1
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Li D, Zhang C, Ding W, Huang S, Yu L, Lu N, Pan W, Li Y, De Clercq E, Pannecouque C, Zhang H, Wang Y, He Y, Chen F. Structure-based linker optimization of 6-(2-cyclohexyl-1-alkyl)-2-(2-oxo-2-phenylethylsulfanyl)pyrimidin-4(3H)-ones as potent non-nucleoside HIV-1 reverse transcriptase inhibitors. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.09.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Wu Y, Tang C, Rui R, Yang L, Ding W, Wang J, Li Y, Lai CC, Wang Y, Luo R, Xiao W, Zhang H, Zheng Y, He Y. Synthesis and biological evaluation of a series of 2-(((5-akly/aryl-1 H-pyrazol-3-yl)methyl)thio)-5-alkyl-6-(cyclohexylmethyl)-pyrimidin-4(3 H)-ones as potential HIV-1 inhibitors. Acta Pharm Sin B 2020; 10:512-528. [PMID: 32140396 PMCID: PMC7049619 DOI: 10.1016/j.apsb.2019.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 01/16/2023] Open
Abstract
A series of 2-(((5-akly/aryl-1H-pyrazol-3-yl)methyl)thio)-5-alkyl-6-(cyclohexylmethyl)-pyrimidin-4(3H)-ones were synthesized and their anti-HIV-1 activities were evaluated. Most of these compounds were highly active against wild-type (WT) HIV-1 strain (IIIB) with EC50 values in the range of 0.0038–0.4759 μmol/L. Among those compounds, I-11 had an EC50 value of 3.8 nmol/L and SI (selectivity index) of up to 25,468 indicating excellent activity against WT HIV-1. In vitro anti-HIV-1 activity and resistance profile studies suggested that compounds I-11 and I-12 displayed potential anti-HIV-1 activity against laboratory adapted strains and primary isolated strains including different subtypes and tropism strains (EC50s range from 4.3 to 63.6 nmol/L and 18.9–219.3 nmol/L, respectively). On the other hand, it was observed that those two compounds were less effective with EC50 values of 2.77 and 4.87 μmol/L for HIV-1A17 (K103N + Y181C). The activity against reverse transcriptase (RT) was also evaluated for those compounds. Both I-11 and I-12 obtained sub-micromolar IC50 values showing their potential in RT inhibition. The pharmacokinetics examination in rats indicated that compound I-11 has acceptable pharmacokinetic properties and bioavailability. Preliminary structure–activity relationships and molecular modeling studies were also discussed.
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Affiliation(s)
- Yumeng Wu
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Chengrun Tang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, the National Kunming High Level Biosafety Research Center for Nonhuman Primate, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Ruomei Rui
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Liumeng Yang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, the National Kunming High Level Biosafety Research Center for Nonhuman Primate, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wei Ding
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Jiangyuan Wang
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Yiming Li
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Christopher C. Lai
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yueping Wang
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Ronghua Luo
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, the National Kunming High Level Biosafety Research Center for Nonhuman Primate, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Weilie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Hongbing Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
- Corresponding authors. Tel./ fax: +86 871 65035538.
| | - Yongtang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, the National Kunming High Level Biosafety Research Center for Nonhuman Primate, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Corresponding authors. Tel./ fax: +86 871 65035538.
| | - Yanping He
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
- Corresponding authors. Tel./ fax: +86 871 65035538.
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3
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El-Brollosy NR, Al-Omar MA, Al-Deeb OA, El-Emam AA, Nielsen C. Synthesis of Novel Uracil Non-Nucleosides Analogues of 3,4-Dihydro-2-Alkylthio-6-benzyl-4-oxopyrimidines and 6-benzyl-1-ethoxymethyl-5-isopropyluracil. JOURNAL OF CHEMICAL RESEARCH 2019. [DOI: 10.3184/030823407x210893] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A series of new uracil non-nucleosides analogues of S-DABO's was synthesised by reaction of 5-alkyl-6-( p-chlorobenzyl)-2-thiouracils with chloroethyl dialkylamine hydrochloride, N-(2-chloroethyl)-pyrrolidine hydrochloride, N-(2-chloroethyl)-piperidine hydrochloride or appropriate haloethers. Novel emivirine analogues were synthesised by silylation of 5-alkyl-6-( p-chlorobenzyl)uracils and treatment with bromomethyl methyl ether, chloromethyl ethyl ether or benzyl chloromethyl ether. Compounds 6-( p-chlorobenzyl)-5-ethyl-1-ethyloxymethyluracil (9e) and 1-benzyloxymethyl-6-(4-chlorobenzyl)-5-ethyluracil (9f) showed activity against wild-type HIV-1 strain III B in MT-4 cells.
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Affiliation(s)
- Nasser R. El-Brollosy
- Department of Pharmaceutical Chemistry, College of Pharmacy. King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed A. Al-Omar
- Department of Pharmaceutical Chemistry, College of Pharmacy. King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar A. Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy. King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy. King Saud University, Riyadh 11451, Saudi Arabia
| | - Claus Nielsen
- Retrovirus Laboratory, Department of Virology, State Serum Institute, DK-2300 Copenhagen, Denmark
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4
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Nawrozkij MB, Forgione M, Yablokov AS, Lucidi A, Tomaselli D, Patsilinakos A, Panella C, Hailu GS, Kirillov IA, Badia R, Riveira-Muñoz E, Crespan E, Armijos Rivera JI, Cirilli R, Ragno R, Esté JA, Maga G, Mai A, Rotili D. Effect of α-Methoxy Substitution on the Anti-HIV Activity of Dihydropyrimidin-4(3H)-ones. J Med Chem 2018; 62:604-621. [DOI: 10.1021/acs.jmedchem.8b01238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Maxim B. Nawrozkij
- Volgograd State Technical University, Lenina Avenue 28, 400005 Volgograd, Russia
| | - Mariantonietta Forgione
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | | | - Alessia Lucidi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Daniela Tomaselli
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Alexandros Patsilinakos
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Cristina Panella
- Centro Nazionale per il Controllo e la Valutazione dei Farmaci, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Gebremedhin S. Hailu
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Ivan A. Kirillov
- Volgograd State Technical University, Lenina Avenue 28, 400005 Volgograd, Russia
| | - Roger Badia
- IrsiCaixa-AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Eva Riveira-Muñoz
- IrsiCaixa-AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | | | - Roberto Cirilli
- Centro Nazionale per il Controllo e la Valutazione dei Farmaci, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Rino Ragno
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - José A. Esté
- IrsiCaixa-AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Giovanni Maga
- Istituto di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
- Istituto Pasteur—Fondazione Cenci Bolognetti, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Dante Rotili
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
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5
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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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6
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C(2)-Functionalization of pyrimidin-4(3H)-one derivatives in the synthesis of its biologically active derivatives. Russ Chem Bull 2016. [DOI: 10.1007/s11172-015-1190-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Massa S, Mai A, Artico M, Sbardella G, Tramontano E, Loi AG, Scano P, La Colla P. Synthesis and Antiviral Activity of New 3,4-Dihydro-2-Alkoxy-6-Benzyl-4-Oxopyrimidines (DABOs), Specific Inhibitors of Human Immunodeficiency Virus Type 1. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029500600101] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
3,4-Dihydro-2-alkoxy-6-benzyl-4-oxopyrimidines (DABOs) have emerged as non-nucleoside inhibitors of human immunodeficiency virus type 1 [Artico et al. (1993), Antiviral Chem Chemother 4: 361-368]. With a view to increasing their potency, a new series of DABO derivatives, differently substituted at positions C-2 and/or C-5 of the pyrimidine ring and 3′ or 3′,5′ of the benzyl moiety, have been synthesized. DABOs were prepared by reacting O-methylisourea with the appropriate methyl 2-alkyl-4-phenylacetylacetate, with formation of 3,4-dihydro-2-methoxy-6-arylmethyl-4-oxopyrimidines. Subsequent displacement of the methoxy group linked at the 2-position of the pyrimidine ring by treatment with alkoxy and cycloalkoxy potassium salts led to the required derivatives. In vitro, the most potent compounds were 12e and 12p, which had an EC50 of 0.8 μM and a selective index of 400.
