADMET and Molecular Docking Studies of Some Quinoline-Pyrimidine Hybrid Compounds: 3-(2-Amino-6-arylpyrimidin-4- yl)-4-hydroxy-1-methylquinolin-2(1H)-ones. Med Chem 2020; 18:36-50. [PMID: 33380305 DOI: 10.2174/1573406417666201230092615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/01/2020] [Accepted: 10/12/2020] [Indexed: 11/22/2022]
Abstract
AIMS Synthesis of 3-(2-amino-6-arylpyrimidin-4-yl)-4-hydroxy-1-methylquinolin-2(1H)-ones and estimation their anticancer activities on HepG2 and KB cancer lines. BACKGROUND Many derivatives of quinoline-2-on have been consider to synthesize and evaluate their biological properties by organic chemists due to their various biological effects, including antibacterial, antioxidant, anti-inflammatory, anticancer activities. Quinolinepyrimidine hybrid compounds exhibited various biological activities, such as antituberculosis, antibacterial, anticancer, antifungal, etc. The connection of 4-hydroxyquinoline-2-one with 2-amino-pyrimidine could initiate the new activities. OBJECTIVE α,β-Unsaturated ketones of 3-acetyl-4-hydroxy-N-methylquinolin-2-one were prepared. Novel 2-amino-6-aryl-4-(4'-hydroxy-Nmethylquinolin- 2'-on-3'-yl)pyrimidines have been synthesized by reaction of these corresponding α,β-unsaturated ketones with guanidine hydrochloride. Human hepatocellular carcinoma HepG2 and squamous cell carcinoma KB cancer lines were used for screening their cytotoxicity. METHOD 3-Acetyl-4-hydroxy-N-methylquinolin-2-one was prepared from N-methylaniline and diethyl malonate. Reaction of (un)substituted benzaldehydes with this 4-hydroxyquinoline-2-one produced corresponding substituted α ,β-unsaturated ketones in the presence of piperidine as catalyst. 2-Amino-6-aryl-4-(4'-hydroxy-N-methylquinolin-2'-on-3'-yl)pyrimidines have been synthesized from these α,β-unsaturated ketones of 3-acetyl-4-hydroxy-N-methylquinolin-2-one by reaction of corresponding α ,β-unsaturated ketones with guanidine hydrochloride. All obtained pyrimidines were screened for anticancer activity using MTT bio-assay method. RESULT Seven substituted (E)-4-hydroxy-3-(3-(aryl)acryloyl)-1-methylquinolin-2(1H)-ones were prepared and converted to corresponding substituted 2-amino-6-aryl-4-(4'-hydroxy-N-methylquinolin-2'-on-3'-yl)pyrimidines with yields of 58-74%. All the synthesized pyrimidines were screened for their in vitro anticancer activity against human hepatocellular carcinoma HepG2 and squamous cell carcinoma KB cancer lines. Compounds 6b and 6e had the best activity in the series, with IC50 values equal to 1.32 and 1.33 μM, respectively. ADMET properties showed that compounds 6b, 6e, and 6f possessed the drug-likeness behavior. Cross-docking results indicated that residues GLN778(A), DT8(C), DT9(D), DA12(F), and DG13(F) in the binding pocket as potential ligand binding hot-spot residues for compounds 6b, 6e, and 6f. CONCLUSION New substituted 2-amino-6-aryl-4-(4'-hydroxy-N-methylquinolin-2'-on-3'-yl)pyrimidines were obtained and displayed significant inhibition against human hepatocellular carcinoma HepG2 and squamous cell carcinoma KB cancer lines.
