1
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Nie MZ, Zhang SS, Gu SX, Long J, Zhu YY. Advances in diarylpyrimidines and related analogues as HIV-1 nonnucleoside reverse transcriptase inhibitors (2019-2023). Eur J Med Chem 2024; 280:116973. [PMID: 39432934 DOI: 10.1016/j.ejmech.2024.116973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 09/21/2024] [Accepted: 10/14/2024] [Indexed: 10/23/2024]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) have emerged as a vital cornerstone of highly active antiretroviral therapy (HAART) regimens, owing to their unique antiviral activity, low toxicity and high specificity. Diarylpyrimidines (DAPYs) as the second generation NNRTIs, represented by etravirine and rilpivirine, have attracted extensive attention due to their high anti-HIV potency. However, rapid emergence of resistant mutations, suboptimal pharmacokinetics (PK), and toxicity remain significant challenges. Recent structural modifications of DAPY analogues have focused on improving resistance profiles, optimizing PK properties (such as half-life and bioavailability), diversifying core structures through scaffold hopping, refining side-chain structures to enhance activity and selectivity, and reducing toxicity and side effects. Moreover, developing new DAPY analogues with broad-spectrum antiviral activity has become a key research priority. This review provides a comprehensive overview of the evolution of DAPYs from 2019 to 2023, including scaffold hopping and structural modifications of the right wing, left wing, central pyrimidine core, and linker, affording valuable insights for the future development of effective HIV-1 inhibitors.
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Affiliation(s)
- Mu-Zi Nie
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Shuang-Shuang Zhang
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Shuang-Xi Gu
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, 430205, China.
| | - Jiao Long
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, 430205, China.
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
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2
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Zhang K, Zhang YJ, Li M, Pannecouque C, De Clercq E, Wang S, Chen FE. Deciphering the enigmas of non-nucleoside reverse transcriptase inhibitors (NNRTIs): A medicinal chemistry expedition towards combating HIV drug resistance. Med Res Rev 2024. [PMID: 39188075 DOI: 10.1002/med.22080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/11/2024] [Accepted: 08/13/2024] [Indexed: 08/28/2024]
Abstract
The pivotal involvement of reverse transcriptase activity in the pathogenesis of the progressive HIV virus has stimulated gradual advancements in drug discovery initiatives spanning three decades. Consequently, nonnucleoside reverse transcriptase inhibitors (NNRTIs) have emerged as a preeminent category of therapeutic agents for HIV management. Academic institutions and pharmaceutical companies have developed numerous NNRTIs, an essential component of antiretroviral therapy. Six NNRTIs have received Food and Drug Administration approval and are widely used in clinical practice, significantly improving the quality of HIV patients. However, the rapid emergence of drug resistance has limited the effectiveness of these medications, underscoring the necessity for perpetual research and development of novel therapeutic alternatives. To supplement the existing literatures on NNRTIs, a comprehensive review has been compiled to synthesize this extensive dataset into a comprehensible format for the medicinal chemistry community. In this review, a thorough investigation and meticulous analysis were conducted on the progressions achieved in NNRTIs within the past 8 years (2016-2023), and the experiences and insights gained in the development of inhibitors with varying chemical structures were also summarized. The provision of a crucial point of reference for the development of wide-ranging anti-HIV medications is anticipated.
