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Wang JS, Zhao KX, Zhang K, Pannecouque C, De Clercq E, Wang S, Chen FE. Structure-guided design of novel biphenyl-quinazoline derivatives as potent non-nucleoside reverse transcriptase inhibitors featuring improved anti-resistance, selectivity, and solubility. Bioorg Chem 2024; 147:107340. [PMID: 38593532 DOI: 10.1016/j.bioorg.2024.107340] [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: 03/18/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
In pursuit of enhancing the anti-resistance efficacy and solubility of our previously identified NNRTI 1, a series of biphenyl-quinazoline derivatives were synthesized employing a structure-based drug design strategy. Noteworthy advancements in anti-resistance efficacy were discerned among some of these analogs, prominently exemplified by compound 7ag, which exhibited a remarkable 1.37 to 602.41-fold increase in potency against mutant strains (Y181C, L100I, Y188L, F227L + V106A, and K103N + Y181C) in comparison to compound 1. Compound 7ag also demonstrated comparable anti-HIV activity against both WT HIV and K103N, albeit with a marginal reduction in activity against E138K. Of significance, this analog showed augmented selectivity index (SI > 5368) relative to compound 1 (SI > 37764), Nevirapine (SI > 158), Efavirenz (SI > 269), and Etravirine (SI > 1519). Moreover, it displayed a significant enhancement in water solubility, surpassing that of compound 1, Etravirine, and Rilpivirine. To elucidate the underlying molecular mechanisms, molecular docking studies were undertaken to probe the critical interactions between 7ag and both WT and mutant strains of HIV-1 RT. These findings furnish invaluable insights driving further advancements in the development of DAPYs for HIV therapy.
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Affiliation(s)
- Jin-Si Wang
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou 450001, China; 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
| | - Ke-Xin Zhao
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou 450001, China; 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
| | - Kun Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou 450001, China; 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, 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
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou 450001, China; 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.
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2
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Khalifa Z, Patel AB. Tri-substituted 1,3,5-triazine-based analogs as effective HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs): A systematic review. Drug Dev Res 2024; 85:e22154. [PMID: 38349259 DOI: 10.1002/ddr.22154] [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: 10/16/2023] [Revised: 12/19/2023] [Accepted: 01/13/2024] [Indexed: 02/15/2024]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) have significantly impacted the HIV-1 wild-type due to their high specificity and superior potency. As well as different combinations of NNRTIs have been used on clinically approved combining highly active antiretroviral therapy (HAART) to resist the growth of HIV-1 and decrease the mortality rate of HIV/AIDS. Although the feeble strength against the drug-resistant mutant strains and the long-term damaging effects have been reducing the effectiveness of HAART, it could be a crucial challenge to develop novel Anti-HIV leads with a vital mode of action and the least side effects. The extensive chemical reactivity and the diverse chemotherapeutic applications of the 1,3,5-triazine have provided a wide scope of research in medicinal chemistry via a structural modification. In this review, we focused on the Anti-HIV profile of the tri-substituted s-triazine derivatives with structure-based features and also discussed the active mode of action to evaluate the significant findings. The tri-substituted 1,3,5-triazine derivatives have been found more promising to inhibit the growth of the drug-sensitive and drug-resistant variants of HIV-1, especially HIV-1 wild-type, HIV-1 K103N/Y181C, and HIV-1 Tyr181Cys. It has been observed that these derivatives have interacted with the enzyme protein residues via a significantπ $\pi $ -π $\pi $ interaction and hydrogen bonding to resist the proliferation of the viral genomes. Further, the SAR and the active binding modes are critically described and highlight the role of structural variations with functional groups along with the binding affinity of targeted enzymes, which may be beneficial for rational drug discovery to develop highly dynamic Anti-HIV agents.