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Affiliation(s)
- S. Massa
- Dipartimento di Studi Farmaceutici, Università di Roma ‘La Sapienza’, P. le A. Moro 5, 00185 Roma, Italy
| | - A. Mai
- Dipartimento di Studi Farmaceutici, Università di Roma ‘La Sapienza’, P. le A. Moro 5, 00185 Roma, Italy
| | - M. Artico
- Dipartimento di Studi Farmaceutici, Università di Roma ‘La Sapienza’, P. le A. Moro 5, 00185 Roma, Italy
| | - G. Sbardella
- Dipartimento di Studi Farmaceutici, Università di Roma ‘La Sapienza’, P. le A. Moro 5, 00185 Roma, Italy
| | - E. Tramontano
- Dipartimento di Biologia Sperimentale, Università di Cagliari, V. le Regina Margherita 45, 09124 Cagliari, Italy
| | - A. G. Loi
- Dipartimento di Biologia Sperimentale, Università di Cagliari, V. le Regina Margherita 45, 09124 Cagliari, Italy
| | - P. Scano
- Dipartimento di Biologia Sperimentale, Università di Cagliari, V. le Regina Margherita 45, 09124 Cagliari, Italy
| | - P. La Colla
- Dipartimento di Biologia Sperimentale, Università di Cagliari, V. le Regina Margherita 45, 09124 Cagliari, Italy
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8
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Al-Tamimi AMS, Ghabbour HA, El-Emam AA. Crystal structure of 6-oxo-4-propyl-2-(propylthio)-1,6-dihydropyrimidine-5-carbonitrile, C 11H 15N 3OS. Z KRIST-NEW CRYST ST 2016. [DOI: 10.1515/ncrs-2015-0198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C11H15N3OS, triclinic, P1̅ (no. 2), a = 4.6579(2) Å, b = 9.6316(5) Å, c = 13.6654(7) Å, α = 87.982(2)°, β = 87.330(2)°, γ = 78.403(2)°, V = 599.69(5) Å3, Z = 2, R
gt
(F) = 0.0450, wR
ref
(F
2
) = 0.128, T = 100 K.
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Affiliation(s)
- Abdul-Malek S. Al-Tamimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | | | - Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
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9
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Al-Wabli RI, Ghabbour HA, Lahsasni S, Al-Abdullah ES, El-Emam AA. Crystal structure of 5-ethyl-6-[(3-methylphenyl)sulfanyl]pyrimidine-2,4(1 H,3 H)-dione, C 13H 14N 2O 2S. Z KRIST-NEW CRYST ST 2016. [DOI: 10.1515/ncrs-2015-0207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C13H14N2O2S, triclinic, P1̅ (no. 2), a = 4.8885(2) Å, b = 10.3414(5) Å, c = 12.6056(6) Å, α = 95.162(2)°, β = 97.487(1)°, γ = 101.494°, V = 614.73(5) Å3, Z = 2, R
gt
(F) = 0.0507, wR
ref
(F
2
) = 0.1149, T = 100 K.
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Affiliation(s)
- Reem I. Al-Wabli
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riyadh 11451, Saudi Arabia
| | - Hazem A. Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riyadh 11451, Saudi Arabia
| | - Siham Lahsasni
- Department of Chemistry, College of Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ebtehal S. Al-Abdullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riyadh 11451, Saudi Arabia
| | - Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riyadh 11451, Saudi Arabia
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10
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Loksha YM, Pedersen EB, Loddo R, La Colla P. Synthesis and Anti-HIV-1 Evaluation of Some Novel MC-1220 Analogs as Non-Nucleoside Reverse Transcriptase Inhibitors. Arch Pharm (Weinheim) 2016; 349:363-72. [PMID: 26996241 DOI: 10.1002/ardp.201600008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/11/2022]
Abstract
Some novel MC-1220 analogs were synthesized by condensation of 4,6-dichloro-N-methylpyrimidin-2-amine derivatives (1a,b and 15) and/or 4-chloro-6-methoxy-N,N,5-trimethylpyrimidin-2-amine (2a) with the sodium salt of 2,6-difluorophenylacetonitrile followed by treatment with aqueous sodium hydroxide in methanol, alkylation, reduction, halogenation, and/or acidic hydrolysis. All synthesized compounds were evaluated for their activity against HIV-1. The most active compound in this study was compound 7, which showed activity against HIV-1 comparable to that of MC-1220. The only difference in structure between compound 7 and MC-1220 is a fluoro atom instead of a CH3 group.
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Affiliation(s)
- Yasser M Loksha
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, Odense M, Denmark.,Faculty of Pharmacy and Pharmaceutical Industries, Department of Pharmaceutical Chemistry, Sinai University, Al-Arish, North Sinai, Egypt
| | - Erik B Pedersen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, Odense M, Denmark
| | - Roberta Loddo
- Dipartimento di Scienze e Tecnologie Biomediche, Sezione di Microbiologia e Virologia Generale e Biotecnologie Microbiche, Universita di Cagliari, Monserrato, Italy
| | - Paolo La Colla
- Dipartimento di Scienze e Tecnologie Biomediche, Sezione di Microbiologia e Virologia Generale e Biotecnologie Microbiche, Universita di Cagliari, Monserrato, Italy
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11
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El-Emam AA, Ghabbour HA, Al-Deeb OA, Abdelbaky MSM, García-Granda S. Crystal structure of 2-[(4-fluorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile, C 16H 16FN 3OS. Z KRIST-NEW CRYST ST 2016. [DOI: 10.1515/ncrs-2015-0123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C16H16FN3OS, triclinic, P1̅ (no. 2), a = 5.6885(3) Å, b = 9.4378(4) Å, c = 15.0736(7) Å, α = 84.037(4)°, β = 81.442(4)°, γ = 74.271(4)°, V = 768.56(7) Å3, Z = 2, R
gt
(F) = 0.0518, wR
ref
(F
2
) = 0.1430, T = 100 K.
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Affiliation(s)
- Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
| | - Hazem A. Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
| | - Omar A. Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
| | - Mohammed S. M. Abdelbaky
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo – CINN, C/Julian Clavería, 8, 33006 Oviedo, (Asturias), Spain
| | - Santiago García-Granda
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
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12
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Spectroscopic and electronic structure calculation of a potential chemotherapeutic agent 5-propyl-6-(p-tolylsulfanyl)pyrimidine-2,4(1H,3H)-dione using first principles. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Dong M, Ren Y. Molecular modeling studies of dihydro-alkyloxy-benzyl-oxopyrimidines (DABOs) as non-nucleoside inhibitors of HIV-1 reverse transcriptase using 3D-QSAR, Topomer CoMFA and molecular docking simulations. RSC Adv 2015. [DOI: 10.1039/c4ra15397a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is generally regarded as a target for the treatment of acquired immune deficiency syndrome (AIDS).
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Affiliation(s)
- Minghui Dong
- School of Chemical and Environmental Engineering
- Shanghai Institute of Technology
- Shanghai
- P. R. China
| | - Yujie Ren
- School of Chemical and Environmental Engineering
- Shanghai Institute of Technology
- Shanghai
- P. R. China
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14
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Khalifa NM, Al-Omar MA. Synthesis and biological evaluation of 2-thioxopyrimidin-4(1H)-one derivatives as potential non-nucleoside HIV-1 reverse transcriptase inhibitors. Int J Mol Sci 2014; 15:20723-35. [PMID: 25397597 PMCID: PMC4264192 DOI: 10.3390/ijms151120723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/18/2014] [Accepted: 11/03/2014] [Indexed: 11/28/2022] Open
Abstract
A series of new 5-allyl-6-benzylpyrimidin-4(3H)-ones bearing different substituents at the C-2 position of the pyrimidine core have been synthesized and evaluated for their in vitro activities against human immunodeficiency virus type 1 (HIV-1) in the human T-lymphotropic type (MT-4 cell cultures). The majority of the title compounds showed moderate to good activities against HIV-1. Amongst them, 5-allyl-6-benzyl-2-(3-hydroxypropylthio)pyrimidin-4(3H)-one analogue 11c exhibited the most potent anti-HIV-1 activity (IC50 0.32 µM). The biological testing results clearly indicated that the substitution at C-2 position of the pyrimidine ring could increase the anti-HIV-1 reverse transcriptase (RT) activity.