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Affiliation(s)
- Duong Ngoc Toan
- Faculty of Chemistry, Thai Nguyen University of Education, 20 Luong Ngoc Quyen, Thai Nguyen. Vietnam
| | - Nguyen Dinh Thanh
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi. Vietnam
| | - Mai Xuan Truong
- Faculty of Chemistry, Thai Nguyen University of Education, 20 Luong Ngoc Quyen, Thai Nguyen. Vietnam
| | - Dinh Thuy Van
- Faculty of Chemistry, Thai Nguyen University of Education, 20 Luong Ngoc Quyen, Thai Nguyen. Vietnam
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Song R, Wang Y, Wang M, Gao R, Yang T, Yang S, Yang CG, Jin Y, Zou S, Cai J, Fan R, He Q. Design and synthesis of novel desfluoroquinolone-aminopyrimidine hybrids as potent anti-MRSA agents with low hERG activity. Bioorg Chem 2020; 103:104176. [PMID: 32891858 DOI: 10.1016/j.bioorg.2020.104176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 01/05/2023]
Abstract
Despite the fact that the introduction of a fluorine atom at the C-6 position has resulted in the evolution of fluoroquinolones, fluoroquinolone-induced cardiac toxicity has drawn considerable attention. In this context, desfluoroquinolone-based hybrids with involvement of C-7 aminopyrimidine functional group were designed and synthesized. The biological results showed majority of these hybrids still demonstrated potent anti-MRSA activity with MIC values between 0.38 and 1.5 μg/mL, despite the lack of the typical C-6 fluorine atom. Particularly, the most active B14 exhibited activities at submicromolar concentrations against a panel of MRSA strains including vancomycin-intermediate strains, levofloxacin-resistant isolates, and linezolid-resistant isolates, etc. As expected, it also displayed highly selective toxicity toward bacterial cells and low hERG inhibition. Further resistance development study indicated MRSA is unlikely to acquire resistance against B14. The docking study revealed that two hydrogen bonds were formed between the C-7 substituent and the surrounding DNA bases, which might contribute to overcome resistance by reducing the dependence on the magnesium-water bridge interactions with topoisomerase IV. These results indicate a promising strategy for developing new antibiotic quinolones to combat multidrug resistance and cardiotoxicity.
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Affiliation(s)
- Runzhe Song
- Department of Chemistry, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yue Wang
- Department of Chemistry, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Minghui Wang
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Ruixuan Gao
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Teng Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yongsheng Jin
- School of Pharmacy, The Second Military Medical University, Shanghai 200433, China
| | - Siyuan Zou
- Department of Chemistry, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States.
| | - Renhua Fan
- Department of Chemistry, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China.
| | - Qiuqin He
- Department of Chemistry, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China.
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Zhuang C, Pannecouque C, De Clercq E, Chen F. Development of non-nucleoside reverse transcriptase inhibitors (NNRTIs): our past twenty years. Acta Pharm Sin B 2020; 10:961-978. [PMID: 32642405 PMCID: PMC7332669 DOI: 10.1016/j.apsb.2019.11.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/08/2019] [Accepted: 11/08/2019] [Indexed: 11/30/2022] Open
Abstract
Human immunodeficiency virus (HIV) is the primary infectious agent of acquired immunodeficiency syndrome (AIDS), and non-nucleoside reverse transcriptase inhibitors (NNRTIs) are the cornerstone of HIV treatment. In the last 20 years, our medicinal chemistry group has made great strides in developing several distinct novel NNRTIs, including 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT), thio-dihydro-alkoxy-benzyl-oxopyrimidine (S-DABO), diaryltriazine (DATA), diarylpyrimidine (DAPY) analogues, and their hybrid derivatives. Application of integrated modern medicinal strategies, including structure-based drug design, fragment-based optimization, scaffold/fragment hopping, molecular/fragment hybridization, and bioisosterism, led to the development of several highly potent analogues for further evaluations. In this paper, we review the development of NNRTIs in the last two decades using the above optimization strategies, including their structure–activity relationships, molecular modeling, and their binding modes with HIV-1 reverse transcriptase (RT). Future directions and perspectives on the design and associated challenges are also discussed.
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Key Words
- AIDS, acquired immunodeficiency syndrome
- Bioisosterism
- DAPY, diarylpyrimidine
- DAPYs
- DATA, diaryltriazine
- DATAs
- DLV, delavirdine
- DOR, doravirine
- ECD, electronic circular dichroism
- EFV, efavirenz
- ETR, etravirine
- FDA, U.S. Food and Drug Administration
- Fragment-based drug design
- HAART, highly active antiretroviral therapy
- HENT, napthyl-HEPT
- HENTs
- HEPT, 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine
- HIV, human immunodeficiency virus
- HIV-1
- INSTI, integrase inhibitor
- Molecular hybridization
- NNIBP, NNRTI binding pocket
- NNRTI, non-nucleoside reverse transcriptase inhibitor
- NNRTIs
- NRTI, nucleoside reverse transcriptase inhibitor
- NVP, nevirapine
- PI, protease inhibitor
- PK, pharmacokinetic
- PROTAC, proteolysis targeting chimera
- RPV, rilpivirine
- RT, reverse transcriptase
- S-DABO, thio-dihydro-alkoxy-benzyl-oxopyrimidine
- S-DABOs
- SAR, structure–activity relationship
- SBDD, structure-based drug design
- SFC, supercritical fluid chromatography
- SI, selectivity index
- Structure-based optimization
- UNAIDS, the Joint United Nations Programme on HIV/AIDS
- ee, enantiomeric excess
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Affiliation(s)
- Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Leuven B-3000, Belgium
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
- Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
- Corresponding author.