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Affiliation(s)
- Zebabanu Khalifa
- Department of Chemistry, Government College, Daman (Affiliated to Veer Narmad South Gujarat University, Surat), Daman, India
| | - Amit B Patel
- Department of Chemistry, Government College, Daman (Affiliated to Veer Narmad South Gujarat University, Surat), Daman, India
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3
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Yan J, Li Y, Ding L, Hou R, Xing C, Jiang C, Miao Z, Zhuang C. Fragment-Based Discovery of Azocyclic Alkyl Naphthalenesulfonamides as Keap1-Nrf2 Inhibitors for Acute Lung Injury Treatment. J Med Chem 2023. [PMID: 37257073 DOI: 10.1021/acs.jmedchem.3c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Blocking the Kelch-like epichlorohydrin-related protein 1 (Keap1)-nuclear factor-erythroid 2 related factor 2 (Nrf2) pathway is a promising strategy to alleviate acute lung injury (ALI). A naphthalensulfonamide NXPZ-2, targeting Keap1-Nrf2 interaction to release Nrf2, was confirmed to exhibit significant anti-inflammatory activities, however, accompanying nonideal solubility and PK profiles. To further improve the properties, twenty-nine novel naphthalenesulfonamide derivatives were designed by a fragment-based strategy. Among them, compound 10u with a (R)-azetidine group displayed the highest PPI inhibitory activity (KD2 = 0.22 μM). The hydrochloric acid form of 10u exhibited a 9-fold improvement on water solubility (S = 484 μg/mL, pH = 7.0) compared to NXPZ-2 (S = 55 μg/mL, pH = 7.0). It could significantly reduce LPS-induced lung oxidative damages and inflammations in vitro and in vivo. Furthermore, a satisfactory pharmacokinetic property was revealed. In conclusion, the novel azetidine-containing naphthalenesulfonamide represents a promising drug candidate for Keap1-targeting ALI treatment.
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Affiliation(s)
- Jianyu Yan
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Yue Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Li Ding
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Ruilin Hou
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Chengguo Xing
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Chengshi Jiang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Zhenyuan Miao
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
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Structure-directed expansion of biphenyl-pyridone derivatives as potent non-nucleoside reverse transcriptase inhibitors with significantly improved potency and safety. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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5
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Sang YL, Pannecouque C, De Clercq E, Wang S, Chen FE. Picomolar inhibitor of reverse transcriptase featuring significantly improved metabolic stability. Acta Pharm Sin B 2023. [PMID: 37521857 PMCID: PMC10372819 DOI: 10.1016/j.apsb.2023.03.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Considering the undesirable metabolic stability of our recently identified NNRTI 5 (t1/2 = 96 min) in human liver microsomes, we directed our efforts to improve its metabolic stability by introducing a new favorable hydroxymethyl side chain to the C-5 position of pyrimidine. This strategy provided a series of novel methylol-biphenyl-diarylpyrimidines with excellent anti-HIV-1 activity. The best compound 9g was endowed with remarkably improved metabolic stability in human liver microsomes (t1/2 = 2754 min), which was about 29-fold longer than that of 5 (t1/2 = 96 min). This compound conferred picomolar inhibition of WT HIV-1 (EC50 = 0.9 nmol/L) and low nanomolar activity against five clinically drug-resistant mutant strains. It maintained particularly low cytotoxicity (CC50 = 264 μmol/L) and good selectivity (SI = 256,438). Molecular docking studies revealed that compound 9g exhibited a more stable conformation than 5 due to the newly constructed hydrogen bond of the hydroxymethyl group with E138. Also, compound 9g was characterized by good safety profiles. It displayed no apparent inhibition of CYP enzymes and hERG. The acute toxicity assay did not cause death and pathological damage in mice at a single dose of 2 g/kg. These findings paved the way for the discovery and development of new-generation anti-HIV-1 drugs.