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Affiliation(s)
- Nagy M Khalifa
- Pharmaceutical Chemistry Department, Drug Exploration & Development Chair, College of Pharmacy, King Saud University, Riyadh 11451, Saudia Arabia.
| | - Mohamed A Al-Omar
- Pharmaceutical Chemistry Department, Drug Exploration & Development Chair, College of Pharmacy, King Saud University, Riyadh 11451, Saudia Arabia.
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15
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Rotili D, Tarantino D, Nawrozkij MB, Babushkin AS, Botta G, Marrocco B, Cirilli R, Menta S, Badia R, Crespan E, Ballante F, Ragno R, Esté JA, Maga G, Mai A. Exploring the Role of 2-Chloro-6-fluoro Substitution in 2-Alkylthio-6-benzyl-5-alkylpyrimidin-4(3H)-ones: Effects in HIV-1-Infected Cells and in HIV-1 Reverse Transcriptase Enzymes. J Med Chem 2014; 57:5212-25. [DOI: 10.1021/jm500284x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Dante Rotili
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Domenico Tarantino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Maxim B. Nawrozkij
- Volgograd State Technical University, pr. Lenina, 28, 400131 Volgograd, Russia
| | | | - Giorgia Botta
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Roberto Cirilli
- Dipartimento
del Farmaco, Istituto Superiore di Sanità,, Viale Regina Elena 299, 00161 Rome, Italy
| | - Sergio Menta
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Roger Badia
- IrsiCaixa,
Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Emmanuele Crespan
- Istituto
di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Flavio Ballante
- Rome Center
for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
- Department
of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, 700 South Euclid Avenue, St. Louis, Missouri 00185, United States
| | - Rino Ragno
- Rome Center
for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - José A. Esté
- IrsiCaixa,
Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Giovanni Maga
- Istituto
di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Antonello Mai
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
- Istituto
Pasteur—Fondazione Cenci Bolognetti, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
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16
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Zhang L, Tang X, Cao Y, Wu S, Zhang Y, Zhao J, Guo Y, Tian C, Zhang Z, Liu J, Wang X. Synthesis and biological evaluation of novel 2-arylalkylthio-5-iodine-6-substituted-benzyl-pyrimidine-4(3H)-ones as potent HIV-1 non-nucleoside reverse transcriptase inhibitors. Molecules 2014; 19:7104-21. [PMID: 24886938 PMCID: PMC6271041 DOI: 10.3390/molecules19067104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/26/2014] [Accepted: 05/28/2014] [Indexed: 11/25/2022] Open
Abstract
A novel series of 2-arylalkylthio-5-iodine-6-substitutedbenzyl-pyrimidine-4(3H)-ones (S-DABOs) 8a-x had been synthesized via an efficient method. Their biological activity against HIV virus and RT assay were evaluated. Some compounds, especially 8h, 8l and 8n, displayed promising activity against HIV-1 RT with IC50 values in a range of 0.41 μM to 0.71 μM, which were much better than that of nevirapine. Molecular modeling studies revealed that the binding mode would be affected via forming an additional hydrogen bond by incorporating an oxygen atom on the C-2 side chain. The biological activity was in accordance with the docking results.
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Affiliation(s)
- Liang Zhang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaowan Tang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuanyuan Cao
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Shaotong Wu
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yu Zhang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jianxiong Zhao
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ying Guo
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chao Tian
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhili Zhang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Junyi Liu
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Xiaowei Wang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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17
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Towards new C6-rigid S-DABO HIV-1 reverse transcriptase inhibitors: synthesis, biological investigation and molecular modeling studies. Bioorg Med Chem 2013; 21:6477-83. [PMID: 24055077 DOI: 10.1016/j.bmc.2013.08.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/19/2013] [Accepted: 08/21/2013] [Indexed: 11/21/2022]
Abstract
A series of C6-rigid S-DABO analogs characterized by a substituted benzoyl group at C6 position of the pyrimidine ring has been synthesized and biological evaluation as NNRTIs against wild-type HIV-1 strain IIIB, double RT mutant (K103N+Y181C) strain RES056 as well as HIV-2 strain ROD in MT-4 cell cultures. Most of the compounds exhibited moderate antiviral activities. Among them, compound 7q displayed the highest anti-HIV-1 activity with an EC50 value of 0.26μM and a selectivity index (SI) of 541. The preliminary structure-activity relationship (SAR) of these new S-DABOs was investigated, the target RT was confirmed and docking study was performed.
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18
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6-(Arylmethyl)pyrimidin-4(3H)-ones: anthology and prospects of highly efficient anti-HIV agents. Russ Chem Bull 2013. [DOI: 10.1007/s11172-012-0182-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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19
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Esposito F, Corona A, Zinzula L, Kharlamova T, Tramontano E. New anthraquinone derivatives as inhibitors of the HIV-1 reverse transcriptase-associated ribonuclease H function. Chemotherapy 2012; 58:299-307. [PMID: 23128501 DOI: 10.1159/000343101] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 08/31/2012] [Indexed: 02/02/2023]
Abstract
BACKGROUND The degradative activity of the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), termed ribonuclease H (RNase H), which hydrolyzes the RNA component of the heteroduplex RNA:DNA replication intermediate, is an excellent target for drug discovery. Anthraquinones (AQs) and their derivatives, which are common secondary metabolites occurring in bacteria, fungi, lichens and a large number of families in higher plants, have been reported to have several biological activities including that of inhibiting HIV-1 RT activities in biochemical assays. METHODS We have assayed new AQ derivatives on HIV-1 RNase H activities in biochemical assays. RESULTS Six series of new AQ derivatives with various substituents at positions 1, 2, 3 and 4 of the AQ ring were tested, and new analogs able to inhibit HIV-1 RT-associated RNase H activity in the low micromolar range were found. CONCLUSIONS Our results demonstrate that AQ derivatives are promising anti-RNase H inhibitors.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy.
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20
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Romeo R, Giofrè SV, Macchi B, Balestrieri E, Mastino A, Merino P, Carnovale C, Romeo G, Chiacchio U. Truncated Reverse Isoxazolidinyl Nucleosides: A New Class of Allosteric HIV-1 Reverse Transcriptase Inhibitors. ChemMedChem 2012; 7:565-9. [DOI: 10.1002/cmdc.201200022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Indexed: 01/03/2023]
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21
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Al-Abdullah ES, Al-Obaid ARM, Al-Deeb OA, Habib EE, El-Emam AA. Synthesis of novel 6-phenyl-2,4-disubstituted pyrimidine-5-carbonitriles as potential antimicrobial agents. Eur J Med Chem 2011; 46:4642-7. [PMID: 21849221 DOI: 10.1016/j.ejmech.2011.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 08/01/2011] [Accepted: 08/02/2011] [Indexed: 10/18/2022]
Abstract
New series of 6-phenyl-2,4-disubstituted pyrimidine-5-carbonitriles namely, 2-substitued thio-6-phenyl-3,4-dihydro-4-oxopyrimidine-5-carbonitriles (5a-d, 6, 7a-d, 8), 2-(4-chlorobenzylthio)-4-chloro-6-phenylpyrimidine-5-carbonitrile (9), 2-(4-chlorobenzylthio)-4-arylthio-6-phenylpyrimidine-5-carbonitriles (10a-d) and 2-(4-chlorobenzylthio)-4-arylamino-6-phenylpyrimidine-5-carbonitriles (11a-d) was synthesized and tested for in vitro activities against a panel of Gram-positive and Gram-negative bacteria and the yeast-like pathogenic fungus Candida albicans. Compounds 5b, 5c, 6, 7a, 7b, 7c, 9 and 11a displayed marked antibacterial activity particularly against the tested Gram-positive bacteria, while compounds 6, 7c, 7d and 9 were moderately or weakly active against C. albicans.