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10
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Batalha PN, da S M Forezi L, Tolentino NMDC, Sagrillo FS, de Oliveira VG, de Souza MCBV, da C S Boechat F. 4-Oxoquinoline Derivatives as Antivirals: A Ten Years Overview. Curr Top Med Chem 2020; 20:244-255. [PMID: 31995008 DOI: 10.2174/1568026620666200129100219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/30/2019] [Accepted: 01/06/2020] [Indexed: 11/22/2022]
Abstract
4-Oxoquinoline derivatives constitute an important family of biologically important substances, associated with different bioactivities, which can be synthesized by different synthetic methods, allowing the design and preparation of libraries of substances with specific structural variations capable of modulating their pharmacological action. Over the last years, these substances have been extensively explored by the scientific community in efforts to develop new biologically active agents, with greater efficiency for the treatment of a variety of diseases. Viral infections have been one of the targets of these studies, although to a lesser extent than other diseases such as cancer and bacterial infections. Nevertheless, the literature provides examples that corroborate with the fact that these substances may act on different pharmacological targets in different viral pathogens. This review provides a compilation of some of the major studies published in recent years showing the discovery and/or development of new antiviral oxoquinoline agents, highlighting, whenever possible, their mechanisms of action.
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Affiliation(s)
- Pedro N Batalha
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Baptista, 24020-141 Niteroi, RJ, Brazil
| | - Luana da S M Forezi
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Baptista, 24020-141 Niteroi, RJ, Brazil
| | - Nathalia M de C Tolentino
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Baptista, 24020-141 Niteroi, RJ, Brazil
| | - Fernanda S Sagrillo
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Baptista, 24020-141 Niteroi, RJ, Brazil
| | - Vanessa G de Oliveira
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Baptista, 24020-141 Niteroi, RJ, Brazil
| | - Maria Cecília B V de Souza
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Baptista, 24020-141 Niteroi, RJ, Brazil
| | - Fernanda da C S Boechat
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Baptista, 24020-141 Niteroi, RJ, Brazil
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Wang R, Xu K, Shi W. Quinolone derivatives: Potential anti‐HIV agent—development and application. Arch Pharm (Weinheim) 2019; 352:e1900045. [DOI: 10.1002/ardp.201900045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Ruo Wang
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
| | - Kai Xu
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
| | - Weixiong Shi
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
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12
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Gill MSA, Hassan SS, Ahemad N. Evolution of HIV-1 reverse transcriptase and integrase dual inhibitors: Recent advances and developments. Eur J Med Chem 2019; 179:423-448. [PMID: 31265935 DOI: 10.1016/j.ejmech.2019.06.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 01/10/2023]
Abstract
HIV infection is a major challenge to mankind and a definitive cure or a viable vaccine for HIV is still elusive. HIV-1 is constantly evolving and developing resistant against clinically used anti-HIV drugs thus posing serious hurdles in the treatment of HIV infection. This prompts the need to developed new anti-HIV drugs; preferentially adopting intelligent ways to counteract an evolving virus. Highly Active Anti-Retroviral Therapy (HAART): a strategy involving multiple targeting through various drugs has proven beneficial in the management of AIDS. However, it is a complex regimen with high drug load, increased risk of drug interactions and adverse effects, which lead to poor patient compliance. Reverse transcriptase (RT) and Integrase (IN) are two pivotal enzymes in HIV-1 lifecycle with high structural and functional analogy to be perceived as drug-able targets for novel dual-purpose inhibitors. Designed multi-functional ligand (DML) is a modern strategy by which multiple targets can be exploited using a single chemical entity. A single chemical entity acting on multiple targets can be much more effective than a complex multi-drug regimen. The development of such multifunctional ligands is highly valued in anti-HIV drug discovery with the proposed advantage of being able to stop two or more stages of viral replication cycle. This review will encompass the evolution of the RT-IN dual inhibitory scaffolds reported so far and the contribution made by the leading research groups over the years in this field.