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6
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Discovery of novel biphenyl-substituted pyridone derivatives as potent non-nucleoside reverse transcriptase inhibitors with promising oral bioavailability. Eur J Med Chem 2022; 240:114581. [DOI: 10.1016/j.ejmech.2022.114581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022]
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7
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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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Kumar A, Wahan SK, Virendra SA, Chawla PA. Recent Advances on the Role of Nitrogen‐Based Heterocyclic Scaffolds in Targeting HIV through Reverse Transcriptase Inhibition. ChemistrySelect 2022. [DOI: 10.1002/slct.202202637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ankur Kumar
- Department of Pharmaceutical Chemistry ISF College of Pharmacy GT Road Ghal Kalan Moga 142001 India
| | - Simranpreet K. Wahan
- Department of Pharmaceutical Chemistry ISF College of Pharmacy GT Road Ghal Kalan Moga 142001 India
| | - Sharma Arvind Virendra
- Department of Pharmaceutical Chemistry ISF College of Pharmacy GT Road Ghal Kalan Moga 142001 India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry ISF College of Pharmacy GT Road Ghal Kalan Moga 142001 India
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9
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Ling X, Hao QQ, Pannecouque C, Clercq ED, Chen FE. Expansion of the S–CN-DABO scaffold to exploit the impact on inhibitory activities against the non-nucleoside HIV-1 reverse transcriptase. Eur J Med Chem 2022; 238:114512. [DOI: 10.1016/j.ejmech.2022.114512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 11/04/2022]
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10
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Li G, Wang Y, De Clercq E. Approved HIV reverse transcriptase inhibitors in the past decade. Acta Pharm Sin B 2022; 12:1567-1590. [PMID: 35847492 PMCID: PMC9279714 DOI: 10.1016/j.apsb.2021.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 01/09/2023] Open
Abstract
HIV reverse transcriptase (RT) inhibitors are the important components of highly active antiretroviral therapies (HAARTs) for anti-HIV treatment and pre-exposure prophylaxis in clinical practice. Many RT inhibitors and their combination regimens have been approved in the past ten years, but a review on their drug discovery, pharmacology, and clinical efficacy is lacking. Here, we provide a comprehensive review of RT inhibitors (tenofovir alafenamide, rilpivirine, doravirine, dapivirine, azvudine and elsulfavirine) approved in the past decade, regarding their drug discovery, pharmacology, and clinical efficacy in randomized controlled trials. Novel RT inhibitors such as islatravir, MK-8504, MK-8507, MK8583, IQP-0528, and MIV-150 will be also highlighted. Future development may focus on the new generation of novel antiretroviral inhibitors with higher bioavailability, longer elimination half-life, more favorable side-effect profiles, fewer drug-drug interactions, and higher activities against circulating drug-resistant strains.
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Key Words
- 3TC, (−)-2′,3′-dideoxy-3′-thiacytidine (common name, lamivudine)
- ABC, abacavir
- ATV, atazanavir
- AZT, 3′-azido-3′-deoxy-thymidine (common name, zidovudine)
- BIC, bictegravir
- CAB, cabotegravir
- CC50, the 50% cytotoxic concentration
- COBI, cobicistat
- Clinical efficacy
- DOR, doravirine
- DPV, dapivirine
- DRV, darunavir
- DTG, dolutegravir
- EACS, European AIDS Clinical Society
- EC50, half maximal effective concentration
- EFV, efavirenz
- ESV, elsulfavirine
- EVG, elvitegravir
- F, bioavailability
- FDA, US Food and Drug Administration
- FTC, (−)-2′,3′-dideoxy-5-fluoro-3′-thiacytidine (common name, emtricitabine)
- HAART
- HAART, highly active antiretroviral therapy
- HIV treatment
- HIV, human immunodeficiency virus
- IAS-USA, International Antiviral Society-USA
- IC50, half maximal inhibitory concentration
- MSM, men who have sex with men
- NNRTI
- NNRTI, non-nucleoside reverse transcriptase inhibitor
- NRTI
- NRTI, nucleoside/nucleotide reverse transcriptase inhibitor
- RPV, rilpivirine
- TAF, tenofovir alafenamide
- TDF, tenofovir disoproxil fumarate
- t1/2, elimination half-life
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Affiliation(s)
- Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Yali Wang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Erik De Clercq
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven B-3000, Belgium
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11
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Ding L, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Discovery of Novel Pyridine-Dimethyl-Phenyl-DAPY Hybrids by Molecular Fusing of Methyl-Pyrimidine-DAPYs and Difluoro-Pyridinyl-DAPYs: Improving the Druggability toward High Inhibitory Activity, Solubility, Safety, and PK. J Med Chem 2022; 65:2122-2138. [DOI: 10.1021/acs.jmedchem.1c01676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- 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, Herestraat 49, Leuven B-3000, Belgium
| | - 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
| | - Fen-Er Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- 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, 18 Chao Wang Road, Hangzhou 310014, China
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12