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Affiliation(s)
- Ebtehal S Al-Abdullah
- Department of Pharmaceutical Chemistry, PO Box 2457, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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22
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Sbardella G, Mai A, Bartolini S, Castellano S, Cirilli R, Rotili D, Milite C, Santoriello M, Orlando S, Sciamanna I, Serafino A, Lavia P, Spadafora C. Modulation of Cell Differentiation, Proliferation, and Tumor Growth by Dihydrobenzyloxopyrimidine Non-Nucleoside Reverse Transcriptase Inhibitors. J Med Chem 2011; 54:5927-36. [DOI: 10.1021/jm200734j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Gianluca Sbardella
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Antonello Mai
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P.le A. Moro 5, I-00185 Rome, Italy
| | - Sara Bartolini
- Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Rome, Italy
| | - Sabrina Castellano
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Roberto Cirilli
- Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Rome, Italy
| | - Dante Rotili
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P.le A. Moro 5, I-00185 Rome, Italy
| | - Ciro Milite
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Marisabella Santoriello
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Serena Orlando
- Istituto di Biologia Molecolare e Patologia, CNR, c/o Sapienza Università di Roma, Via degli Apuli 4, I-00185 Rome, Italy
| | - Ilaria Sciamanna
- Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Rome, Italy
| | - Annalucia Serafino
- Istituto di Farmacologia Traslazionale, CNR, Via Fosso del Cavaliere 100, 00133, Rome, Italy
| | - Patrizia Lavia
- Istituto di Biologia Molecolare e Patologia, CNR, c/o Sapienza Università di Roma, Via degli Apuli 4, I-00185 Rome, Italy
| | - Corrado Spadafora
- Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Rome, Italy
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23
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Zhan P, Chen X, Li D, Fang Z, De Clercq E, Liu X. HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design. Med Res Rev 2011; 33 Suppl 1:E1-72. [PMID: 21523792 DOI: 10.1002/med.20241] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) nowadays represent very potent and most promising anti-AIDS agents that specifically target the HIV-1 reverse transcriptase (RT). However, the effectiveness of NNRTI drugs can be hampered by rapid emergence of drug-resistant viruses and severe side effects upon long-term use. Therefore, there is an urgent need to develop novel, highly potent NNRTIs with broad spectrum antiviral activity and improved pharmacokinetic properties, and more efficient strategies that facilitate and shorten the drug discovery process would be extremely beneficial. Fortunately, the structural diversity of NNRTIs provided a wide space for novel lead discovery, and the pharmacophore similarity of NNRTIs gave valuable hints for lead discovery and optimization. More importantly, with the continued efforts in the development of computational tools and increased crystallographic information on RT/NNRTI complexes, structure-based approaches using a combination of traditional medicinal chemistry, structural biology, and computational chemistry are being used increasingly in the design of NNRTIs. First, this review covers two decades of research and development for various NNRTI families based on their chemical scaffolds, and then describes the structural similarity of NNRTIs. We have attempted to assemble a comprehensive overview of the general approaches in NNRTI lead discovery and optimization reported in the literature during the last decade. The successful applications of medicinal chemistry strategies, crystallography, and computational tools for designing novel NNRTIs are highlighted. Future directions for research are also outlined.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, PR China
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24
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Yu M, Li Z, Liu S, Fan E, Pannecouque C, De Clercq E, Liu X. Synthesis and biological evaluation of 6-substituted 5-alkyl-2-(phenylaminocarbonylmethylthio)pyrimidin-4(3H)-ones as potent HIV-1 NNRTIs. ChemMedChem 2011; 6:826-33. [PMID: 21322110 DOI: 10.1002/cmdc.201000555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 01/05/2011] [Indexed: 01/28/2023]
Abstract
A series of new 5-alkyl-2-phenylaminocarbonylmethylthiopyrimidin-4(3H)-ones bearing variously substituted arylmethyl moieties at the C6 position of the pyrimidine ring were synthesized and evaluated for anti-HIV activity in MT-4 cells. Most of these new congeners exhibited moderate to good activities against the wild-type virus, with EC(50) values in the range of 1.40-0.19 μM. Among them, 2-[(4-cyanophenylamino)carbonylmethylthio]-6-(2-chloro-6-fluorobenzyl)-5-ethylpyrimidin-4(3H)-one 4 b6 is one of the compounds endowed with the highest broad-spectrum HIV-1 inhibitory activity, with EC(50) values of 0.19±0.005 μM against the wild-type virus, 1.05±0.24 μM (twofold resistance) against the E138K strain, and 2.38±0.13 μM (4.5-fold resistance) against the Y181C strain. Furthermore, reverse transcriptase (RT) inhibition assays against wild-type HIV-1 RT were performed with selected derivatives, confirming that the main target of these compounds is HIV-1 RT and that these new S-DABO analogues act as non-nucleoside RT inhibitors (NNRTIs). Structure-activity relationship and molecular modeling analyses of these new congeners are also discussed.
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Affiliation(s)
- Mingyan Yu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
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25
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Yu M, Liu X, Li Z, Liu S, Pannecouque C, Clercq ED. Synthesis and biological evaluation of novel 2-(substituted phenylaminocarbonylmethylthio)-6-(2,6-dichlorobenzyl)-pyrimidin-4(3H)-ones as potent HIV-1 NNRTIs. Bioorg Med Chem 2009; 17:7749-54. [DOI: 10.1016/j.bmc.2009.09.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 09/17/2009] [Accepted: 09/18/2009] [Indexed: 11/27/2022]
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26
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Prajapati DG, Ramajayam R, Yadav MR, Giridhar R. The search for potent, small molecule NNRTIs: A review. Bioorg Med Chem 2009; 17:5744-62. [PMID: 19632850 DOI: 10.1016/j.bmc.2009.06.060] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/22/2009] [Accepted: 06/23/2009] [Indexed: 11/29/2022]
Abstract
AIDS has become the leading pandemic disease, and is the cause of death worldwide. Presently, HAART treatment, a combination of reverse transcriptase (RT) and protease inhibitors is also unsuccessful due to the virus getting resistant to the drugs because of mutational changes. Two types of RT inhibitors exist namely nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). The NNRTIs which bind to an allosteric site on RT are an important arsenal of drugs against HIV-1. The specificity of NNRTIs towards HIV-1 has led to extensive structural and molecular modelling studies of enzyme complexes and chemical synthesis of second and third-generation NNRTIs. The major drawbacks of NNRTIs are generation of resistance and pharmacokinetic problems. By mutational studies of non-nucleoside inhibitor binding pocket (NNIBP) some amino acids which were found to play an important role in proper binding resulted less prone to mutation. In this review we present a chronological history of NNRTI development, also highlighting the need for small molecules belonging to the NNRTI class for the management of AIDS.
