1
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Batran RZ, Sabt A, Khedr MA, Allayeh AK, Pannecouque C, Kassem AF. 4-Phenylcoumarin derivatives as new HIV-1 NNRTIs: Design, synthesis, biological activities, and computational studies. Bioorg Chem 2023; 141:106918. [PMID: 37866206 DOI: 10.1016/j.bioorg.2023.106918] [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: 08/23/2023] [Revised: 10/05/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023]
Abstract
A series of 4-phenylcoumarin derivatives was synthesized and evaluated for their cellular anti-HIV-1 and HIV-2 activities as well as their inhibitory effects against HIV-1 reverse transcriptase (RT). The hydrazone compound 8b and the ethylthiosemicarbazide derivative 4c showed the best inhibition activity against wild-type (WT) HIV-1. The promising compounds were further evaluated against HIV-1 RT and exhibited significant inhibitory activity with compound 8b showing comparable effect to the reference NNRTI Efavirenz (IC50 = 9.01 nM). Structure activity relationship study revealed the importance of 6-chloro and 4-phenyl substituents for optimum activity, as well as the 5-atoms linker (=N-NH-CO-CH2-O-) at position 7 of coumarin scaffold that can support the rotation and flexibility of compound 8b to fit well in the binding pocket. The molecular docking of compound 8b demonstrated a typical seahorse binding mode with better binding interactions that covered more residues when compared to Efavirenz.
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Affiliation(s)
- Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt.
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Mohammed A Khedr
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, Kuwait
| | - Abdou K Allayeh
- Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | | | - Asmaa F Kassem
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
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2
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Nandy A, Kazi I, Guha S, Sekar G. Visible-Light-Driven Halogen-Bond-Assisted Direct Synthesis of Heteroaryl Thioethers Using Transition-Metal-Free One-Pot C–I Bond Formation/C–S Cross-Coupling Reaction. J Org Chem 2021; 86:2570-2581. [DOI: 10.1021/acs.joc.0c02672] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Anuradha Nandy
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036 Tamil Nadu, India
| | - Imran Kazi
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036 Tamil Nadu, India
| | - Somraj Guha
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036 Tamil Nadu, India
| | - Govindasamy Sekar
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036 Tamil Nadu, India
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3
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Sangwan R, Dubey A, Tiwari A, Mandal PK. The strategic use of para-quinone methides to access synthetically challenging and chemoselective α,α'-diarylmethyl N-glycosides from unprotected carbohydrate amines. Org Biomol Chem 2020; 18:1343-1348. [PMID: 32003394 DOI: 10.1039/d0ob00039f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Reported herein is a practical route to access synthetically challenging and chemoselective α,α'-diarylmethyl N-glycosides via Sc(OTf)3-catalyzed 1,6-conjugate addition of amino sugars with para-quinone methides (p-QMs). The reactions proceed smoothly without a base and under mild reaction conditions with a broad substrate scope and moderate to good yields.
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Affiliation(s)
- Rekha Sangwan
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram extn, Sitapur Road, P.O. Box 173, Lucknow 226031, India. and Academy of Scientific and Innovative Research, New Delhi 110001, India
| | - Atul Dubey
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram extn, Sitapur Road, P.O. Box 173, Lucknow 226031, India.
| | - Ashwani Tiwari
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram extn, Sitapur Road, P.O. Box 173, Lucknow 226031, India.
| | - Pintu Kumar Mandal
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram extn, Sitapur Road, P.O. Box 173, Lucknow 226031, India. and Academy of Scientific and Innovative Research, New Delhi 110001, India
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4
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Xu C, Xin Y, Chen M, Ba M, Guo Q, Zhu C, Guo Y, Shi J. Discovery, synthesis, and optimization of an N-alkoxy indolylacetamide against HIV-1 carrying NNRTI-resistant mutations from the Isatis indigotica root. Eur J Med Chem 2020; 189:112071. [PMID: 32004936 PMCID: PMC7111291 DOI: 10.1016/j.ejmech.2020.112071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/04/2020] [Accepted: 01/13/2020] [Indexed: 12/27/2022]
Abstract
From an aqueous decoction of the traditional Chinese medicine "ban lan gen" (the Isatis indigotica root), an antiviral natural product CI - 39 was isolated as an NNRTI (non-nucleoside reverse transcriptase inhibitor) (EC50 = 3.40 μM). Its novel structure was determined as methyl (1-methoxy-1H-indol-3-yl)acetamidobenzoate by spectroscopic data and confirmed by single crystal X-ray diffraction. Through synthesis and structure-activity relationship (SAR) investigation of CI - 39 and 57 new derivatives (24 with EC50 values of 0.06-8.55 μM), two optimized derivatives 10f and 10i (EC50: 0.06 μM and 0.06 μM) having activity comparable to that of NVP (EC50 = 0.03 μM) were obtained. Further evaluation verified that 10f and 10i were RT DNA polymerase inhibitors and exhibited better activities and drug resistance folds compared to NVP against seven NNRTI-resistant strains carrying different mutations. Especially, 10i (EC50 = 0.43 μM) was more active to the L100I/K103N double-mutant strain as compared to both NVP (EC50 = 0.76 μM) and EFV (EC50 = 1.08 μM). The molecular docking demonstrated a possible binding pattern between 10i and RT and revealed activity mechanism of 10i against the NNRTI-resistant strains.
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Affiliation(s)
- Chengbo Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yijing Xin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Minghua Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Mingyu Ba
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qinglan Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Chenggen Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ying Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Jiangong Shi
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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5
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Gao RX, Luan XQ, Xie ZY, Yang L, Pei Y. Fe-Catalyzed decarbonylative cascade reaction of N-aryl cinnamamides with aliphatic aldehydes to construct 3,4-dihydroquinolin-2(1H)-ones. Org Biomol Chem 2019; 17:5262-5268. [PMID: 31086867 DOI: 10.1039/c9ob00492k] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A practical Fe-catalyzed decarbonylative cascade reaction of N-aryl cinnamamides with aliphatic aldehydes to provide C3 alkylated 3,4-dihydroquinolin-2(1H)-ones is developed. Aliphatic aldehydes were oxidatively decarbonylated into 1°, 2° and 3° alkyl radicals conveniently, allowing for the subsequent cascade construction of C(sp3)-C(sp3) and C(sp3)-C(sp2) bonds via radical addition and HAS-type cyclization. The importance of the amide linkage and the selectivity of the 6-endo-trig over 5-exo-trig cyclization pathway were elucidated by experimental results and DFT calculations.
