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Vanangamudi M, Palaniappan S, Kathiravan MK, Namasivayam V. Strategies in the Design and Development of Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs). Viruses 2023; 15:1992. [PMID: 37896769 PMCID: PMC10610861 DOI: 10.3390/v15101992] [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: 08/15/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
AIDS (acquired immunodeficiency syndrome) is a potentially life-threatening infectious disease caused by human immunodeficiency virus (HIV). To date, thousands of people have lost their lives annually due to HIV infection, and it continues to be a big public health issue globally. Since the discovery of the first drug, Zidovudine (AZT), a nucleoside reverse transcriptase inhibitor (NRTI), to date, 30 drugs have been approved by the FDA, primarily targeting reverse transcriptase, integrase, and/or protease enzymes. The majority of these drugs target the catalytic and allosteric sites of the HIV enzyme reverse transcriptase. Compared to the NRTI family of drugs, the diverse chemical class of non-nucleoside reverse transcriptase inhibitors (NNRTIs) has special anti-HIV activity with high specificity and low toxicity. However, current clinical usage of NRTI and NNRTI drugs has limited therapeutic value due to their adverse drug reactions and the emergence of multidrug-resistant (MDR) strains. To overcome drug resistance and efficacy issues, combination therapy is widely prescribed for HIV patients. Combination antiretroviral therapy (cART) includes more than one antiretroviral agent targeting two or more enzymes in the life cycle of the virus. Medicinal chemistry researchers apply different optimization strategies including structure- and fragment-based drug design, prodrug approach, scaffold hopping, molecular/fragment hybridization, bioisosterism, high-throughput screening, covalent-binding, targeting highly hydrophobic channel, targeting dual site, and multi-target-directed ligand to identify and develop novel NNRTIs with high antiviral activity against wild-type (WT) and mutant strains. The formulation experts design various delivery systems with single or combination therapies and long-acting regimens of NNRTIs to improve pharmacokinetic profiles and provide sustained therapeutic effects.
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Affiliation(s)
- Murugesan Vanangamudi
- Department of Pharmaceutical Chemistry, Amity Institute of Pharmacy, Amity University Madhya Pradesh, Gwalior 474005, Madhya Pradesh, India;
| | - Senthilkumar Palaniappan
- Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore 641021, Tamilnadu, India;
- Center for Active Pharmaceutical Ingredients, Karpagam Academy of Higher Education, Coimbatore 641021, Tamilnadu, India
| | - Muthu Kumaradoss Kathiravan
- Dr. APJ Abdul Kalam Research Lab, SRM College of Pharmacy, SRMIST, Kattankulathur 603203, Tamilnadu, India;
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Kattankulathur 603203, Tamilnadu, India
| | - Vigneshwaran Namasivayam
- Pharmaceutical Chemistry, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
- LIED, University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538 Lübeck, Germany
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Design, Synthesis and Bioactivity of Novel Pyrimidine Sulfonate Esters Containing Thioether Moiety. Int J Mol Sci 2023; 24:ijms24054691. [PMID: 36902121 PMCID: PMC10003536 DOI: 10.3390/ijms24054691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/04/2023] Open
Abstract
Pesticides play an important role in crop disease and pest control. However, their irrational use leads to the emergence of drug resistance. Therefore, it is necessary to search for new pesticide-lead compounds with new structures. We designed and synthesized 33 novel pyrimidine derivatives containing sulfonate groups and evaluated their antibacterial and insecticidal activities. Results: Most of the synthesized compounds showed good antibacterial activity against Xanthomonas oryzae pv. Oryzae (Xoo), Xanthomonas axonopodis pv. Citri (Xac), Pseudomonas syringae pv. actinidiae (Psa) and Ralstonia solanacearum (Rs), and certain insecticidal activity. A5, A31 and A33 showed strong antibacterial activity against Xoo, with EC50 values of 4.24, 6.77 and 9.35 μg/mL, respectively. Compounds A1, A3, A5 and A33 showed remarkable activity against Xac (EC50 was 79.02, 82.28, 70.80 and 44.11 μg/mL, respectively). In addition, A5 could significantly improve the defense enzyme (superoxide dismutase, peroxidase, phenylalanine ammonia-lyase and catalase) activity of plants against pathogens and thus improve the disease resistance of plants. Moreover, a few compounds also showed good insecticidal activity against Plutella xylostella and Myzus persicae. The results of this study provide insight into the development of new broad-spectrum pesticides.