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Affiliation(s)
- Dhaval G Prajapati
- Pharmacy Department, Kalabhavan, The M.S. University of Baroda, Vadodara, India
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27
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Samuele A, Facchini M, Rotili D, Mai A, Artico M, Armand-Ugón M, Esté J, Maga G. Substrate-Induced Stable Enzyme-Inhibitor Complex Formation Allows Tight Binding of Novel 2-Aminopyrimidin-4(3H)-ones to Drug-Resistant HIV-1 Reverse Transcriptase Mutants. ChemMedChem 2008; 3:1412-8. [DOI: 10.1002/cmdc.200800051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Brito MAD, Rodrigues CR, Cirino JJV, de Alencastro RB, Castro HC, Albuquerque MG. 3D-QSAR CoMFA of a Series of DABO Derivatives as HIV-1 Reverse Transcriptase Non-Nucleoside Inhibitors. J Chem Inf Model 2008; 48:1706-15. [DOI: 10.1021/ci8001217] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Monique Araújo de Brito
- Programa de Pós-Graduação em Química Orgânica, Departamento de Química Orgânica, Laboratório de Modelagem Molecular (LabMMol), Instituto de Química, CCMN, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-909, Departamento de Medicamentos, Laboratório de Modelagem Molecular e QSAR (ModMolQSAR), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, CCS, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-590, and Departamento de Biologia Celular e Molecular, Laboratório de Antibióticos, Bioquímica
| | - Carlos Rangel Rodrigues
- Programa de Pós-Graduação em Química Orgânica, Departamento de Química Orgânica, Laboratório de Modelagem Molecular (LabMMol), Instituto de Química, CCMN, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-909, Departamento de Medicamentos, Laboratório de Modelagem Molecular e QSAR (ModMolQSAR), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, CCS, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-590, and Departamento de Biologia Celular e Molecular, Laboratório de Antibióticos, Bioquímica
| | - José Jair Vianna Cirino
- Programa de Pós-Graduação em Química Orgânica, Departamento de Química Orgânica, Laboratório de Modelagem Molecular (LabMMol), Instituto de Química, CCMN, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-909, Departamento de Medicamentos, Laboratório de Modelagem Molecular e QSAR (ModMolQSAR), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, CCS, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-590, and Departamento de Biologia Celular e Molecular, Laboratório de Antibióticos, Bioquímica
| | - Ricardo Bicca de Alencastro
- Programa de Pós-Graduação em Química Orgânica, Departamento de Química Orgânica, Laboratório de Modelagem Molecular (LabMMol), Instituto de Química, CCMN, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-909, Departamento de Medicamentos, Laboratório de Modelagem Molecular e QSAR (ModMolQSAR), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, CCS, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-590, and Departamento de Biologia Celular e Molecular, Laboratório de Antibióticos, Bioquímica
| | - Helena Carla Castro
- Programa de Pós-Graduação em Química Orgânica, Departamento de Química Orgânica, Laboratório de Modelagem Molecular (LabMMol), Instituto de Química, CCMN, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-909, Departamento de Medicamentos, Laboratório de Modelagem Molecular e QSAR (ModMolQSAR), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, CCS, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-590, and Departamento de Biologia Celular e Molecular, Laboratório de Antibióticos, Bioquímica
| | - Magaly Girão Albuquerque
- Programa de Pós-Graduação em Química Orgânica, Departamento de Química Orgânica, Laboratório de Modelagem Molecular (LabMMol), Instituto de Química, CCMN, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-909, Departamento de Medicamentos, Laboratório de Modelagem Molecular e QSAR (ModMolQSAR), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, CCS, UFRJ, Rio de Janeiro, RJ, Brazil, CEP 21941-590, and Departamento de Biologia Celular e Molecular, Laboratório de Antibióticos, Bioquímica
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29
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Nawrozkij MB, Rotili D, Tarantino D, Botta G, Eremiychuk AS, Musmuca I, Ragno R, Samuele A, Zanoli S, Armand-Ugón M, Clotet-Codina I, Novakov IA, Orlinson BS, Maga G, Esté JA, Artico M, Mai A. 5-Alkyl-6-benzyl-2-(2-oxo-2-phenylethylsulfanyl)pyrimidin-4(3H)-ones, a series of anti-HIV-1 agents of the dihydro-alkoxy-benzyl-oxopyrimidine family with peculiar structure-activity relationship profile. J Med Chem 2008; 51:4641-52. [PMID: 18630898 DOI: 10.1021/jm800340w] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of dihydro-alkylthio-benzyl-oxopyrimidines (S-DABOs) bearing a 2-aryl-2-oxoethylsulfanyl chain at pyrimidine C2, an alkyl group at C5, and a 2,6-dichloro-, 2-chloro-6-fluoro-, and 2,6-difluoro-benzyl substitution at C6 (oxophenethyl- S-DABOs, 6-8) is here described. The new compounds showed low micromolar to low nanomolar (in one case subnanomolar) inhibitory activity against wt HIV-1. Against clinically relevant HIV-1 mutants (K103N, Y181C, and Y188L) as well as in enzyme (wt and K103N, Y181I, and L100I mutated RTs) assays, compounds carrying an ethyl/ iso-propyl group at C5 and a 2,6-dichloro-/2-chloro-6-fluoro-benzyl moiety at C6 were the most potent derivatives, also characterized by low fold resistance ratio. Interestingly, the structure-activity relationship (SAR) data drawn from this DABO series are more related to HEPT than to DABO derivatives. These findings were at least in part rationalized by the description of a fair superimposition between the 6-8 and TNK-651 (a HEPT analogue) binding modes in both WT and Y181C RTs.
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Affiliation(s)
- Maxim B Nawrozkij
- Volgograd State Technical UniVersity, Pr Lenina, 28, 400131 Volgograd, Russia
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Mai A, Artico M, Rotili D, Tarantino D, Clotet-Codina I, Armand-Ugón M, Ragno R, Simeoni S, Sbardella G, Nawrozkij MB, Samuele A, Maga G, Esté JA. Synthesis and biological properties of novel 2-aminopyrimidin-4(3H)-ones highly potent against HIV-1 mutant strains. J Med Chem 2007; 50:5412-24. [PMID: 17910429 DOI: 10.1021/jm070811e] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following the disclosure of dihydro-alkoxy-, dihydro-alkylthio-, and dihydro-alkylamino-benzyl-oxopyrimidines (DABOs, S-DABOs, and NH-DABOs) as potent and selective anti-HIV-1 agents belonging to the non-nucleoside reverse transcriptase inhibitor (NNRTI) class, we report here the synthesis and biological evaluation of a novel series of DABOs bearing a N,N-disubstituted amino group or a cyclic amine at the pyrimidine-C2 position, a hydrogen atom or a small alkyl group at C5 and/or at the benzylic position, and the favorable 2,6-difluorobenzyl moiety at the C6 position (F2-N,N-DABOs). The new compounds were highly active up to the subnanomolar level against both wt HIV-1 and the Y181C mutant and at the submicromolar to nanomolar range against the K103N and Y188L mutant strains. Such derivatives were more potent than S-DABOs, NH-DABOs, and nevirapine and efavirenz were chosen as reference drugs. The higher inhibitor adaptability to the HIV-1 RT non-nucleoside binding site (NNBS) may account for the higher inhibitory effect exerted by the new molecules against the mutated RTs.
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Affiliation(s)
- Antonello Mai
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università degli Studi di Roma La Sapienza, P. le A. Moro 5, 00185 Roma, Italy.
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Cancio R, Mai A, Rotili D, Artico M, Sbardella G, Clotet-Codina I, Esté JA, Crespan E, Zanoli S, Hübscher U, Spadari S, Maga G. Slow-, Tight-Binding HIV-1 Reverse Transcriptase Non-Nucleoside Inhibitors Highly Active against Drug-Resistant Mutants. ChemMedChem 2007; 2:445-8. [PMID: 17323401 DOI: 10.1002/cmdc.200600310] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Reynel Cancio
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche via Abbiategrasso 207, 27100 Pavia, Italy
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33
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Ji L, Chen FE, De Clercq E, Balzarini J, Pannecouque C. Synthesis and anti-HIV-1 activity evaluation of 5-alkyl-2-alkylthio-6-(arylcarbonyl or alpha-cyanoarylmethyl)-3,4-dihydropyrimidin-4(3H)-ones as novel non-nucleoside HIV-1 reverse transcriptase inhibitors. J Med Chem 2007; 50:1778-86. [PMID: 17381078 DOI: 10.1021/jm061167r] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A series of novel S-DABO analogues (S-DABOs, 1) were synthesized and evaluated as inhibitors of human immunodeficiency virus type-1 (HIV-1). Key structural modifications included replacement of the 6-arylmethyl group by a 6-arylcarbonyl or 6-(alpha-cyanoarylmethyl) group. Most of the compounds showed only micromolar potency against HIV-1 in MT-4 cells in vitro, though two of them (3e and 3g) were unusually potent (IC50=0.09 and 0.23 [corrected] microM, respectively) and selective (SI=1500 and 1033 [corrected] respectively). Structure-activity relationships among the newly synthesized S-DABOs are discussed.