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Affiliation(s)
- Ru-Xin Gao
- Key Laboratory for Environmentally Friendly Chemistry and Application of the Ministry of Education, Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Hunan, 411105, PR China.
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6
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Wang R, Xu K, Shi W. Quinolone derivatives: Potential anti‐HIV agent—development and application. Arch Pharm (Weinheim) 2019; 352:e1900045. [DOI: 10.1002/ardp.201900045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Ruo Wang
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
| | - Kai Xu
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
| | - Weixiong Shi
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
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7
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Silva VLM, Silva AMS. Palladium-Catalysed Synthesis and Transformation of Quinolones. Molecules 2019; 24:E228. [PMID: 30634524 PMCID: PMC6359680 DOI: 10.3390/molecules24020228] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 12/31/2018] [Accepted: 01/04/2019] [Indexed: 11/16/2022] Open
Abstract
Palladium-catalysed reactions have had a large impact on synthetic organic chemistry and have found many applications in target-oriented synthesis. Their widespread use in organic synthesis is due to the mild conditions associated with the reactions together with their tolerance of a wide range of functional groups. Moreover, these types of reactions allow the rapid construction of complex molecules through multiple bond-forming reactions in a single step, the so-called tandem processes. Pd-catalysed reactions have been applied to the synthesis of a large number of natural products and bioactive compounds, some of them of complex molecular structures. This review article aims to present an overview of the most important Pd-catalysed reactions employed in the synthesis and transformations of quinolin-2(1H)-ones and quinolin-4(1H)-ones. These compounds are widely recognized by their diverse bioactivity, being privileged structures in medicinal chemistry and useful structural moieties for the development of new drug candidates. Furthermore, they hold significant interest due to their host⁻guest chemistry; applications in chemical, biochemical and environmental analyses and use in the development of new synthetic methods. In some cases, the quinolone formation step cannot be ascribed to a claimed Pd-catalysed reaction but this reaction is crucial to get the appropriate substrate for cyclization into the quinolone. Herein we present and discuss different economical, efficient and selective synthetic strategies to access quinolone-type compounds.
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Affiliation(s)
- Vera L M Silva
- Department of Chemistry QOPNA and LAQV-REQUIMTE, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Artur M S Silva
- Department of Chemistry QOPNA and LAQV-REQUIMTE, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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8
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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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9
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Anderson RG, Jett BM, McNally A. Selective formation of heteroaryl thioethers via a phosphonium ion coupling reaction. Tetrahedron 2018; 74:3129-3136. [PMID: 30479455 PMCID: PMC6252084 DOI: 10.1016/j.tet.2017.12.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Heteroaryl thioethers, comprised of pyridines and diazines, are an important class of compounds with relevance to medicinal chemistry. Metal-catalyzed cross-couplings and SNAr are traditionally used to form C-S bonds in these systems but are limited by available halogenated precursors. An alternative approach is presented where pyridines and diazines are transformed into heterocyclic phosphonium salts and then C-S bonds are formed by adding thiolate nucleophiles. The process is 4-selective for pyridines, simple to execute and can be used to make derivatives of complex pharmaceuticals.
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Affiliation(s)
- Ryan G. Anderson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, CO 80523, USA
| | - Brianna M. Jett
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, CO 80523, USA
| | - Andrew McNally
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, CO 80523, USA
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10
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Cabrera A, Hernández LH, Chávez D, Medina-Franco JL. Molecular Modeling of Potential Dual Inhibitors of HIV Reverse Transcriptase and Integrase. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/cmb.2018.81001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Wang Y, Yan F, Jia Q, Dai Y, Wang Q. Quantitative structure-activity relationship of anti-HIV integrase and reverse transcriptase inhibitors using norm indexes. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:1025-1044. [PMID: 29157005 DOI: 10.1080/1062936x.2017.1397055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023]
Abstract
The development of new and safe anti-human immunodeficiency virus (anti-HIV) drugs has been an urgent task for medical research recently. Herein, based on the norm-index descriptors proposed in this work and previous works, a couple of models were developed for investigating the quantitative structure-activity/toxicity relationship (QSAR/QSTR) of dual-target anti-HIV integrase (IN) and reverse transcriptase (RT) inhibitors. The validation results proved that the developed models were stable and reliable, both in statistical quality and predictive capacity. Moreover, potential dual-target inhibitors with high activity and low toxicity were deduced from the developed models; molecular docking results indicated that these inhibitors could interact with some important residues of HIV IN and RT through H-bonding. Accordingly, the norm indexes descriptors proposed by this work might be helpful for the research and development of dual-target anti-HIV drugs.
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Affiliation(s)
- Y Wang
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - F Yan
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - Q Jia
- b School of Marine and Environmental Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - Y Dai
- c School of Bioengineering , Tianjin University of Science and Technology , Tianjin , PR China
| | - Q Wang
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
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12
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El-Sheref EM, Aly AA, Mourad AFE, Brown AB, Bräse S, Bakheet MEM. Synthesis of pyrano[3,2-c]quinoline-4-carboxylates and 2-(4-oxo-1,4-dihydroquinolin-3-yl)fumarates. CHEMICAL PAPERS 2017. [DOI: 10.1007/s11696-017-0269-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Li X, Pan J, Wu H, Jiao N. Rh-catalyzed aerobic oxidative cyclization of anilines, alkynes, and CO. Chem Sci 2017; 8:6266-6273. [PMID: 28989660 PMCID: PMC5628386 DOI: 10.1039/c7sc02181j] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/01/2017] [Indexed: 11/21/2022] Open
Abstract
We describe a novel Rh-catalyzed C–H cyclization of a wide range of anilines with alkynes and CO. Particularly, simple primary anilines and readily prepared tertiary anilines can be easily converted to quinolin-2(1H)-ones via C–N bond cleavage.