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Affiliation(s)
- Muhammad Shoaib Ali Gill
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia; Institute of Pharmaceutical Sciences (IPS), University of Veterinary & Animal Sciences (UVAS), Lahore, 54000, Pakistan
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia; Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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13
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Senerovic L, Opsenica D, Moric I, Aleksic I, Spasić M, Vasiljevic B. Quinolines and Quinolones as Antibacterial, Antifungal, Anti-virulence, Antiviral and Anti-parasitic Agents. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1282:37-69. [PMID: 31515709 DOI: 10.1007/5584_2019_428] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Infective diseases have become health threat of a global proportion due to appearance and spread of microorganisms resistant to majority of therapeutics currently used for their treatment. Therefore, there is a constant need for development of new antimicrobial agents, as well as novel therapeutic strategies. Quinolines and quinolones, isolated from plants, animals, and microorganisms, have demonstrated numerous biological activities such as antimicrobial, insecticidal, anti-inflammatory, antiplatelet, and antitumor. For more than two centuries quinoline/quinolone moiety has been used as a scaffold for drug development and even today it represents an inexhaustible inspiration for design and development of novel semi-synthetic or synthetic agents exhibiting broad spectrum of bioactivities. The structural diversity of synthetized compounds provides high and selective activity attained through different mechanisms of action, as well as low toxicity on human cells. This review describes quinoline and quinolone derivatives with antibacterial, antifungal, anti-virulent, antiviral, and anti-parasitic activities with the focus on the last 10 years literature.
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Affiliation(s)
- Lidija Senerovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
| | - Dejan Opsenica
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
- Center of excellence in Environmental Chemistry and Engineering, ICTM - University of Belgrade, Belgrade, Serbia
| | - Ivana Moric
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Ivana Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marta Spasić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Branka Vasiljevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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14
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Xu Z, Zhao SJ, Lv ZS, Gao F, Wang Y, Zhang F, Bai L, Deng JL. Fluoroquinolone-isatin hybrids and their biological activities. Eur J Med Chem 2018; 162:396-406. [PMID: 30453247 DOI: 10.1016/j.ejmech.2018.11.032] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/04/2018] [Accepted: 11/10/2018] [Indexed: 12/20/2022]
Abstract
Hybridization of different pharmacophores from various bioactive substances into a single molecule is the potential weapon to prevent the drug resistance since this strategy can provide new leads with complimentary activities and/or multiple pharmacological targets. Fluoroquinolone and isatin are common pharmacophores, and their derivatives possess various biological activities. Obviously, hybridization of these two pharmacophores into one molecule may result in novel candidates with broader spectrum, higher efficiency, lower toxicity as well as multiple mechanisms of action. Therefore, fluoroquinolone-isatin hybrids have the potential for clinical deployment in the control and eradication of various diseases. This review covers the recent advances of fluoroquinolone-isatin hybrids as potential anti-bacterial, anti-tubercular, anti-viral and anti-cancer agents. The structure-activity relationship is also discussed to pave the way for the further rational development of this kind of hybrids.
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Affiliation(s)
- Zhi Xu
- Huanghuai University, College of Chemistry and Pharmaceutical Engineering, Zhumadian, PR China.
| | - Shi-Jia Zhao
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, Wuhan University of Science and Technology, Wuhan, PR China
| | - Zao-Sheng Lv
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, Wuhan University of Science and Technology, Wuhan, PR China
| | - Feng Gao
- Academy of Advanced Interdisciplinary Studies, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Yinling Wang
- Huanghuai University, College of Chemistry and Pharmaceutical Engineering, Zhumadian, PR China
| | - Feng Zhang
- Huanghuai University, College of Chemistry and Pharmaceutical Engineering, Zhumadian, PR China
| | - Liuyang Bai
- Huanghuai University, College of Chemistry and Pharmaceutical Engineering, Zhumadian, PR China
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15
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Gu SX, Lu HH, Liu GY, Ju XL, Zhu YY. Advances in diarylpyrimidines and related analogues as HIV-1 nonnucleoside reverse transcriptase inhibitors. Eur J Med Chem 2018; 158:371-392. [PMID: 30223123 DOI: 10.1016/j.ejmech.2018.09.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/01/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022]
Abstract
HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs) have been playing an important role in the fight against acquired immunodeficiency syndrome (AIDS). Diarylpyrimidines (DAPYs) as the second generation NNRTIs, represented by etravirine (TMC125) and rilpivirine (TMC278), have attracted extensive attention due to their extraordinary potency, high specificity and low toxicity. However, the rapid emergence of drug-resistant virus strains and dissatisfactory pharmacokinetics of DAPYs present new challenges. In the past two decades, an increasing number of novel DAPY derivatives have emerged, which significantly enriched the structure-activity relationship of DAPYs. Studies of crystallography and molecular modeling have afforded a lot of useful information on structural requirements of NNRTIs, which contributes greatly to the improvement of their resistance profiles. In this review, we reviewed the discovery history and their evolution of DAPYs including their structural modification, derivatization and scaffold hopping in continuous pursuit of excellent anti-HIV drugs. And also, we discussed the prospect of DAPYs and the directions of future efforts.