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Xu S, Song S, Sun L, Gao P, Gao S, Ma Y, Kang D, Cheng Y, Zhang X, Cherukupalli S, De Clercq E, Pannecouque C, Liu X, Zhan P. Indolylarylsulfones bearing phenylboronic acid and phenylboronate ester functionalities as potent HIV‑1 non-nucleoside reverse transcriptase inhibitors. Bioorg Med Chem 2022; 53:116531. [PMID: 34890994 DOI: 10.1016/j.bmc.2021.116531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/02/2022]
Abstract
To explore the chemical space around the entrance channel of the HIV-1 reverse transcriptase (RT) binding pocket, we innovatively designed and synthesized a series of novel indolylarylsulfones (IASs) bearing phenylboronic acid and phenylboronate ester functionalities at the indole-2-carboxamide as new HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) through structure-based drug design. All the newly synthesized compounds exhibited excellent to moderate potency against wild-type (WT) HIV-1 with EC50 values ranging from 6.7 to 42.6 nM. Among all, (3-ethylphenyl)boronic acid substituted indole-2-carboxamide and (4-ethylphenyl) boronate ester substituted indole-2-carboxamide were found to be the most potent inhibitors (EC50 = 8.5 nM, SI = 3310; EC50 = 6.7 nM, SI = 3549, respectively). Notably, (3-ethylphenyl)boronic acid substituted indole-2-carboxamide maintained excellent activities against the single HIV-1 mutants L100I (EC50 = 7.3 nM), K103N (EC50 = 9.2 nM), as well as the double mutant V106A/F227L (EC50 = 21.1 nM). Preliminary SARs and molecular modelling studies are also discussed in detail.
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Affiliation(s)
- Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shu Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Yue Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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13
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Zenchenko AA, Drenichev MS, Il’icheva IA, Mikhailov SN. Antiviral and Antimicrobial Nucleoside Derivatives: Structural Features and Mechanisms of Action. Mol Biol 2021; 55:786-812. [PMID: 34955556 PMCID: PMC8682041 DOI: 10.1134/s0026893321040105] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/03/2021] [Accepted: 04/09/2021] [Indexed: 11/23/2022]
Abstract
The emergence of new viruses and resistant strains of pathogenic microorganisms has become a powerful stimulus in the search for new drugs. Nucleosides are a promising class of natural compounds, and more than a hundred drugs have already been created based on them, including antiviral, antibacterial and antitumor agents. The review considers the structural and functional features and mechanisms of action of known nucleoside analogs with antiviral, antibacterial or antiprotozoal activity. Particular attention is paid to the mechanisms that determine the antiviral effect of nucleoside analogs containing hydrophobic fragments. Depending on the structure and position of the hydrophobic substituent, such nucleosides can either block the process of penetration of viruses into cells or inhibit the stage of genome replication. The mechanisms of inhibition of viral enzymes by compounds of nucleoside and non-nucleoside nature have been compared. The stages of creation of antiparasitic drugs, which are based on the peculiarities of metabolic transformations of nucleosides in humans body and parasites, have been considered. A new approach to the creation of drugs is described, based on the use of prodrugs of modified nucleosides, which, as a result of metabolic processes, are converted into an effective drug directly in the target organ or tissue. This strategy makes it possible to reduce the general toxicity of the drug to humans and to increase the effectiveness of its action on cells infected by the virus.
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Affiliation(s)
- A. A. Zenchenko
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - M. S. Drenichev
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - I. A. Il’icheva
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - S. N. Mikhailov
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
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14
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Jin X, Piao HR, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Design of the naphthyl-diarylpyrimidines as potent non-nucleoside reverse transcriptase inhibitors (NNRTIs) via structure-based extension into the entrance channel. Eur J Med Chem 2021; 226:113868. [PMID: 34583311 DOI: 10.1016/j.ejmech.2021.113868] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/27/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
A series of novel naphthyl-diarylpyrimidine (DAPY) derivatives were designed and synthesized to explore the entrance channel of the non-nucleoside reverse transcriptase inhibitors binding pocket (NNIBP) by incorporating different flexible side chains at the C-6 position. The biological evaluation results showed that all analogues possessed promising HIV-1 inhibitory activity at the nanomolar concentration range. Three compounds (7, 9 and 39) displayed excellent potency against WT HIV-1 strain with EC50 values ranging from 5 to 10 nM and high selectivity indexes (SI = 3504, 30488 and 22846, respectively), which were higher than for nevirapine and comparable to the values for etravirine. The RT inhibition activity, preliminary structure-activity relationship and molecular docking study showed that the side chain at the C-6 position of the DAPYs occupied the entrance channel and significantly influenced anti-HIV activity and selectivity. Additionally, the physicochemical properties were investigated to evaluate the drug-like features, which indicated that introducing various substituents on the pyrimidine ring can improve solubility.