Transition-metal-catalyzed oxidative C–H cyclization of anilines has been an attractive and powerful strategy for the efficient construction of N-heterocycles. However, primary and tertiary anilines are rarely employed in this strategy due to the relative instability with strong oxidants or the presence of three C–N bonds. We describe here a novel Rh-catalyzed C–H cyclization of a wide range of anilines with alkynes and CO, using an aerobic oxidative protocol. Particularly, the simple primary anilines and readily prepared tertiary anilines could be easily converted to quinolin-2(1H)-ones, which are high value-added, biologically significant N-heterocycles, via C–N bond cleavage.
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Affiliation(s)
- Xinyao Li
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , School of Pharmaceutical Sciences , Xue Yuan Rd. 38 , Beijing 100191 , China .
| | - Jun Pan
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , School of Pharmaceutical Sciences , Xue Yuan Rd. 38 , Beijing 100191 , China .
| | - Hao Wu
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , School of Pharmaceutical Sciences , Xue Yuan Rd. 38 , Beijing 100191 , China .
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , School of Pharmaceutical Sciences , Xue Yuan Rd. 38 , Beijing 100191 , China . .,State Key Laboratory of Elemento-organic Chemistry , Nankai University , Weijin Rd. 94 , Tianjin 300071 , China
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14
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Cao Y, Zhao H, Zhang-Negrerie D, Du Y, Zhao K. Metal-Free Synthesis of 3-Arylquinolin-2-ones fromN,2-Diaryl- acrylamidesviaPhenyliodine(III) Bis(2,2-dimethylpropanoate)- Mediated Direct Oxidative C−C Bond Formation. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yang Cao
- Tianjin Key Laboratory for Modern Drug Delivery &; High-Efficiency, School of Pharmaceutical Science and Technology; Tianjin University; Tianjin 300072 People's Republic of China
| | - Hui Zhao
- College of Chemistry and Material Science; Shandong Agricultural University; Taian City, Shandong Province 271018 People's Republic of China
| | - Daisy Zhang-Negrerie
- Tianjin Key Laboratory for Modern Drug Delivery &; High-Efficiency, School of Pharmaceutical Science and Technology; Tianjin University; Tianjin 300072 People's Republic of China
| | - Yunfei Du
- Tianjin Key Laboratory for Modern Drug Delivery &; High-Efficiency, School of Pharmaceutical Science and Technology; Tianjin University; Tianjin 300072 People's Republic of China
| | - Kang Zhao
- Tianjin Key Laboratory for Modern Drug Delivery &; High-Efficiency, School of Pharmaceutical Science and Technology; Tianjin University; Tianjin 300072 People's Republic of China
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15
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Zhu F, Li Y, Wang Z, Wu XF. Iridium-Catalyzed Carbonylative Synthesis of Halogen-Containing Quinolin-2(1H)-ones from Internal Alkynes and Simple Anilines. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600680] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Fengxiang Zhu
- Leibniz-Institut für Katalyse e.V. an der; Universität Rostock; Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Yahui Li
- Leibniz-Institut für Katalyse e.V. an der; Universität Rostock; Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Zechao Wang
- Leibniz-Institut für Katalyse e.V. an der; Universität Rostock; Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Xiao-Feng Wu
- Leibniz-Institut für Katalyse e.V. an der; Universität Rostock; Albert-Einstein-Strasse 29a 18059 Rostock Germany
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16
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Dousson C, Alexandre FR, Amador A, Bonaric S, Bot S, Caillet C, Convard T, da Costa D, Lioure MP, Roland A, Rosinovsky E, Maldonado S, Parsy C, Trochet C, Storer R, Stewart A, Wang J, Mayes BA, Musiu C, Poddesu B, Vargiu L, Liuzzi M, Moussa A, Jakubik J, Hubbard L, Seifer M, Standring D. Discovery of the Aryl-phospho-indole IDX899, a Highly Potent Anti-HIV Non-nucleoside Reverse Transcriptase Inhibitor. J Med Chem 2016; 59:1891-8. [PMID: 26804933 DOI: 10.1021/acs.jmedchem.5b01430] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Here, we describe the design, synthesis, biological evaluation, and identification of a clinical candidate non-nucleoside reverse transcriptase inhibitors (NNRTIs) with a novel aryl-phospho-indole (APhI) scaffold. NNRTIs are recommended components of highly active antiretroviral therapy (HAART) for the treatment of HIV-1. Since a major problem associated with NNRTI treatment is the emergence of drug resistant virus, this work focused on optimization of the APhI against clinically relevant HIV-1 Y181C and K103N mutants and the Y181C/K103N double mutant. Optimization of the phosphinate aryl substituent led to the discovery of the 3-Me,5-acrylonitrile-phenyl analogue RP-13s (IDX899) having an EC50 of 11 nM against the Y181C/K103N double mutant.
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Affiliation(s)
- Cyril Dousson
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - François-René Alexandre
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Agnès Amador
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Séverine Bonaric
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Stéphanie Bot
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Catherine Caillet
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Thierry Convard
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Daniel da Costa
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Marie-Pierre Lioure
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Arlène Roland
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Elodie Rosinovsky
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Sébastien Maldonado
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Christophe Parsy
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Christophe Trochet
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Richard Storer
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Alistair Stewart
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Jingyang Wang
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Benjamin A Mayes
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Chiara Musiu
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Barbara Poddesu
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Luana Vargiu
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Michel Liuzzi
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Adel Moussa
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Jocelyn Jakubik
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Luke Hubbard
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Maria Seifer
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - David Standring
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
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17
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Cabrera A, Miranda LD, Reyes H, Aguirre G, Chávez D. Crystal structure of ethyl 2,4-di-chloro-quinoline-3-carboxyl-ate. Acta Crystallogr E Crystallogr Commun 2015; 71:o939. [PMID: 26870538 PMCID: PMC4719891 DOI: 10.1107/s2056989015020587] [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: 07/09/2015] [Accepted: 10/30/2015] [Indexed: 11/10/2022]
Abstract
In the crystal structure of the title compound, C12H9Cl2NO2, the mean planes through the quinoline and carboxyl-ate groups have r.m.s. deviations of 0.006 and 0.021 Å, respectively, and form a dihedral angle of 87.06 (19)°. In the crystal, mol-ecules are linked via very weak C-H⋯O hydrogen bonds, forming chains, which propagate along the c-axis direction.