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Ming W, Lu WL, Pannecouque C, Chen J, Wang HF, Xiao YQ, Hu S, Gu SX, Zhu YY, Chen FE. Hybrids of delavirdine and piperdin-4-yl-aminopyrimidines (DPAPYs) as potent HIV-1 NNRTIs: Design, synthesis and biological activities. Eur J Med Chem 2023; 248:115114. [PMID: 36640458 DOI: 10.1016/j.ejmech.2023.115114] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/01/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
The hybrids of delavirdine and piperdin-4-yl-aminopyrimidine (DPAPYs) were designed from two excellent HIV-1 NNRTIs delavirdine and piperidin-4-yl-aminopyrimidine via molecular hybridization. The target compounds 4a-r were prepared and evaluated for their cellular anti-HIV activities and cytotoxicities as well as the inhibitory activities against HIV-1 reverse transcriptase (RT). All the newly synthesized compounds demonstrated moderate to excellent potency against wild-type (WT) HIV-1 with EC50 values in a range of 5.7 to 0.0086 μM and against RT with IC50 values ranging from 12.0 to 0.11 μM, indicating that the DPAPYs were specific RT inhibitors. Among all, 4d displayed the most potent activity against WT HIV-1 (EC50 = 8.6 nM, SI = 2151). Gratifyingly, it exhibited good to excellent potency against the single HIV-1 mutants L100I, K103N, Y181C, Y188L, E138K, as well as the double mutant F227L + V106A. Furthermore, the preliminary structure-activity relationships were summarized, molecular modeling was conducted to explore the binding mode of DPAPYs and HIV-1 RT, and their physicochemical properties were also predicted.
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Affiliation(s)
- Wei Ming
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Wen-Long Lu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Christophe Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000, Leuven, Belgium
| | - Jiong Chen
- 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
| | - Ya-Qi Xiao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Sha Hu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China
| | - 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.
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
| | - Fen-Er Chen
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China; Department of Chemistry, Fudan University, Shanghai, 200433, China; Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, 430205, China.
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Abstract
Background Rilpivirine (RPV) was approved by the U.S. FDA (Food and Drug Administration) in 2011 to treat individuals infected with human immunodeficiency virus 1 (HIV-1). Significantly, rilpivirine is three fold more potent than etravirine. Once-daily, it is used with a low oral dose (25 mg/tablet), decreasing the drug administration and bringing a better choice to the patients. However, there are many shortcomings in the existing synthesis route of RPV, such as the high cost, prolonged reaction time and low yield (18.5%). Results This article describes our efforts to develop an efficient and practical microwave-promoted method to synthesize rilpivirine using less toxic organic reagents and low boiling solvents. The last step's reaction time decreased from 69 h to 90 min through this optimized synthetic procedure, and the overall yield improved from 18.5 to 21%. In addition, the yield of intermediate 3 increased from 52 to 62% compared to the original patent. Conclusion Overall, through a series of process optimization, we have developed a practical synthesis method of rilpivirine, which is easy to scale with higher yield and shorter reaction time.