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Affiliation(s)
- Xin Jin
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China
| | - Hu-Ri Piao
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - 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.
| | - Fen-Er Chen
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China; Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium.
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15
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Ding L, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Improving Druggability of Novel Diarylpyrimidine NNRTIs by a Fragment-Based Replacement Strategy: From Biphenyl-DAPYs to Heteroaromatic-Biphenyl-DAPYs. J Med Chem 2021; 64:10297-10311. [PMID: 34197708 DOI: 10.1021/acs.jmedchem.1c00708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A series of novel heteroaromatic-difluoro-biphenyl-diarylpyrimidines were designed as non-nucleoside anti-HIV inhibitors targeting reverse transcriptase by a fragment-based replacement strategy with the purpose of improving the druggability. Hopping five- or six-membered heterocycle groups on the biphenyl moiety as bioisosterism for intrinsically cyanophenyl gave 23 derivatives. All of these compounds possessed excellent HIV-1 inhibitory activity in the nanomolar range. Among them, 12g with a 4-pyridine group displayed excellent inhibitory activity toward WT and mutant HIV virus possessing significant selectivity. Moreover, this compound exhibited a decent improvement in druggability than etravirine and rilpivirine: (1) The hydrochloric acid salt of 12g exhibited significantly improved water solubility in different pH conditions. (2) 12g did not show apparent CYP enzymatic inhibitory activity or acute toxicity. (3) Excellent oral bioavailability was also revealed (F = 126%, rats) in 12g. Collectively, these novel heteroaromatic-biphenyl-DAPYs represent promising drug candidates for HIV clinical therapy.
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Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,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, Herestraat 49, B-3000 Leuven, Belgium
| | - 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
| | - Fen-Er Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,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, 18 Chao Wang Road, Hangzhou 310014, China
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16
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Fu Z, Zhang T, Zhou Z, Kang D, Sun L, Gao S, Cherukupalli S, De Clercq E, Pannecouque C, Liu X, Zhan P. Exploiting the hydrophobic channel of the NNIBP: Discovery of novel diarylpyrimidines as HIV-1 NNRTIs against wild-type and K103N mutant viruses. Bioorg Med Chem 2021; 42:116239. [PMID: 34090079 DOI: 10.1016/j.bmc.2021.116239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 01/19/2023]
Abstract
To further explore the chemical space surrounding the "hydrophobic channel" of the NNRTI binding pocket (NNIBP), a new series of diarylpyrimidines (DAPYs) were designed and synthesized as potent HIV-1 non-nucleoside RT inhibitors (NNRTIs). The target compounds were evaluated for anti-HIV potency in MT-4 cells. Most of the synthesized DAPYs exhibited moderate to excellent activity against the HIV-1 wild-type (WT) strain with EC50 values ranging from 16 nM to 0.722 µM. Interestingly, few compounds displayed remarkable activity in inhibiting K103N mutant virus with EC50 values ranging from 39 nM to 1.708 µM. Notably, FS2 (EC50(IIIB) = 16 nM, EC50(K103N) = 39 nM, SI = 294) was identified as the most significant compound, which was considerably more potent than nevirapine, lamivudine, and comparable to zidovudine. Additionally, the HIV-1 RT inhibition assay confirmed their binding target. Preliminary structure-activity relationships (SARs) and molecular modeling studies were also performed, providing significant suggestions for further optimization.