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Affiliation(s)
- Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China.
| | - Huan-Huan Lu
- Yichang Humanwell Pharmaceutical Co., Ltd, Yichang, 443005, PR China
| | - Gen-Yan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China
| | - Xiu-Lian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430205, PR China.
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16
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Umamatheswari S, Sankar C. Synthesis, identification and in vitro biological evaluation of some novel quinoline incorporated 1,3-thiazinan-4-one derivatives. Bioorg Med Chem Lett 2017; 27:695-699. [PMID: 28065567 DOI: 10.1016/j.bmcl.2016.06.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 05/31/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
The present study describes the synthesis of two new series of 3-hydroxy-N-(4-oxo-2-phenyl-1,3-thiazinan-3-yl)-8-(trifluoromethyl)quinoline-2-carboxamide derivatives (4a-j) and 3-((7-chloroquinolin-4-ylamino)methyl)-2-phenyl-1,3-thiazinan-4-one derivatives (5a-7j). All the compounds were synthesized in moderate to good yield by one-pot three component cyclo-condensation reaction. The newly synthesized compounds were characterized by FT-IR, 1H, 13C NMR and elemental analysis. The compounds were screened for their in vitro antibacterial activity against a panel of pathogenic bacterial strains, antitubercular activity against Mycobacterium tuberculosis H37Rv and also for their in vitro antimalarial activity against Plasmodium falciparum. Among the synthesized compounds two of them (4f and 5f) showed excellent antibacterial activity against C. tetani at 15.6μg/mL. Some of them exhibited excellent antitubercular (4f &5f) and good antimalarial (4f, 5f &6f) activity compared with the first line drugs.
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Affiliation(s)
- S Umamatheswari
- Department of Chemistry, Govt. Arts College, Tiruchirappalli, Tamil Nadu 620022, India
| | - C Sankar
- Department of Chemistry, TRP Engineering College, Irungalur, Tiruchirappalli, Tamil Nadu 621 105, India.
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Gu SX, Xue P, Ju XL, Zhu YY. Advances in rationally designed dual inhibitors of HIV-1 reverse transcriptase and integrase. Bioorg Med Chem 2016; 24:5007-5016. [PMID: 27658796 DOI: 10.1016/j.bmc.2016.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/09/2016] [Accepted: 09/10/2016] [Indexed: 01/07/2023]
Abstract
Reverse transcriptase (RT) and integrase (IN) are two indispensable enzymes in human immunodeficiency virus type 1 (HIV-1) replication. RT is responsible for the transformation of the single-stranded RNA viral genome into double-stranded DNA, and IN catalyzes the integration of viral DNA into the host DNA. Although highly active antiretroviral therapy (HAART) combining nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs) with nonnucleoside reverse transcriptase inhibitors (NNRTIs) or protease inhibitors (PIs) could suppress successfully HIV viral load and reduce evidently the mortality of HIV infected people, it involves the difficulty of perfect adherence, and other drawbacks such as viral rebound, toxicities and multi-drug resistances. Recently, rational drug design has become a dominant technique for the development of multi-target drugs. And the rationally designed dual inhibitors of HIV-1 RT and IN have become a hot topic of anti-HIV research. In this review, the advances in rationally designed dual inhibitors of HIV-1 RT and IN were summarized, including structurally diverse inhibitors, their structure-activity relationship (SAR) studies as well as binding mode analysis.
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Affiliation(s)
- Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China.
| | - Ping Xue
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China
| | - Xiu-Lian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430073, China.
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18
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Khan SA, Asiri AM. Fluorescence quenching of environmentally benign highly fluorescence donor (D)-π-acceptor (A)-π-donor (D) quinoline dye by silver nanoparticles and anionic surfactant in liquid stage. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.05.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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