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Affiliation(s)
- Lei Ji
- Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
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34
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Sbardella G, Bartolini S, Castellano S, Artico M, Paesano N, Rotili D, Spadafora C, Mai A. 6-Alkylthio-4-[1-(2,6-difluorophenyl)alkyl]-1H-[1,3,5]triazin-2-ones (ADATs): Novel Regulators of Cell Differentiation and Proliferation. ChemMedChem 2006; 1:1073-80. [PMID: 16944545 DOI: 10.1002/cmdc.200600139] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Novel triazine analogues of 5-alkyl-2-alkylthio-6-[1-(2,6-difluorophenyl)alkyl]-3,4-dihydropyrimidin-4(3H)-ones (F(2)-DABOs), previously described by us as nonnucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs), were tested for their antiproliferative and cytodifferentiating activity on the A-375 human melanoma cell line. Most of the tested derivatives were effective in decreasing cell proliferation, facilitating morphological differentiation, and reprogramming gene expression. All these effects were reversible upon withdrawal of RT inhibitors. Among the compounds tested, 3 f showed the highest antiproliferative effect, whereas compound 6 c, although not affecting cell proliferation, is endowed with a strong cytodifferentiating effect, which is probably related to a marked upregulation of the e-cad gene. These results support the potential of NNRTIs as valuable antitumor agents.
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Affiliation(s)
- Gianluca Sbardella
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Salerno Via Ponte Don Melillo, Fisciano SA, Italy
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Synthesis of novel N2-adamantyl derivatives of 2-amino-6-methyl-4(3H)-pyrimidinone as potential activators of tumor necrosis factor (TNF) release. Chem Heterocycl Compd (N Y) 2006. [DOI: 10.1007/s10593-006-0243-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Characteristics of the halogenation of 2-substituted 6-benzhydryl-4(3H)-pyrimidinones. Chem Heterocycl Compd (N Y) 2006. [DOI: 10.1007/s10593-006-0231-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Bartolini S, Mai A, Artico M, Paesano N, Rotili D, Spadafora C, Sbardella G. 6-[1-(2,6-difluorophenyl)ethyl]pyrimidinones antagonize cell proliferation and induce cell differentiation by inhibiting (a nontelomeric) endogenous reverse transcriptase. J Med Chem 2005; 48:6776-8. [PMID: 16250634 DOI: 10.1021/jm0507330] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two 2,6-difluoro-DABO derivatives (MC 1047, 1, and MC 1220, 2, respectively) were tested against endogenous, nontelomeric reverse transcriptase (endo-RT) in human differentiating cell systems to investigate their antiproliferative and cytodifferentiating activity. The two compounds significantly reduced cell proliferation and facilitated the morphological differentiation of cells. These results propose F(2)-DABOs as useful tools in preventive and/or curative therapy to counteract the loss of differentiation in dedifferentiating pathologies and as antiproliferative drugs in tumor therapy.
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Affiliation(s)
- Sara Bartolini
- Istituto Superiore di Sanità, Viale Regina Elena 299, Via del Castro Laurenziano 25, 00161 Rome, Italy
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38
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Mai A, Artico M, Ragno R, Sbardella G, Massa S, Musiu C, Mura M, Marturana F, Cadeddu A, Maga G, La Colla P. 5-Alkyl-2-alkylamino-6-(2,6-difluorophenylalkyl)-3,4-dihydropyrimidin-4(3H)-ones, a new series of potent, broad-spectrum non-nucleoside reverse transcriptase inhibitors belonging to the DABO family. Bioorg Med Chem 2005; 13:2065-77. [PMID: 15727860 DOI: 10.1016/j.bmc.2005.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2004] [Revised: 12/30/2004] [Accepted: 01/07/2005] [Indexed: 11/22/2022]
Abstract
2-Alkylamino-6-[1-(2,6-difluorophenyl)alkyl]-3,4-dihydro-5-alkylpyrimidin-4(3H)-ones (F(2)-NH-DABOs) 4, 5 belonging to the dihydro-alkoxy-benzyl-oxopyrimidine (DABO) family and bearing different alkyl- and arylamino side chains at the C(2)-position of the pyrimidine ring were designed as active against wild type (wt) human immunodeficiency virus type 1 (HIV-1) and some relevant HIV-1 mutants. Biological evaluation indicated the importance of the further anchor point of compounds 4, 5 into the non-nucleoside binding site (NNBS): newly synthesized compounds were highly active against both wild type and the Y181C HIV-1 strains. In anti-wt HIV-1 assay the potency of amino derivatives did not depend on the size or shape of the C(2)-amino side chain, but it associated with the presence of one or two methyl groups (one at the pyrimidine C(5)-position and the other at the benzylic carbon), being thymine, alpha-methyluracil or alpha-methylthymine derivatives almost equally active in reducing wt HIV-1-induced cytopathogenicity in MT-4 cells. Against the Y181C mutant strain, 2,6-difluorobenzyl-alpha-methylthymine derivatives 4d, 5h'-n' showed the highest potency and selectivity among tested compounds, both a properly sized C(2)-NH side chain and the presence of two methyl groups (at C(5) and benzylic positions) being crucial for high antiviral action.
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Affiliation(s)
- Antonello Mai
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università degli Studi di Roma La Sapienza, P. le A. Moro 5, I-00185 Roma, Italy.
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39
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Wang J, Kang X, Kuntz ID, Kollman PA. Hierarchical Database Screenings for HIV-1 Reverse Transcriptase Using a Pharmacophore Model, Rigid Docking, Solvation Docking, and MM−PB/SA. J Med Chem 2005; 48:2432-44. [PMID: 15801834 DOI: 10.1021/jm049606e] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, an efficient strategy was presented to search drug leads for human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) using hierarchical database screenings, which included a pharmacophore model, multiple-conformation rigid docking, solvation docking, and molecular mechanics-Poisson-Boltzmann/surface area (MM-PB/SA) sequentially. Encouraging results were achieved in searching a refined available chemical directory (ACD) database: the enrichment factor after the first three filters was estimated to be 25-fold; the hit rate for all the four filters was predicted to be 41% in a control test using 37 known HIV-1 non-nucleoside reverse transcriptase inhibitors; 10 out of 30 promising solvation-docking hits had MM-PB/SA binding free energies better than -6.8 kcal/mol and the best one, HIT15, had -17.0 kcal/mol. In conclusion, the hierarchical multiple-filter database searching strategy is an attractive strategy in drug lead exploration.
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Affiliation(s)
- Junmei Wang
- Encysive Pharmaceuticals Inc., 7000 Fannin, Houston, Texas 77030, USA.
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40
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He Y, Chen F, Yu X, Wang Y, De Clercq E, Balzarini J, Pannecouque C. Nonnucleoside HIV-1 reverse transcriptase inhibitors; part 3. Synthesis and antiviral activity of 5-alkyl-2-[(aryl and alkyloxyl-carbonylmethyl)thio]-6-(1-naphthylmethyl) pyrimidin-4(3H)-ones. Bioorg Chem 2004; 32:536-48. [PMID: 15530994 DOI: 10.1016/j.bioorg.2004.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2004] [Indexed: 11/29/2022]
Abstract
A series of 6-naphthylmethyl substituted S-alkylated dihydroalkoxybenzyloxopyrimidine (S-DABO) analogues with a beta-carbonyl group on the C-2 side chain were synthesized. All of the new compounds were evaluated for their anti-HIV activities in MT-4 cells. The most active compound, 5-isopropyl-2-[(4'-methoxyphenylcarbonyl-methyl)thio]-6-(1-naphthylmethyl)pyrimidin-4(3H)-one showed activity against HIV-1 and against the double mutated strain of HIV(Y181C and K103N) in the micromolar range. Furthermore, some of the compounds are active against both HIV-1 and HIV-2 in cell culture. In view of the fact that the loss of antiviral activity of these compounds when tested against S0561945 was much less pronounced than the loss of activity of typical NNRTIs, it is concluded that some of the compounds might interfere with another target or act on reverse transcriptase in a different way than the typical NNRTIs.