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Affiliation(s)
- Zhipeng Fu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Tao Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zhongxia Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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17
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Kiriwan D, Choowongkomon K. In silico structural elucidation of the rabies RNA-dependent RNA polymerase (RdRp) toward the identification of potential rabies virus inhibitors. J Mol Model 2021; 27:183. [PMID: 34031746 PMCID: PMC8143072 DOI: 10.1007/s00894-021-04798-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 05/17/2021] [Indexed: 11/25/2022]
Abstract
The rabies virus (RABV) is a non-segmented, negative single-stranded RNA virus which causes acute infection of the central nervous system in humans. Once symptoms appear, the result is nearly always death, and to date, post-exposure prophylaxis (PEP) is the only treatment applicable only immediately after an exposure. Previous studies have identified viral RNA-dependent RNA polymerase (RdRp) as a potential drug target due to its significant role in viral replication and transcription. Herein we generated an energy-minimized homology model of RABIES-RdRp and used it for virtual screening against 2045 NCI Diversity Set III library. The best five ligand-RdRp complexes were picked for further energy minimization via molecular dynamics (MDs) where the complex with ligand Z01690699 shows a minimum score characterized with stable hydrogen bonds and hydrophobic interactions with the catalytic site residues. Our study identified an important ligand for development of remedial approach for treatment of rabies infection.
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Affiliation(s)
- Duangnapa Kiriwan
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand. .,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand.
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18
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Ding L, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Hydrophobic Pocket Occupation Design of Difluoro-Biphenyl-Diarylpyrimidines as Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors: from N-Alkylation to Methyl Hopping on the Pyrimidine Ring. J Med Chem 2021; 64:5067-5081. [PMID: 33851529 DOI: 10.1021/acs.jmedchem.1c00128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Considering the nonideal metabolic stability of the difluoro-biphenyl-diarylpyrimidine lead compound 4, a series of novel alkylated difluoro-biphenyl-diarylpyrimidines were designed and synthesized based on their structure. Introducing alkyl or substituted alkyl groups on the linker region to block the potential metabolic sensitive sites generated 22 derivatives. Among them, compound 12a with an N-methyl group displayed excellent anti-HIV-1 activity and selectivity. The methyl group was hopped to the central pyrimidine to occupy the small linker region and maintain the water-mediated hydrogen bond observed in the binding of compound 4 with RT. The resulting compound 16y exhibited an improved anti-HIV-1 activity, much lower cytotoxicity, and nanomolar activity toward multiple mutants. In addition, 16y has a better stability in human liver microsomes than 4. Moreover, no apparent in vivo acute toxicity was observed in 16y-treated female, especially pregnant mice. This series of alkylated compounds with highly potency and safety represent a promising lead template for future discovery.
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Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,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, Herestraat 49, B-3000 Leuven, Belgium
| | - 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
| | - Fen-Er Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,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, 18 Chao Wang Road, 310014 Hangzhou, China
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19
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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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20
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Feng D, Zuo X, Jing L, Chen CH, Olotu FA, Lin H, Soliman M, De Clercq E, Pannecouque C, Lee KH, Kang D, Liu X, Zhan P. Design, synthesis, and evaluation of "dual-site"-binding diarylpyrimidines targeting both NNIBP and the NNRTI adjacent site of the HIV-1 reverse transcriptase. Eur J Med Chem 2020; 211:113063. [PMID: 33340914 DOI: 10.1016/j.ejmech.2020.113063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/22/2020] [Accepted: 11/28/2020] [Indexed: 12/16/2022]
Abstract
Inspired by our previous efforts to improve the drug-resistance profiles of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), a novel series of "dual-site" binding diarylpyrimidine (DAPY) derivatives targeting both the NNRTI adjacent site and NNRTIs binding pocket (NNIBP) were designed, synthesized, and evaluated for their anti-HIV potency in TZM-bl and MT-4 cells. Eight compounds exhibited moderate to excellent potencies in inhibiting wild-type (WT) HIV-1 replication with EC50 values ranging from 2.45 nM to 5.36 nM, and 14c (EC50 = 2.45 nM) proved to be the most promising inhibitor. Of note, 14c exhibited potent activity against the single mutant strain E138K (EC50 = 10.6 nM), being comparable with ETR (EC50 = 9.80 nM) and 3.5-fold more potent than that of compound 7 (EC50 = 37.3 nM). Moreover, 14c acted as a classical NNRTI with high affinity for WT HIV-1 RT (IC50 = 0.0589 μM). The detailed structure-activity relationships (SARs) of the representative compounds were also determined, and further supported by molecular dynamics simulation. Overall, we envision that the "dual-site"-binding NNRTIs have significant prospects and pave the way for the next round of rational design of potent anti-HIV-1 agents.