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Affiliation(s)
- Kun Zhang
- Department of Chemistry, 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 Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yu-Jie Zhang
- Department of Chemistry, 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 Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Min Li
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Shuai Wang
- Department of Chemistry, 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
| | - Fen-Er Chen
- Department of Chemistry, 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 Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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Wang Z, Wang W, Gao Z, Gao H, Clercq ED, Pannecouque C, Chen CH, Kang D, Zhan P, Liu X. Structure-based design, synthesis, and biological characterization of indolylarylsulfone derivatives as novel human immunodeficiency virus type 1 inhibitors with potent antiviral activities and favorable drug-like profiles. J Med Virol 2024; 96:e29830. [PMID: 39072764 DOI: 10.1002/jmv.29830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/08/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
In the current antiretroviral landscape, continuous efforts are still needed to search for novel chemotypes of human immunodeficiency virus type 1 (HIV-1) inhibitors with improved drug resistance profiles and favorable drug-like properties. Herein, we report the design, synthesis, biological characterization, and druggability evaluation of a class of non-nucleoside reverse transcriptase inhibitors. Guided by the available crystallographic information, a series of novel indolylarylsulfone derivatives were rationally discovered via the substituent decorating strategy to fully explore the chemical space of the entrance channel. Among them, compound 11h bearing the cyano-substituted benzyl moiety proved to be the most effective inhibitor against HIV-1 wild-type and mutant strains (EC50 = 0.0039-0.338 μM), being far more potent than or comparable to etravirine and doravirine. Besides, 11h did not exhibit cytotoxicity at the maximum test concentration. Meanwhile, the binding target of 11h was further confirmed to be reverse transcriptase (IC50 = 0.055 μM). Preliminary structure-activity relationship were discussed to guide further optimization work. Molecular docking and dynamics simulation studies were investigated in detail to rationalize the biological evaluation results. Further drug-likeness assessment indicated that 11h possessed excellent physicochemical properties. Moreover, no apparent hERG blockade liability and cytochrome P450 inhibition were observed for 11h. Notably, 11h was characterized by favorable in vitro metabolic stability with moderate clearance rates and long half-lives in human plasma and liver microsomes. Overall, 11h holds great promise as an ideal Anti-HIV-1 lead compound due to its potent antiviral efficacy, low toxicity, and favorable drug-like profiles.
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Affiliation(s)
- Zhao Wang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, China
- Suzhou Research Institute of Shandong University, Suzhou, Jiangsu, China
| | - Wenbo Wang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhen Gao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Huizhan Gao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Leuven, Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Leuven, Belgium
| | - Chin-Ho Chen
- Surgical Oncology Research Facility, Duke University Medical Center, Durham, North Carolina, USA
| | - Dongwei Kang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, China
| | - Peng Zhan
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, China
| | - Xinyong Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, China
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4
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Hao QQ, Chen XM, Pannecouque C, De Clercq E, Wang S, Chen FE. Structure-directed linker optimization of novel HEPTs as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg Chem 2023; 133:106413. [PMID: 36791619 DOI: 10.1016/j.bioorg.2023.106413] [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: 12/17/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
1-[(2-Hydroxyethoxy)methyl]-6-(phenylthio)thymines (HEPTs) have been previously described as an important class of HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs). In our continuously pursuing HEPT optimization efforts, a series of novel HEPTs, featuring -C(OH)CH2R, -CC, or -CHCH2R linker at the benzylic α-methylene unit, were developed as NNRTIs. Among these new HEPTs, the compound C20 with -CHCH3 group at the benzylic α-methylene unit conferred the highest potency toward WT HIV-1 and selectivity (EC50 = 0.23 μM, SI = 150.20), which was better than the lead compound HEPT (EC50 = 7 μM, SI = 106). Also, C20 was endowed with high efficacy against clinically relevant mutant strains (EC50(L100I) = 1.07 μM; EC50(K103N) = 4.33 μM; EC50(Y181C) = 5.57 μM; EC50(E138K) = 1.06 μM; EC50(F227L+V106A) = 5.45 μM) and wild-type HIV-1 reverse transcriptase (RT) with an IC50 value of 0.55 μM. Molecular docking and molecular dynamics simulations, as well as preliminary structure-activity relationship (SAR) analysis of these new compounds, provided a deeper insight into the key structural features of the interactions between HEPT analogs and HIV-1 RT and laid the foundation for further modification on HEPT scaffold.