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Affiliation(s)
- Yanping He
- Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
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He Y, Chen F, Sun G, Wang Y, De Clercq E, Balzarini J, Pannecouque C. 5-Alkyl-2-[(aryl and alkyloxylcarbonylmethyl)thio]-6-(1-naphthylmethyl) pyrimidin-4(3H)-ones as an unique HIV reverse transcriptase inhibitors of S-DABO series. Bioorg Med Chem Lett 2004; 14:3173-6. [PMID: 15149669 DOI: 10.1016/j.bmcl.2004.04.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Accepted: 04/02/2004] [Indexed: 10/26/2022]
Abstract
The introduction of a beta-carbonyl group to the C-2 side chain of S-DABO led to the finding of a series of novel potent anti-HIV agent. Some derivatives proved to be highly effective in inhibiting HIV-1 replication at nanomolar concentrations. Furthermore, the novel S-DABOs differ from the classical NNRTIs in that some compounds are active against both HIV-1 and HIV-2. They might interfere with another target or at least act on RT in a different way as compared to typical NNRTIs.
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Affiliation(s)
- Yanping He
- Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
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Ragno R, Mai A, Sbardella G, Artico M, Massa S, Musiu C, Mura M, Marturana F, Cadeddu A, La Colla P. Computer-Aided Design, Synthesis, and Anti-HIV-1 Activity in Vitro of 2-Alkylamino-6-[1-(2,6-difluorophenyl)alkyl]-3,4-dihydro-5-alkylpyrimidin-4(3H)- ones as Novel Potent Non-Nucleoside Reverse Transcriptase Inhibitors, Also Active Against the Y181C Variant. J Med Chem 2004; 47:928-34. [PMID: 14761194 DOI: 10.1021/jm0309856] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydro-alkoxy-benzyl-oxopyrimidines (DABOs) are a family of potent NNRTIs developed in the past decade. Attempts to improve their potency and selectivity led to thio-DABOs (S-DABOs), DATNOs, and difluoro-thio-DABOs (F(2)-S-DABOs). More recently, we reported the synthesis and molecular modeling studies of a novel conformationally constrained subtype of the S-DABO series characterized by the presence of substituents on the methylene linkage connecting the pyrimidine ring to the aryl moiety (Mai, A., et al. J. Med. Chem. 2001, 44, 2544-2554). Now we report the computer-aided design, synthesis, and biological evaluation of four new DABO prototypes (5-alkyl-2-cyclopentylamino-6-[1-(2,6-difluorophenyl)alkyl]-3,4-dihydropyrimidin-4(3H)-ones, F(2)-NH-DABOs) in which the sulfur atom of the related F(2)-S-DABOs is replaced by an amino group. For these studies, we used as a reference model the cocrystallized MKC-442/RT complex. Docking studies with Autodock of the newly designed F(2)-NH-DABOs on the ligand-derived RT confirmed the findings previously described for the F(2)-S-DABOs. The F(2)-NH-DABO binding mode resembles that reported for F(2)-S-DABOs, with the difference that the NH moiety at the C-2 position represents a new anchor site for ligand/enzyme complexation. The predicted inhibition constant (K(i)) values by the internal scoring function of Autodock, and the predicted IC(50) values by the application of a VALIDATE II/HIV-RT model strongly suggested the synthesis of the designed amino-DABOs. F(2)-NH-DABOs were shown to be highly active in both anti-RT and anti-HIV biological assays with IC(50) and EC(50) comparable with that of the reference compound MKC-442. Interestingly, 2-cyclopentylamino-6-[1-(2,6-difluorophenyl)ethyl]-3,4-dihydro-5-methyl pyrimidin-4(3H)-one (9d) was active against the Y181C HIV-1 mutant strain at submicromolar concentration, with a resistance value similar to that of efavirenz, the last FDA-approved NNRTI for AIDS therapy, and 2-fold lower than that of its 2-cyclopentylthio counterpart 8d. The introduction in 9d of a new anchor point (pyrimidine C-2 NH group), with the formation of a new hydrogen bond with Lys101, could compensate for the lack of positive hydrophobic ligand/NNBP interactions due to the Tyr181 to Cys181 mutation.
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Affiliation(s)
- Rino Ragno
- Dipartimento di Studi di Chimica e Tecnologie delle Sostanze Biologicamente Attive, Università degli Studi di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
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43
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Saladino R, Ciambecchini U, Nencioni L, Palamara AT. Recent advances in the chemistry of parainfluenza-1 (Sendai) virus inhibitors. Med Res Rev 2003; 23:427-55. [PMID: 12710019 DOI: 10.1002/med.10036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Purine and pyrimidine derivatives, antioxidants, fusion inhibitors, statins, prostaglandins, antibiotic nucleosides, inhibitors of Ca(2+) homeostasis, carbohydrate derivatives, antisense polynucleotides and chimeras, are described as inhibitors of parainfluenza-1 (Sendai) viral infections.
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Affiliation(s)
- Raffaele Saladino
- Agrobiological and Agrochemical Department, University of Tuscia, via San Camillo de Lellis snc, 00100, Viterbo, Italy.
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44
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Silvestri R, Artico M, De Martino G, Ragno R, Massa S, Loddo R, Murgioni C, Loi AG, La Colla P, Pani A. Synthesis, biological evaluation, and binding mode of novel 1-[2-(diarylmethoxy)ethyl]-2-methyl-5-nitroimidazoles targeted at the HIV-1 reverse transcriptase. J Med Chem 2002; 45:1567-76. [PMID: 11931611 DOI: 10.1021/jm010904a] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel series of 1-[2-(diarylmethoxy)ethyl]-2-methyl-5-nitroimidazole (DAMNI) analogues were synthesized and tested in cell-based assays and in enzyme assays against HIV-1 recombinant reverse transcriptase (RT). Preparation of the new derivatives was performed by reacting the appropriate benzhydrols or the corresponding bromides with 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole or the 3-hydroxypropyl homologue. Several compounds showed anti-HIV-1 activity in the submicromolar range. Structure-activity relationship studies suggested that meta substitution at one phenyl ring of the diarylmethane moiety strongly influences the antiviral activity. The 3,5-disubstitution at the same phenyl ring led to less potent derivatives. Molecular modeling and docking studies within the RT non-nucleoside binding site confirmed that DAMNIs, similar to other NNRTIs such as TNK-651 and delavirdine (BHAP U90152), assume a butterfly-like conformation that appears to be halfway between that of classical NNRTIs, such as nevirapine, HEPT, TBZ, TIBO, and DABOs, and the conformation of BHAPs. In particular, the diphenylmethane moiety mimics the wings whereas the 1-(2-methyl-5-nitroimidazolyl)ethane portion resembles the BHAP 5-methanesulfonamidoindole-2-carbonylpiperazine portion.
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Affiliation(s)
- Romano Silvestri
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università di Roma La Sapienza, BOX 36, Roma 62, P.le Aldo Moro 5, I-00185 Roma, Italy
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45
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Loksha YM, Jørgensen PT, Pedersen EB, El-Badawi MA, El-Barbary AA, Nielsen C. Synthesis of imidazoles as novel emivirine and S-DABO analogues. J Heterocycl Chem 2002. [DOI: 10.1002/jhet.5570390222] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Saladino R, Crestini C, Palamara AT, Danti MC, Manetti F, Corelli F, Garaci E, Botta M. Synthesis, biological evaluation, and pharmacophore generation of uracil, 4(3H)-pyrimidinone, and uridine derivatives as potent and selective inhibitors of parainfluenza 1 (Sendai) virus. J Med Chem 2001; 44:4554-62. [PMID: 11741474 DOI: 10.1021/jm010938i] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Several new 6-oxiranyl-, 6-oxiranylmethyluracils, and pyrimidinone derivatives, synthesized by lithiation-alkylation sequence of 1,3,6-trimethyluracil, 1,3-dimethyl-6-chloromethyluracil, and 2-alkoxy-6-methyl-4(3H)-pyrimidinones, showed a potent and selective antiviral activity against Sendai virus (SV) replication. To gain insight into the structural features required for SV inhibition activity, the new compounds were submitted to a pharmacophore generation procedure using the program Catalyst. The resulting pharmacophore model showed high correlation and predictive power. It also rationalized the relationships between structural properties and biological data of these inhibitors of SV replication.