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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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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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Li TT, Pannecouque C, De Clercq E, Zhuang CL, Chen FE. Scaffold Hopping in Discovery of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors: From CH(CN)-DABOs to CH(CN)-DAPYs. Molecules 2020; 25:E1581. [PMID: 32235557 PMCID: PMC7180830 DOI: 10.3390/molecules25071581] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 01/15/2023] Open
Abstract
Scaffold hopping is a frequently-used strategy in the development of non-nucleoside reverse transcriptase inhibitors. Herein, CH(CN)-DAPYs were designed by hopping the cyano-methylene linker of our previous published CH(CN)-DABOs onto the etravirine (ETR). Eighteen CH(CN)-DAPYs were synthesized and evaluated for their anti-HIV activity. Most compounds exhibited promising activity against wild-type (WT) HIV-1. Compounds B4 (EC50 = 6 nM) and B6 (EC50 = 8 nM) showed single-digit nanomolar potency against WT HIV-1. Moreover, these two compounds had EC50 values of 0.06 and 0.08 μM toward the K103N mutant, respectively, which were comparable to the reference efavirenz (EFV) (EC50 = 0.08 μM). The preliminary structure-activity relationship (SAR) indicated that introducing substitutions on C2 of the 4-cyanophenyl group could improve antiviral activity. Molecular docking predicted that the cyano-methylene linker was positioned into the hydrophobic cavity formed by Y181/Y188 and V179 residues.
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Affiliation(s)
- Ting-Ting Li
- Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China;
| | - 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.)
| | - Chun-Lin Zhuang
- Department of Chemistry, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Fen-Er Chen
- Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China;
- 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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Xiao T, Tang JF, Meng G, Pannecouque C, Zhu YY, Liu GY, Xu ZQ, Wu FS, Gu SX, Chen FE. Indazolyl-substituted piperidin-4-yl-aminopyrimidines as HIV-1 NNRTIs: Design, synthesis and biological activities. Eur J Med Chem 2020; 186:111864. [DOI: 10.1016/j.ejmech.2019.111864] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/25/2019] [Accepted: 11/06/2019] [Indexed: 11/25/2022]
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Said MA, Eldehna WM, Nocentini A, Bonardi A, Fahim SH, Bua S, Soliman DH, Abdel-Aziz HA, Gratteri P, Abou-Seri SM, Supuran CT. Synthesis, biological and molecular dynamics investigations with a series of triazolopyrimidine/triazole-based benzenesulfonamides as novel carbonic anhydrase inhibitors. Eur J Med Chem 2020; 185:111843. [PMID: 31718943 DOI: 10.1016/j.ejmech.2019.111843] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023]
Abstract
In the presented work, we report the design and synthesis of different new sets of triazolopyrimidine-based (9a-d) and triazole-based (11a-h, 13a-c, 15a,b, 17a,b and 21a-g) benzenesulfonamides. The newly synthesized sulfonamides were assessed for their inhibitory activities toward four human (h) metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) isoforms; hCA I, II, IX and XII. The four examined isoforms were inhibited by the prepared sulfonamides (9a-d, 11a-h, 13a-c, 15a,b, 17a,b and 21a-g) in variable degrees with KIs ranges: 94.4-4953.5 nM for hCA I, 6.9-837.6 nM for hCA II, 3.3-85.0 nM for hCA XI, and 4.4-105.0 nM for hCA XII. In particular, sulfonamides 11e, 21a and 21e emerged as single-digit nanomolar hCA IX and hCA XII inhibitors. Interestingly, triazolopyrimidine-based sulfonamide 9d and triazole-based sulfonamide 21e were found to be the most selective hCA IX inhibitors over hCA I (SI = 100.85 and 210.58, respectively) and hCA II (SI = 18.54 and 38.36, respectively). Thereafter, sulfonamides 9d and 21e were docked into the active site of CAs II, IX and XII, then poses showing the best scoring values and favorable binding interactions were subjected to a MM-GBSA based refinement and, limited to CA IX and XII, to a cycle of 100 ns molecular dynamics.
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Affiliation(s)
- Mohamed A Said
- Department of Pharmaceutical Chemistry, College of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33516, Egypt.
| | - Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy; Department of NEUROFARBA - Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Alessandro Bonardi
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy; Department of NEUROFARBA - Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Samar H Fahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Silvia Bua
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Dalia H Soliman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al Azhar University, Cairo, P.O. Box 11471, Egypt
| | - Hatem A Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Cairo, 12622, Egypt
| | - Paola Gratteri
- Department of NEUROFARBA - Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Sahar M Abou-Seri
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy.