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Affiliation(s)
- Da Feng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xiaofang Zuo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Chin-Ho Chen
- Natural Products Research Laboratories, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Hao Lin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Mahmoud Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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21
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vonRanke NL, Ribeiro MMJ, Miceli LA, de Souza NP, Abrahim-Vieira BA, Castro HC, Teixeira VL, Rodrigues CR, Souza AMT. Structure-activity relationship, molecular docking, and molecular dynamic studies of diterpenes from marine natural products with anti-HIV activity. J Biomol Struct Dyn 2020; 40:3185-3195. [PMID: 33183161 DOI: 10.1080/07391102.2020.1845977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
HIV-1 infection is a global epidemic whose treatment is limited majorly by viral resistance and adverse effects. Natural products from algae have been studied for many years, including antiviral, being an alternative to anti-HIV drug design. Since the isolation of natural products can be a hurdle, molecular modeling is an important tool to study these compounds. Herein, structure-activity relationship, molecular docking, and molecular dynamic studies were performed to direct the studies of ten marine natural products with anti-HIV activity. In the structure-activity relationship, descriptors were identified associating the anti-HIV activity of five diterpenes with possible action on the reverse transcriptase allosteric site. These diterpenes were evaluated by molecular docking, and it was identified that only dolabelladienetriol interacted in the allosteric site. Molecular dynamics suggested that the dolabelladienetriol might interfere with the viral RNA binding to HIV-1 RT by inducing a conformational change of the enzyme. Also, in silico ADMET simulations predicts that the dolabelladienetriol present a high potential to be successfully developed as a drug. Thus, applying in silico approaches was possible to suggest potential anti-HIV compounds derived from marine natural products.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- N L vonRanke
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M M J Ribeiro
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - L A Miceli
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Biology Institute, Federal Fluminense University, Niteroi, Brazil
| | - N P de Souza
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - B A Abrahim-Vieira
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - H C Castro
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Biology Institute, Federal Fluminense University, Niteroi, Brazil
| | - V L Teixeira
- Center for Biological Sciences and Health (CCBS), Rectory, Federal University of Rio de Janeiro State, Rio de Janeiro, Brazil
| | - C R Rodrigues
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A M T Souza
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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22
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Gu SX, Zhu YY, Wang C, Wang HF, Liu GY, Cao S, Huang L. Recent discoveries in HIV-1 reverse transcriptase inhibitors. Curr Opin Pharmacol 2020; 54:166-172. [PMID: 33176248 DOI: 10.1016/j.coph.2020.09.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/20/2022]
Abstract
HIV-1 reverse transcriptase inhibitors (RTIs) are indispensable components of highly active antiretroviral therapy (HAART), which has achieved great success in controlling AIDS epidemic in reducing drastically the morbidity and mortality of HIV-infected patients. RTIs are divided into two categories, nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs). In this review, the recent discoveries in NRTIs and NNRTIs, including approved anti-HIV drugs and noteworthy drug candidates in different development stages, are summarized, and their future direction is prospected.
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Affiliation(s)
- Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou 450001, China.