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Affiliation(s)
- Alberto Cabrera
- Centro de Graduados e Investigación en Química del Instituto, Tecnológico de, Tijuana, Apdo. Postal 1166, 22500, Tijuana, B.C., Mexico
| | - Luis D. Miranda
- Instituto de Química, Universidad Nacional Autónoma de, México, Circuito, Exterior, S. N., Ciudad Universitaria, Coyoacán, México, D. F. 04510, México
| | - Héctor Reyes
- Centro de Graduados e Investigación en Química del Instituto, Tecnológico de, Tijuana, Apdo. Postal 1166, 22500, Tijuana, B.C., Mexico
| | - Gerardo Aguirre
- Centro de Graduados e Investigación en Química del Instituto, Tecnológico de, Tijuana, Apdo. Postal 1166, 22500, Tijuana, B.C., Mexico
| | - Daniel Chávez
- Centro de Graduados e Investigación en Química del Instituto, Tecnológico de, Tijuana, Apdo. Postal 1166, 22500, Tijuana, B.C., Mexico
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18
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Budnikova YH, Sinyashin OG. Phosphorylation of C–H bonds of aromatic compounds using metals and metal complexes. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4525] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Li W, Li X, De Clercq E, Zhan P, Liu X. Discovery of potent HIV-1 non-nucleoside reverse transcriptase inhibitors from arylthioacetanilide structural motif. Eur J Med Chem 2015; 102:167-79. [DOI: 10.1016/j.ejmech.2015.07.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 11/26/2022]
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20
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Wan ZY, Yao J, Mao TQ, Wang XL, Wang HF, Chen WX, Yin H, Chen FE, De Clercq E, Daelemans D, Pannecouque C. Pyrimidine sulfonylacetanilides with improved potency against key mutant viruses of HIV-1 by specific targeting of a highly conserved residue. Eur J Med Chem 2015; 102:215-22. [DOI: 10.1016/j.ejmech.2015.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/21/2015] [Accepted: 08/02/2015] [Indexed: 10/23/2022]
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21
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Li X, Li X, Jiao N. Rh-Catalyzed Construction of Quinolin-2(1H)-ones via C–H Bond Activation of Simple Anilines with CO and Alkynes. J Am Chem Soc 2015; 137:9246-9. [DOI: 10.1021/jacs.5b05843] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xinyao Li
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Xue
Yuan Road 38, Beijing 100191, China
| | - Xinwei Li
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Xue
Yuan Road 38, Beijing 100191, China
| | - Ning Jiao
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Xue
Yuan Road 38, Beijing 100191, China
- State
Key Laboratory of Elemento-organic Chemistry, Nankai University, Weijin
Road 94, Tianjin 300071, China
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22
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Barot KP, Jain SV, Kremer L, Singh S, Ghate MD. Recent advances and therapeutic journey of coumarins: current status and perspectives. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1350-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Chen YF, Lin YC, Morris-Natschke SL, Wei CF, Shen TC, Lin HY, Hsu MH, Chou LC, Zhao Y, Kuo SC, Lee KH, Huang LJ. Synthesis and SAR studies of novel 6,7,8-substituted 4-substituted benzyloxyquinolin-2(1H)-one derivatives for anticancer activity. Br J Pharmacol 2015; 172:1195-221. [PMID: 25363404 DOI: 10.1111/bph.12992] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/29/2014] [Accepted: 10/20/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND AND PURPOSE 4-Phenylquinolin-2(1H)-one (4-PQ) derivatives can induce cancer cell apoptosis. Additional new 4-PQ analogs were investigated as more effective, less toxic antitumour agents. EXPERIMENTAL APPROACH Forty-five 6,7,8-substituted 4-substituted benzyloxyquinolin-2(1H)-one derivatives were synthesized. Antiproliferative activities were evaluated using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliun bromide assay and structure-activity relationship correlations were established. Compounds 9b, 9c, 9e and 11e were also evaluated against the National Cancer Institute-60 human cancer cell line panel. Hoechst 33258 and Annexin V-FITC/PI staining assays were used to detect apoptosis, while inhibition of microtubule polymerization was assayed by fluorescence microscopy. Effects on the cell cycle were assessed by flow cytometry and on apoptosis-related proteins (active caspase-3, -8 and -9, procaspase-3, -8, -9, PARP, Bid, Bcl-xL and Bcl-2) by Western blotting. KEY RESULTS Nine 6,7,8-substituted 4-substituted benzyloxyquinolin-2(1H)-one derivatives (7e, 8e, 9b, 9c, 9e, 10c, 10e, 11c and 11e) displayed high potency against HL-60, Hep3B, H460, and COLO 205 cancer cells (IC₅₀ < 1 μM) without affecting Detroit 551 normal human cells (IC₅₀ > 50 μM). Particularly, compound 11e exhibited nanomolar potency against COLO 205 cancer cells. Mechanistic studies indicated that compound 11e disrupted microtubule assembly and induced G2/M arrest, polyploidy and apoptosis via the intrinsic and extrinsic signalling pathways. Activation of JNK could play a role in TRAIL-induced COLO 205 apoptosis. CONCLUSION AND IMPLICATIONS New quinolone derivatives were identified as potential pro-apoptotic agents. Compound 11e could be a promising lead compound for future antitumour agent development.