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Gu SX, Lu HH, Liu GY, Ju XL, Zhu YY. Advances in diarylpyrimidines and related analogues as HIV-1 nonnucleoside reverse transcriptase inhibitors. Eur J Med Chem 2018; 158:371-392. [PMID: 30223123 DOI: 10.1016/j.ejmech.2018.09.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/01/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022]
Abstract
HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs) have been playing an important role in the fight against acquired immunodeficiency syndrome (AIDS). Diarylpyrimidines (DAPYs) as the second generation NNRTIs, represented by etravirine (TMC125) and rilpivirine (TMC278), have attracted extensive attention due to their extraordinary potency, high specificity and low toxicity. However, the rapid emergence of drug-resistant virus strains and dissatisfactory pharmacokinetics of DAPYs present new challenges. In the past two decades, an increasing number of novel DAPY derivatives have emerged, which significantly enriched the structure-activity relationship of DAPYs. Studies of crystallography and molecular modeling have afforded a lot of useful information on structural requirements of NNRTIs, which contributes greatly to the improvement of their resistance profiles. In this review, we reviewed the discovery history and their evolution of DAPYs including their structural modification, derivatization and scaffold hopping in continuous pursuit of excellent anti-HIV drugs. And also, we discussed the prospect of DAPYs and the directions of future efforts.
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Affiliation(s)
- Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China.
| | - Huan-Huan Lu
- Yichang Humanwell Pharmaceutical Co., Ltd, Yichang, 443005, PR China
| | - Gen-Yan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China
| | - Xiu-Lian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430205, PR China.
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Liu G, Wang W, Wan Y, Ju X, Gu S. Application of 3D-QSAR, Pharmacophore, and Molecular Docking in the Molecular Design of Diarylpyrimidine Derivatives as HIV-1 Nonnucleoside Reverse Transcriptase Inhibitors. Int J Mol Sci 2018; 19:ijms19051436. [PMID: 29751616 PMCID: PMC5983643 DOI: 10.3390/ijms19051436] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 12/17/2022] Open
Abstract
Diarylpyrimidines (DAPYs), acting as HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs), have been considered to be one of the most potent drug families in the fight against acquired immunodeficiency syndrome (AIDS). To better understand the structural requirements of HIV-1 NNRTIs, three-dimensional quantitative structure–activity relationship (3D-QSAR), pharmacophore, and molecular docking studies were performed on 52 DAPY analogues that were synthesized in our previous studies. The internal and external validation parameters indicated that the generated 3D-QSAR models, including comparative molecular field analysis (CoMFA, q2 = 0.679, R2 = 0.983, and rpred2 = 0.884) and comparative molecular similarity indices analysis (CoMSIA, q2 = 0.734, R2 = 0.985, and rpred2 = 0.891), exhibited good predictive abilities and significant statistical reliability. The docking results demonstrated that the phenyl ring at the C4-position of the pyrimidine ring was better than the cycloalkanes for the activity, as the phenyl group was able to participate in π–π stacking interactions with the aromatic residues of the binding site, whereas the cycloalkanes were not. The pharmacophore model and 3D-QSAR contour maps provided significant insights into the key structural features of DAPYs that were responsible for the activity. On the basis of the obtained information, a series of novel DAPY analogues of HIV-1 NNRTIs with potentially higher predicted activity was designed. This work might provide useful information for guiding the rational design of potential HIV-1 NNRTI DAPYs.
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Affiliation(s)
- Genyan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Wenjie Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Youlan Wan
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Xiulian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Shuangxi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China.