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Affiliation(s)
- Qing-Qing Hao
- 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; Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xiao-Mei Chen
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Shuai Wang
- 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.
| | - Fen-Er 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; Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
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Prener L, Baszczyňski O, Kaiser MM, Dračínský M, Stepan G, Lee YJ, Brumshtein B, Yu H, Jansa P, Lansdon EB, Janeba Z. Design and Synthesis of Novel HIV-1 NNRTIs with Bicyclic Cores and with Improved Physicochemical Properties. J Med Chem 2023; 66:1761-1777. [PMID: 36652602 PMCID: PMC10017027 DOI: 10.1021/acs.jmedchem.2c01574] [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: 10/03/2022] [Indexed: 01/19/2023]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) represent cornerstones of current regimens for treatment of human immunodeficiency virus type 1 (HIV-1) infections. However, NNRTIs usually suffer from low aqueous solubility and the emergence of resistant viral strains. In the present work, novel bicyclic NNRTIs derived from etravirine (ETV) and rilpivirine (RPV), bearing modified purine, tetrahydropteridine, and pyrimidodiazepine cores, were designed and prepared. Compounds 2, 4, and 6 carrying the acrylonitrile moiety displayed single-digit nanomolar activities against the wild-type (WT) virus (EC50 = 2.5, 2.7, and 3.0 nM, respectively), where the low nanomolar activity was retained against HXB2 (EC50 = 2.2-2.8 nM) and the K103N and Y181C mutated strains (fold change, 1.2-6.7×). Most importantly, compound 2 exhibited significantly improved phosphate-buffered saline solubility (10.4 μM) compared to ETV and RPV (≪1 μM). Additionally, the binding modes of compounds 2, 4, and 6 to the reverse transcriptase were studied by X-ray crystallography.
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Affiliation(s)
- Ladislav Prener
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Ondřej Baszczyňski
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128
43, Czech Republic
| | - Martin M. Kaiser
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - George Stepan
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Yu-Jen Lee
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Boris Brumshtein
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Helen Yu
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Petr Jansa
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Eric B. Lansdon
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Zlatko Janeba
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
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Zhang T, Zhou Z, Zhao F, Sang Z, De Clercq E, Pannecouque C, Kang D, Zhan P, Liu X. Identification of Novel Diarylpyrimidines as Potent HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors by Exploring the Primer Grip Region. Pharmaceuticals (Basel) 2022; 15:ph15111438. [PMID: 36422568 PMCID: PMC9697031 DOI: 10.3390/ph15111438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
HIV-1 reverse transcriptase (RT) plays a crucial role in the viral replication cycle, and RT inhibitors can represent a promising pathway in treating AIDS. To explore the primer grip region of HIV-1 RT, using -CH2O- as a linker, substituted benzene or pyridine rings were introduced into the left wing of diarylpyrimidines (DAPYs). A total of 17 compounds with new structures were synthesized. It showed that all compounds exhibited anti-HIV-1 (wild-type) activity values ranging from 7.6−199.0 nM. Among them, TF2 (EC50 = 7.6 nM) showed the most potent activity, which was better than that of NVP (EC50 = 122.6 nM). Notably, compared with RPV (CC50 = 3.98 μM), TF2 (CC50 > 279,329.6 nM) showed low cytotoxicity. For HIV-1 mutant strains K103N and E138K, most compounds showed effective activities. Especially for K103N, TF2 (EC50 = 28.1 nM), TF12 (EC50 = 34.7 nM) and TF13 (EC50 = 28.0 nM) exhibited outstanding activity, being superior to that of NVP (EC50 = 7495.1 nM) and EFV (EC50 = 95.1 nM). Additionally, TF2 also showed the most potent activity against E138K (EC50 = 44.0 nM) and Y181C mutant strains (EC50 = 139.3 nM). In addition, all the compounds showed strong enzyme inhibition (IC50 = 0.036−0.483 μM), which demonstrated that their target was HIV-1 RT. Moreover, molecular dynamics simulation studies were implemented to predict the binding mode of TF2 in the binding pocket of wild-type and K103N HIV-1 RT.
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Affiliation(s)
- Tao Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Zhongxia Zhou
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- Department of Pharmacy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Fabao Zhao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Zihao Sang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (P.Z.); (X.L.)
| | - Peng Zhan
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (P.Z.); (X.L.)
| | - Xinyong Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (P.Z.); (X.L.)
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Deng C, Yan H, Wang J, Liu K, Liu BS, Shi YM. Current scenario on non-nucleoside reverse transcriptase inhibitors (2018-present). ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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