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Affiliation(s)
- Yi-Fong Chen
- The Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung, Taiwan; School of Pharmacy, China Medical University, Taichung, Taiwan
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24
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Structure-based virtual screening and docking studies for the identification of novel inhibitors against wild and drug resistance strains of HIV-1 RT. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1251-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Jain Pancholi N, Gupta S, Sapre N, Sapre NS. Design of novel leads: ligand based computational modeling studies on non-nucleoside reverse transcriptase inhibitors (NNRTIs) of HIV-1. MOLECULAR BIOSYSTEMS 2014; 10:313-25. [PMID: 24292893 DOI: 10.1039/c3mb70218a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Researchers are on the constant lookout for new antiviral agents for the treatment of AIDS. In the present work, ligand based modeling studies are performed on analogues of substituted phenyl-thio-thymines, which act as non-nucleoside reverse transcriptase inhibitors (NNRTIs) and novel leads are extracted. Using alignment-dependent descriptors, based on group center overlap (SALL, HDALL, HAALL and RALL), an alignment-independent descriptor (S log P), a topological descriptor (Balaban index (J)) and a 3D descriptor dipole moment (μ) and shape based descriptors (Kappa 2 index ((2)κ)), a correlation is derived with inhibitory activity. Linear and non-linear techniques have been used to achieve the goal. Support Vector Machine (SVM, R = 0.929, R(2) = 0.863) and Back Propagation Neural Network (BPNN, R = 0.928, R(2) = 0.861) methods yielded near similar results and outperformed Multiple Linear Regression (MLR, R = 0.915, R(2) = 0.837). The predictive ability of the models are cross-validated using a test dataset (SVM: R = 0.846, R(2) = 0.716, BPNN: R = 0.841, R(2) = 0.707 and MLR: R = 0.833, R(2) = 0.694). It is concluded that the hydrophobicity (S log P) and the polarity (μ) of a ligand and the presence of hydrogen donor (HDALL) moieties are the deciding factors in improving antiviral activity and pharmaco-therapeutic properties. Based on the above findings, a virtual dataset is created to extract probable leads with reasonable antiviral activity as well as better pharmacophoric properties.
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Affiliation(s)
- Nilanjana Jain Pancholi
- Department of Applied Chemistry, Shri G.S. Institute of Technology and Sciences, Indore, MP 452001, India.
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26
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De Colibus L, Wang X, Spyrou JAB, Kelly J, Ren J, Grimes J, Puerstinger G, Stonehouse N, Walter TS, Hu Z, Wang J, Li X, Peng W, Rowlands D, Fry EE, Rao Z, Stuart DI. More-powerful virus inhibitors from structure-based analysis of HEV71 capsid-binding molecules. Nat Struct Mol Biol 2014; 21:282-288. [PMID: 24509833 PMCID: PMC4530014 DOI: 10.1038/nsmb.2769] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 01/13/2014] [Indexed: 11/09/2022]
Abstract
Enterovirus 71 (HEV71) epidemics in children and infants result mainly in mild symptoms; however, especially in the Asia-Pacific region, infection can be fatal. At present, no therapies are available. We have used structural analysis of the complete virus to guide the design of HEV71 inhibitors. Analysis of complexes with four 3-(4-pyridyl)-2-imidazolidinone derivatives with varying anti-HEV71 activities pinpointed key structure-activity correlates. We then identified additional potentially beneficial substitutions, developed methods to reliably triage compounds by quantum mechanics-enhanced ligand docking and synthesized two candidates. Structural analysis and in vitro assays confirmed the predicted binding modes and their ability to block viral infection. One ligand (with IC50 of 25 pM) is an order of magnitude more potent than the best previously reported inhibitor and is also more soluble. Our approach may be useful in the design of effective drugs for enterovirus infections.
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Affiliation(s)
- Luigi De Colibus
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK
| | - Xiangxi Wang
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - John A B Spyrou
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK
| | - James Kelly
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK
| | - Jonathan Grimes
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.,Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, UK
| | - Gerhard Puerstinger
- Department of Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Nicola Stonehouse
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Thomas S Walter
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK
| | - Zhongyu Hu
- National Institutes for Food and Drug Control, No. 2, TiantanXili, Beijing, China
| | - Junzhi Wang
- National Institutes for Food and Drug Control, No. 2, TiantanXili, Beijing, China
| | - Xuemei Li
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Wei Peng
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - David Rowlands
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK
| | - Zihe Rao
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.,Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, UK
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27
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Mi X, Huang M, Zhang J, Wang C, Wu Y. Regioselective Palladium-Catalyzed Phosphonation of Coumarins with Dialkyl H-Phosphonates via C–H Functionalization. Org Lett 2013; 15:6266-9. [DOI: 10.1021/ol4031167] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xia Mi
- College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry, Key Laboratory of Applied Chemistry of Henan Universities, Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Mengmeng Huang
- College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry, Key Laboratory of Applied Chemistry of Henan Universities, Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Jianye Zhang
- College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry, Key Laboratory of Applied Chemistry of Henan Universities, Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Chenyang Wang
- College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry, Key Laboratory of Applied Chemistry of Henan Universities, Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Yangjie Wu
- College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry, Key Laboratory of Applied Chemistry of Henan Universities, Zhengzhou University, Zhengzhou 450052, P.R. China
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28
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Carrër A, Brion JD, Messaoudi S, Alami M. Synthesis of 3,4-Disubstituted Quinolin-2-(1H)-onesviaPalladium-Catalyzed Decarboxylative Arylation Reactions. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201300299] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Bruneau A, Brion JD, Alami M, Messaoudi S. Stereoselective copper-catalyzed Chan–Lam–Evans N-arylation of glucosamines with arylboronic acids at room temperature. Chem Commun (Camb) 2013; 49:8359-61. [DOI: 10.1039/c3cc44780d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Kalid O, Toledo Warshaviak D, Shechter S, Sherman W, Shacham S. Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors. J Comput Aided Mol Des 2012; 26:1217-28. [PMID: 23053738 DOI: 10.1007/s10822-012-9611-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/20/2012] [Indexed: 11/29/2022]
Abstract
We present the Consensus Induced Fit Docking (cIFD) approach for adapting a protein binding site to accommodate multiple diverse ligands for virtual screening. This novel approach results in a single binding site structure that can bind diverse chemotypes and is thus highly useful for efficient structure-based virtual screening. We first describe the cIFD method and its validation on three targets that were previously shown to be challenging for docking programs (COX-2, estrogen receptor, and HIV reverse transcriptase). We then demonstrate the application of cIFD to the challenging discovery of irreversible Crm1 inhibitors. We report the identification of 33 novel Crm1 inhibitors, which resulted from the testing of 402 purchased compounds selected from a screening set containing 261,680 compounds. This corresponds to a hit rate of 8.2 %. The novel Crm1 inhibitors reveal diverse chemical structures, validating the utility of the cIFD method in a real-world drug discovery project. This approach offers a pragmatic way to implicitly account for protein flexibility without the additional computational costs of ensemble docking or including full protein flexibility during virtual screening.