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Valuev-Elliston VT, Kochetkov SN. Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors: A Combinatorial Approach. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523068 DOI: 10.1134/s0006297917130107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Highly active antiretroviral therapy (HAART) is one of the most effective means for fighting against HIV-infection. HAART primarily targets HIV-1 reverse transcriptase (RT), and 14 of 28 compounds approved by the FDA as anti-HIV drugs act on this enzyme. HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) hold a special place among HIV RT inhibitors owing to their high specificity and unique mode of action. Nonetheless, these drugs show a tendency to decrease their efficacy due to high HIV-1 variability and formation of resistant virus strains tolerant to clinically applied HIV NNRTIs. A combinatorial approach based on varying substituents within various fragments of the parent molecule that results in development of highly potent compounds is one of the approaches aimed at designing novel HIV NNRTIs. Generation of HIV NNRTIs based on pyrimidine derivatives explicitly exemplifies this approach, which is discussed in this review.
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Affiliation(s)
- V T Valuev-Elliston
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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Lu HH, Xue P, Zhu YY, Ju XL, Zheng XJ, Zhang X, Xiao T, Pannecouque C, Li TT, Gu SX. Structural modifications of diarylpyrimidines (DAPYs) as HIV-1 NNRTIs: Synthesis, anti-HIV activities and SAR. Bioorg Med Chem 2017; 25:2491-2497. [DOI: 10.1016/j.bmc.2017.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/04/2017] [Accepted: 03/05/2017] [Indexed: 12/01/2022]
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Xue P, Lu HH, Zhu YY, Ju XL, Pannecouque C, Zheng XJ, Liu GY, Zhang XL, Gu SX. Design and synthesis of hybrids of diarylpyrimidines and diketo acids as HIV-1 inhibitors. Bioorg Med Chem Lett 2017; 27:1640-1643. [PMID: 28314598 DOI: 10.1016/j.bmcl.2017.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 02/22/2017] [Accepted: 03/06/2017] [Indexed: 10/20/2022]
Abstract
Based on the strategy of molecular hybridization, diketo acid fragment as a classical phamacophore of integrase inhibitors was introduced to reverse transcriptase inhibitors diarylpyrimidines to design a series of diarylpyrimidine-diketo acid hybrids (DAPY-DKAs). The target molecules 10b and 11b showed inhibitory activities against WT HIV-1 with EC50 values of 0.18μM and 0.14μM, respectively. And the results of molecular docking demonstrated the potential binding mode and revealed that the DKA moiety and its ester could both be tolerated in the nonnucleoside binding site (NNBS) of HIV-1 RT.
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Affiliation(s)
- Ping Xue
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Huan-Huan Lu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Xiu-Lian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Christophe Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Xiao-Jiao Zheng
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, 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
| | - Xiu-Lan Zhang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - 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.
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A novel family of diarylpyrimidines (DAPYs) featuring a diatomic linker: Design, synthesis and anti-HIV activities. Bioorg Med Chem 2015; 23:6587-93. [DOI: 10.1016/j.bmc.2015.09.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 11/22/2022]
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Double Variational Binding--(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands. Int J Mol Sci 2015; 16:19553-601. [PMID: 26295229 PMCID: PMC4581313 DOI: 10.3390/ijms160819553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/11/2015] [Indexed: 12/11/2022] Open
Abstract
Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process.
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Laxminarayana B, Kundu LM. Direct Chemoselective Synthesis of N-3-Substituted Pyrimidinones in a Microwave-Assisted Method. SYNTHETIC COMMUN 2015. [DOI: 10.1080/00397911.2015.1017770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | - Lal Mohan Kundu
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, India
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Chen X, Li Y, Ding S, Balzarini J, Pannecouque C, De Clercq E, Liu H, Liu X. Discovery of Piperidine-Linked Pyridine Analogues as Potent Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors. ChemMedChem 2013; 8:1117-26. [DOI: 10.1002/cmdc.201300130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Indexed: 11/10/2022]
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Design, synthesis, anti-HIV evaluation and molecular modeling of piperidine-linked amino-triazine derivatives as potent non-nucleoside reverse transcriptase inhibitors. Bioorg Med Chem 2012; 20:3856-64. [DOI: 10.1016/j.bmc.2012.04.030] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/11/2012] [Accepted: 04/16/2012] [Indexed: 01/17/2023]
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