| | - Yuan-Yuan Zhu
- School of Chemistry & Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Chao Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Hai-Feng Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Gen-Yan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang Cao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Lu Huang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
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23
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Targeting dual tolerant regions of binding pocket: Discovery of novel morpholine-substituted diarylpyrimidines as potent HIV-1 NNRTIs with significantly improved water solubility. Eur J Med Chem 2020; 206:112811. [DOI: 10.1016/j.ejmech.2020.112811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/01/2020] [Accepted: 09/01/2020] [Indexed: 12/21/2022]
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24
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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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Yang Y, Pannecouque C, Clercq ED, Zhuang C, Chen FE. Privileged scaffold inspired design of novel oxime-biphenyl-DAPYs in treatment of HIV-1. Bioorg Chem 2020; 99:103825. [DOI: 10.1016/j.bioorg.2020.103825] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/11/2020] [Accepted: 04/05/2020] [Indexed: 11/24/2022]
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Lei Y, Han S, Yang Y, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Design of Biphenyl-Substituted Diarylpyrimidines with a Cyanomethyl Linker as HIV-1 NNRTIs via a Molecular Hybridization Strategy. Molecules 2020; 25:E1050. [PMID: 32111013 PMCID: PMC7179183 DOI: 10.3390/molecules25051050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
The key problems of human immunodeficiency virus (HIV) therapy are the rapid emergence of drug-resistant mutant strains and significant cumulative drug toxicities. Therefore, there is an urgent demand for new anti-HIV agents with low toxicity and broad-spectrum antiviral potency. A series of biphenyl-substituted diarylpyrimidines with a cyanomethyl linker were designed using a molecular hybridization strategy. The cell-based anti-HIV assay showed that most of the compounds exhibited moderate to good activities against wild-type HIV-1 and clinically relevant mutant strains with a more favorable toxicity, and the enzymatic assay showed they had nanomolar activity against reverse transcriptase (RT). Compound 10p exhibited the best activity against wild-type HIV-1 with an EC50 (50% HIV-1 replication inhibitory concentration) value of 0.027 µM, an acceptable CC50 (50% cytotoxic concentration) value of 36.4 µM, and selectivity index of 1361, with moderate activities against the single mutants (EC50: E138K, 0.17 µM; Y181C, 0.87 µM; K103N, 0.9 µM; L100I, 1.21 µM, respectively), and an IC50 value of 0.059 µM against the RT enzyme, which was six-fold higher than nevirapine (NVP). The preliminary structure-activity relationship (SAR) of these new compounds was concluded. The molecular modeling predicted the binding modes of the new compounds with RT, providing molecular insight for further drug design.
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Affiliation(s)
- Yuan Lei
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; (Y.L.); (Y.Y.)
| | - Sheng Han
- 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
| | - Yang Yang
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; (Y.L.); (Y.Y.)
| | - Christophe Pannecouque
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium; (C.P.); (E.D.C.)
| | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium; (C.P.); (E.D.C.)
| | - 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
| | - Fen-Er Chen
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; (Y.L.); (Y.Y.)
- 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
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Sang Y, Han S, Pannecouque C, De Clercq E, Zhuang C, Chen F. Ligand-Based Design of Nondimethylphenyl-Diarylpyrimidines with Improved Metabolic Stability, Safety, and Oral Pharmacokinetic Profiles. J Med Chem 2019; 62:11430-11436. [PMID: 31714780 DOI: 10.1021/acs.jmedchem.9b01446] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A series of nondimethylphenyl-diarylpyrimidines with much lower cytotoxicities than their dimethyl analogues were developed. Compound B13 with a difluorobiphenyl moiety showed the highest antiviral activity against WT, mutant strains, and RT. The hydrochloride form of B13 exhibited an improved water solubility of 5.6 μg/mL compared with ETR (≪1 μg/mL), better stability in human and rat liver microsomes, and a great oral bioavailability of 44%, making it promising as a drug candidate. In addition, no apparent toxicity was observed in the acute toxicity assay (2 g/kg) and HE staining.
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Affiliation(s)
- Yali Sang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry , Fudan University , Shanghai 200433 , People's Republic of China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs , Shanghai 200433 , People's Republic of China
| | - Sheng Han
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry , Fudan University , Shanghai 200433 , People's Republic of China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs , Shanghai 200433 , People's Republic of China
| | - Christophe Pannecouque
- Rega Institute for Medical Research , KU Leuven , Herestraat 49 , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research , KU Leuven , Herestraat 49 , B-3000 Leuven , Belgium
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry , Fudan University , Shanghai 200433 , People's Republic of China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs , Shanghai 200433 , People's Republic of China
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry , Fudan University , Shanghai 200433 , People's Republic of China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs , Shanghai 200433 , People's Republic of China.,Institute of Pharmaceutical Science and Technology , Zhejiang University of Technology , 18 Chao Wang Road , 310014 Hangzhou , China
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