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Affiliation(s)
- Ori Kalid
- Karyopharm Therapeutics, 2 Mercer Road, Natick, MA 01760, USA.
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31
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de Brito MA, Rodrigues CR, Cirino JJV, Araújo JQ, Honório T, Cabral LM, de Alencastro RB, Castro HC, Albuquerque MG. Residue-ligand interaction energy (ReLIE) on a receptor-dependent 3D-QSAR analysis of S- and NH-DABOs as non-nucleoside reverse transcriptase inhibitors. Molecules 2012; 17:7666-94. [PMID: 22732882 PMCID: PMC6269006 DOI: 10.3390/molecules17077666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/02/2012] [Accepted: 06/05/2012] [Indexed: 11/16/2022] Open
Abstract
A series of 74 dihydroalkoxybenzyloxopyrimidines (DABOs), a class of highly potent non-nucleoside reverse transcriptase inhibitors (NNRTIs), was retrieved from the literature and studied by receptor-dependent (RD) three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis to derive RD-3D-QSAR models. The descriptors in this new method are the steric and electrostatic interaction energies of the protein-ligand complexes (per residue) simulated by molecular dynamics, an approach named Residue-Ligand Interaction Energy (ReLIE). This study was performed using a training set of 59 compounds and the MKC-442/RT complex structure as reference. The ReLIE-3D-QSAR models were constructed and evaluated by genetic algorithm (GA) and partial least squares (PLS). In the best equations, at least one term is related to one of the amino acid residues of the p51 subunit: Asn136, Asn137, Glu138, and Thr139. This fact implies the importance of interchain interaction (p66-p51) in the equations that best describe the structure-activity relationship for this class of compounds. The best equation shows q² = 0.660, SE(cv) = 0.500, r² = 0.930, and SEE = 0.226. The external predictive ability of this best model was evaluated using a test set of 15 compounds. In order to design more potent DABO analogues as anti-HIV/AIDS agents, substituents capable of interactions with residues like Ile94, Lys101, Tyr181, and Tyr188 should be selected. Also, given the importance of the conserved Asn136, this residue could become an attractive target for the design of novel NNRTIs with improved potency and increased ability to avoid the development of drug-resistant viruses.
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Affiliation(s)
- Monique Araújo de Brito
- Laboratory of Computational Medicinal Chemistry (LabQMC), Faculty of Pharmacy, Fluminense Federal University (UFF), Niterói, RJ, 24241-000, Brazil
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
- Authors to whom correspondence should be addressed; (M.A.B.); (M.G.A.); Tel.: +55-21-2629-9599 (M.A.B.); +55-21-2562-7132 (M.G.A.)
| | - Carlos Rangel Rodrigues
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - José Jair Viana Cirino
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Jocley Queiroz Araújo
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Thiago Honório
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - Lúcio Mendes Cabral
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - Ricardo Bicca de Alencastro
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Helena Carla Castro
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Institute of Biology, Fluminense Federal University (UFF), Niterói, RJ, 24210-130, Brazil
| | - Magaly Girão Albuquerque
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
- Authors to whom correspondence should be addressed; (M.A.B.); (M.G.A.); Tel.: +55-21-2629-9599 (M.A.B.); +55-21-2562-7132 (M.G.A.)
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Hassam M, Basson AE, Liotta DC, Morris L, van Otterlo WAL, Pelly SC. Novel Cyclopropyl-Indole Derivatives as HIV Non-Nucleoside Reverse Transcriptase Inhibitors. ACS Med Chem Lett 2012; 3:470-5. [PMID: 24900496 DOI: 10.1021/ml3000462] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/02/2012] [Indexed: 11/28/2022] Open
Abstract
The HIV pandemic represents one of the most serious diseases to face mankind in both a social and economic context, with many developing nations being the worst afflicted. Due to ongoing resistance issues associated with the disease, the design and synthesis of anti-HIV agents presents a constant challenge for medicinal chemists. Utilizing molecular modeling, we have designed a series of novel cyclopropyl indole derivatives as HIV non-nucleoside reverse transcriptase inhibitors and carried out their preparation. These compounds facilitate a double hydrogen bonding interaction to Lys101 and efficiently occupy the hydrophobic pockets in the regions of Tyr181/188 and Val179. Several of these compounds inhibited HIV replication as effectively as nevirapine when tested in a phenotypic assay.
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Affiliation(s)
- Mohammad Hassam
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
| | - Adriaan E. Basson
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Dennis C. Liotta
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Willem A. L. van Otterlo
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
| | - Stephen C. Pelly
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
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33
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Li D, Zhan P, De Clercq E, Liu X. Strategies for the design of HIV-1 non-nucleoside reverse transcriptase inhibitors: lessons from the development of seven representative paradigms. J Med Chem 2012; 55:3595-613. [PMID: 22268494 DOI: 10.1021/jm200990c] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dongyue Li
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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34
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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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Gao C, Herold JM, Kireev D, Wigle T, Norris JL, Frye S. Biophysical probes reveal a "compromise" nature of the methyl-lysine binding pocket in L3MBTL1. J Am Chem Soc 2011; 133:5357-62. [PMID: 21428286 DOI: 10.1021/ja110432e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Histone lysine methylation (Kme) encodes essential information modulating many biological processes including gene expression and transcriptional regulation. However, the atomic-level recognition mechanisms of methylated histones by their respective adaptor proteins are still elusive. For instance, it is unclear how L3MBTL1, a methyl-lysine histone code reader, recognizes equally well both mono- and dimethyl marks but ignores unmodified and trimethylated lysine residues. We made use of molecular dynamics (MD) and free energy perturbation (FEP) techniques in order to investigate the energetics and dynamics of the methyl-lysine recognition. Isothermal titration calorimetry (ITC) was employed to experimentally validate the computational findings. Both computational and experimental methods were applied to a set of designed "biophysical" probes that mimic the shape of a single lysine residue and reproduce the binding affinities of cognate histone peptides. Our results suggest that, besides forming favorable interactions, the L3MBTL1 binding pocket energetically penalizes both methylation states and has most probably evolved as a "compromise" that nonoptimally fits to both mono- and dimethyl-lysine marks.