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Affiliation(s)
- R Saladino
- Dipartimento Agrochimico Agrobiologico, Università degli Studi di Viterbo "La Tuscia", via San Camillo de Lellis, 01100 Viterbo, Italy.
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47
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Botta M, Corelli F, Maga G, Manetti F, Renzulli M, Spadari S. Research on anti-HIV-1 agents. Part 2: Solid-phase synthesis, biological evaluation and molecular modeling studies of 2,5,6-trisubstituted-4(3H)-pyrimidinones targeting HIV-1 reverse transcriptase. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00815-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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48
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Mai A, Sbardella G, Artico M, Ragno R, Massa S, Novellino E, Greco G, Lavecchia A, Musiu C, La Colla M, Murgioni C, La Colla P, Loddo R. Structure-based design, synthesis, and biological evaluation of conformationally restricted novel 2-alkylthio-6-[1-(2,6-difluorophenyl)alkyl]-3,4-dihydro-5-alkylpyrimidin-4(3H)-ones as non-nucleoside inhibitors of HIV-1 reverse transcriptase. J Med Chem 2001; 44:2544-54. [PMID: 11472208 DOI: 10.1021/jm010853h] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Alkyl-2-(alkylthio)-6-(2,6-difluorobenzyl)-3,4-dihydropyrimidin-4(3H)-ones (S-DABOs, 2) have been recently described as a new class of human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) active at nanomolar concentrations (Mai, A. et al. J. Med. Chem. 1999, 42, 619-627). In pursuing our lead optimization efforts, we designed novel conformationally restricted S-DABOs, 3, featuring a methyl at the benzylic carbon (Y = Me) and at the pyrimidine 5-position (R = Me). Conformational analyses and docking simulations suggested that the presence of both methyls would significantly reduce conformational flexibility without compromising, in the R enantiomers, the capability of fitting into the RT non-nucleoside binding pocket. To develop structure-activity relationships, we prepared several congeners of type 3 belonging to the thymine (R = Me) and uracil (R = H) series, featuring various 2-alkylthio side chains (X = Me, i-Pr, n-Bu, i-Bu, s-Bu, c-pentyl, and c-hexyl) and aryl moieties different from the 2,6-difluorophenyl (Ar = phenyl, 2,6-dichlorophenyl, 1-naphthyl). Moreover, alpha-ethyl derivatives (Y = Et) were included in the synthetic project in addition to alpha-methyl derivatives (Y = Me). All of the new compounds were evaluated for their cytotoxicity and anti-HIV-1 activity in MT-4 cells, and some of them were assayed against highly purified recombinant wild-type HIV-1 RT using homopolymeric template primers. The results were expressed as CC(50) (cytotoxicity), EC(50) (anti-HIV-1 activity), SI (selectivity, given by the CC(50)/EC(50) ratio), and IC(50) (RT inhibitory activity) values. In the 2,6-difluorobenzylthymine (R = Me) series, methylation of the benzylic carbon improved anti-HIV-1 and RT inhibitory activities together with selectivity. Compound 3w (Ar = 2,6-F(2)-Ph, R = Y = Me, X = c-pentyl) turned out the most potent and selective among the S-DABOs reported to date (CC(50) > 200 microM, EC(50) = 6 nM, IC(50) = 5 nM, and SI > 33 333). Assays performed on the pure enantiomer (+)-3w, much more active than (-)-3w, yielded the following results: CC(50) > 200 microM, EC(50) = 2 nM, IC(50) = 8 nM, and SI > 100 000, under conditions wherein MKC-442 was less active and selective (CC(50) > 200 microM, EC(50) = 30 nM, IC(50) = 40 nM, SI > 6666). The 2,6-difluorophenylethylthymines (R = Me) were generally endowed with higher potency compared with the uracil counterparts (R = H). In the 2,6-difluorophenyl series the best and the least performant 2-alkylthio side chains were the 2-c-pentylthio and the 2-methylthio, respectively. When the methyl at the benzylic carbon was replaced by an ethyl, activity was retained or decreased slightly, thus suggesting that the dimensions of the cavity within the RT hosting this substituent would not be compatible with groups larger than ethyl. Aryl moieties different from the 2,6-difluorophenyl (phenyl, 1-naphthyl, 2,6-dichlorophenyl) were generally detrimental to activity, consistent with a favorable electronic effect exerted by the 2,6-fluorines on a putative charge-transfer interaction between the aromatic moieties of the inhibitor and Tyr188.
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Affiliation(s)
- A Mai
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Roma, Italy
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Quaglia M, Mai A, Sbardella G, Artico M, Ragno R, Massa S, del Piano D, Setzu G, Doratiotto S, Cotichini V. Chiral resolution and molecular modeling investigation of rac-2-cyclopentylthio-6-[1-(2,6-difluorophenyl)ethyl]-3,4-dihydro-5-methylpyrimidin-4(3H)-one (MC-1047), a potent anti-HIV-1 reverse transcriptase agent of the DABO class. Chirality 2001; 13:75-80. [PMID: 11170249 DOI: 10.1002/1520-636x(2001)13:2<75::aid-chir1001>3.0.co;2-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
rac-2-Cyclopentylthio-6-[1-(2,6-difluorophenyl)ethyl]-3,4-dihydro-5-methylpyrimidin-4(3H)-one (MC-1047) is a potent inhibitor of HIV-1 multiplication in acutely infected cells. MC-1047 racemate has been resolved by chiral HPLC using, as chiral stationary phase (CSP), a commercially available (R,R)-Whelk-01 column. The optical purity and the circular dichroism (CD) of the two resolved enantiomers were determined and their biological activities tested in in vitro assays. Molecular modeling inspection of the binding of (R) and (S) enantiomers to the non-nucleoside binding site (NNBS) of reverse transcriptase (RT) using the defined model of F(2)-S-DABO/RT complex indicates the (R) enantiomer as the more active isomer.
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Affiliation(s)
- M Quaglia
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università degli Studi di Roma "La Sapienza," Roma, Italy.
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Sbardella G, Mai A, Artico M, Chimenti P, Massa S, Loddo R, Marongiu ME, La Collat P, Pani A. Structure-activity relationship studies on new DABOS: effect of substitutions at pyrimidine C-5 and C-6 positions on anti-HIV-1 activity. Antivir Chem Chemother 2001; 12:37-50. [PMID: 11437321 DOI: 10.1177/095632020101200102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Several 5-alkyl, 5-alkenyl, 5-iso-alkyl, 5-halo, 5-aminomethyl and 5-carboxy derivatives of S-DABOs (dihydro-alkyl (or cyclo-alkyl)thio-benzyloxopyrimidines), DATNOs (dihydro-alkylthionaphthylmethyl-oxopyrimidines) and F2-S-DABOs (dihydro-alkyl (or cyclo-alkyl)thio-2,6-difluorobenzyl-oxopyrimidines) have been prepared and tested as anti-HIV-1 agents. S-DABO derivatives bearing at C-6 position monosubstituted phenylmethyl or heteroarylmethyl units have also been synthesized. 2-Alkylthio-3,4-dihydropyrimidin-4(3H)-one derivatives of F2-S-DABO series bearing small alkyl groups at C-5 proved to be potent inhibitors of HIV-1 replication in vitro with selectivity indexes ranging from 250 to >2,500.
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Affiliation(s)
- G Sbardella
- Farmaceutici Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università di Roma, La Sapienza, Italy
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