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Affiliation(s)
- Cen Gao
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7363, USA
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Nikolenko GN, Kotelkin AT, Oreshkova SF, Ilyichev AA. Mechanisms of HIV-1 drug resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors. Mol Biol 2011. [DOI: 10.1134/s0026893311010092] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tang BX, Song RJ, Wu CY, Wang ZQ, Liu Y, Huang XC, Xie YX, Li JH. Ruthenium-catalyzed intramolecular carbocyclization of alkynes with an sp3 carbon involving an oxidative deprotonation process. Chem Sci 2011. [DOI: 10.1039/c1sc00423a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Alexandre FR, Amador A, Bot S, Caillet C, Convard T, Jakubik J, Musiu C, Poddesu B, Vargiu L, Liuzzi M, Roland A, Seifer M, Standring D, Storer R, Dousson CB. Synthesis and biological evaluation of aryl-phospho-indole as novel HIV-1 non-nucleoside reverse transcriptase inhibitors. J Med Chem 2010; 54:392-5. [PMID: 21142105 DOI: 10.1021/jm101142k] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel series of 3-aryl-phospho-indole (API) non-nucleoside reverse transcriptase inhibitors of HIV-1 was developed. Chemical variation in the phosphorus linker led to the discovery of 3-phenyl-methyl-phosphinate-2-carboxamide 14, which possessed excellent potency against wild-type HIV-1 as well as viruses bearing K103N and Y181C single mutants in the reverse transcriptase gene. Chiral separation of the enantiomers showed that only R enantiomer retained the activity. The pharmacokinetic, solubility, and metabolic properties of 14 were assessed.
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Doolittle JM, Gomez SM. Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virol J 2010; 7:82. [PMID: 20426868 PMCID: PMC2877021 DOI: 10.1186/1743-422x-7-82] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 04/28/2010] [Indexed: 01/05/2023] Open
Abstract
Background In the course of infection, viruses such as HIV-1 must enter a cell, travel to sites where they can hijack host machinery to transcribe their genes and translate their proteins, assemble, and then leave the cell again, all while evading the host immune system. Thus, successful infection depends on the pathogen's ability to manipulate the biological pathways and processes of the organism it infects. Interactions between HIV-encoded and human proteins provide one means by which HIV-1 can connect into cellular pathways to carry out these survival processes. Results We developed and applied a computational approach to predict interactions between HIV and human proteins based on structural similarity of 9 HIV-1 proteins to human proteins having known interactions. Using functional data from RNAi studies as a filter, we generated over 2000 interaction predictions between HIV proteins and 406 unique human proteins. Additional filtering based on Gene Ontology cellular component annotation reduced the number of predictions to 502 interactions involving 137 human proteins. We find numerous known interactions as well as novel interactions showing significant functional relevance based on supporting Gene Ontology and literature evidence. Conclusions Understanding the interplay between HIV-1 and its human host will help in understanding the viral lifecycle and the ways in which this virus is able to manipulate its host. The results shown here provide a potential set of interactions that are amenable to further experimental manipulation as well as potential targets for therapeutic intervention.
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Affiliation(s)
- Janet M Doolittle
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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An efficient route to 4-substituted coumarins, 2(5H)-furanones, and pyrones via palladium-catalyzed couplings of alkenyl tosylates with organoindium reagents. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2009.10.096] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Manganese(III)-mediated facile synthesis of 3,4-dihydro-2(1H)-quinolinones: selectivity of the 6-endo and 5-exo cyclization. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.08.068] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Sweeney Z, Kennedy‐Smith J, Wu J, Arora N, Billedeau J, Davidson J, Fretland J, Hang J, Heilek G, Harris S, Hirschfeld D, Inbar P, Javanbakht H, Jernelius J, Jin Q, Li Y, Liang W, Roetz R, Sarma K, Smith M, Stefanidis D, Su G, Suh J, Villaseñor A, Welch M, Zhang F, Klumpp K. Diphenyl Ether Non‐Nucleoside Reverse Transcriptase Inhibitors with Excellent Potency Against Resistant Mutant Viruses and Promising Pharmacokinetic Properties. ChemMedChem 2009; 4:88-99. [DOI: 10.1002/cmdc.200800262] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Zachary K. Sweeney
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - Joshua J. Kennedy‐Smith
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - Jeffrey Wu
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - Nidhi Arora
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - J. Roland Billedeau
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - James P. Davidson
- Department of Chemical Synthesis, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Jennifer Fretland
- Department of Non‐Clinical Safety, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Julie Q. Hang
- Department of Viral Disease Biochemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Gabrielle M. Heilek
- Department of Viral Disease Biology, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Seth F. Harris
- Department of Discovery Sciences and Technologies, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Donald Hirschfeld
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - Petra Inbar
- Department of Discovery Pharmaceutics, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Hassan Javanbakht
- Department of Viral Disease Biology, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Jesper A. Jernelius
- Department of Chemical Synthesis, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Qingwu Jin
- Department of Chemical Synthesis, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Yu Li
- Department of Viral Disease Biochemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Weiling Liang
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - Ralf Roetz
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - Keshab Sarma
- Department of Chemical Synthesis, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Mark Smith
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - Dimitrio Stefanidis
- Department of Discovery Pharmaceutics, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Guoping Su
- Department of Viral Disease Biology, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Judy M. Suh
- Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA), Fax: (+1) 650‐852‐1311
| | - Armando G. Villaseñor
- Department of Discovery Sciences and Technologies, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Michael Welch
- Department of Chemical Synthesis, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Fang‐Jie Zhang
- Department of Chemical Synthesis, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
| | - Klaus Klumpp
- Department of Viral Disease Biochemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304 (USA)
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Abstract
The dominant paradigm in drug discovery is the concept of designing maximally selective ligands to act on individual drug targets. However, many effective drugs act via modulation of multiple proteins rather than single targets. Advances in systems biology are revealing a phenotypic robustness and a network structure that strongly suggests that exquisitely selective compounds, compared with multitarget drugs, may exhibit lower than desired clinical efficacy. This new appreciation of the role of polypharmacology has significant implications for tackling the two major sources of attrition in drug development--efficacy and toxicity. Integrating network biology and polypharmacology holds the promise of expanding the current opportunity space for druggable targets. However, the rational design of polypharmacology faces considerable challenges in the need for new methods to validate target combinations and optimize multiple structure-activity relationships while maintaining drug-like properties. Advances in these areas are creating the foundation of the next paradigm in drug discovery: network pharmacology.
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Affiliation(s)
- Andrew L Hopkins
- Division of Biological Chemistry and Drug Discovery, College of Life Science, University of Dundee, Dundee, UK.
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Sweeney ZK, Harris SF, Arora N, Javanbakht H, Li Y, Fretland J, Davidson JP, Billedeau JR, Gleason SK, Hirschfeld D, Kennedy-Smith JJ, Mirzadegan T, Roetz R, Smith M, Sperry S, Suh JM, Wu J, Tsing S, Villaseñor AG, Paul A, Su G, Heilek G, Hang JQ, Zhou AS, Jernelius JA, Zhang FJ, Klumpp K. Design of Annulated Pyrazoles as Inhibitors of HIV-1 Reverse Transcriptase. J Med Chem 2008; 51:7449-58. [DOI: 10.1021/jm800527x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zachary K. Sweeney
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Seth F. Harris
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Nidhi Arora
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Hassan Javanbakht
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Yu Li
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Jennifer Fretland
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - James P. Davidson
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - J. Roland Billedeau
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Shelley K. Gleason
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Donald Hirschfeld
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Joshua J. Kennedy-Smith
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Taraneh Mirzadegan
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Ralf Roetz
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Mark Smith
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Sarah Sperry
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Judy M. Suh
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Jeffrey Wu
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Stan Tsing
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Armando G. Villaseñor
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Amber Paul
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Guoping Su
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Gabrielle Heilek
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Julie Q. Hang
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Amy S. Zhou
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Jesper A. Jernelius
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Fang-Jie Zhang
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Klaus Klumpp
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
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Ren J, Chamberlain PP, Stamp A, Short SA, Weaver KL, Romines KR, Hazen R, Freeman A, Ferris RG, Andrews CW, Boone L, Chan JH, Stammers DK. Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors. J Med Chem 2008; 51:5000-8. [PMID: 18665583 DOI: 10.1021/jm8004493] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Owing to the emergence of resistant virus, next generation non-nucleoside HIV reverse transcriptase inhibitors (NNRTIs) with improved drug resistance profiles have been developed to treat HIV infection. Crystal structures of HIV-1 RT complexed with benzophenones optimized for inhibition of HIV mutants that were resistant to the prototype benzophenone GF128590 indicate factors contributing to the resilience of later compounds in the series (GW4511, GW678248). Meta-substituents on the benzophenone A-ring had the designed effect of inducing better contacts with the conserved W229 while reducing aromatic stacking interactions with the highly mutable Y181 side chain, which unexpectedly adopted a "down" position. Up to four main-chain hydrogen bonds to the inhibitor also appear significant in contributing to resilience. Structures of mutant RTs (K103N, V106A/Y181C) with benzophenones showed only small rearrangements of the NNRTIs relative to wild-type. Hence, adaptation to a mutated NNRTI pocket by inhibitor rearrangement appears less significant for benzophenones than other next-generation NNRTIs.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
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Zhang X, Crespo A, Fernández A. Turning promiscuous kinase inhibitors into safer drugs. Trends Biotechnol 2008; 26:295-301. [DOI: 10.1016/j.tibtech.2008.02.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 02/23/2008] [Accepted: 02/29/2008] [Indexed: 10/22/2022]
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Nervall M, Hanspers P, Carlsson J, Boukharta L, Aqvist J. Predicting binding modes from free energy calculations. J Med Chem 2008; 51:2657-67. [PMID: 18410080 DOI: 10.1021/jm701218j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To produce reliable predictions of bioactive conformations is a major challenge in the field of structure-based inhibitor design and is a requirement for accurate binding free energy predictions with structure-based methods. A series of HIV-1 reverse transcriptase inhibitors was cross-docked using a non-native crystal structure that resulted in two distinct clusters of possible conformations. One of these clusters was compatible with an existing crystal structure, whereas the other displayed a flipped heterocyclic group. Binding free energies, using the non-native crystal structure, calculated from several scoring functions, were similar for the two clusters, and no conclusion about the binding mode could be drawn from these results. The two clusters could be separated through rescoring with the linear interaction method (LIE) in combination with molecular dynamics simulations, which leads to a binding mode prediction in line with experimental crystallographic data. Further, the LIE model produces the best correlation between experimental and calculated binding free energies among the tested scoring methods.
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Affiliation(s)
- Martin Nervall
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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Ren J, Stammers DK. Structural basis for drug resistance mechanisms for non-nucleoside inhibitors of HIV reverse transcriptase. Virus Res 2008; 134:157-70. [PMID: 18313784 DOI: 10.1016/j.virusres.2007.12.018] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 12/21/2007] [Accepted: 12/21/2007] [Indexed: 11/25/2022]
Abstract
The selection of drug resistant virus is a significant obstacle to the continued successful treatment of HIV infection. Reverse transcriptase is the target for numerous approved anti-HIV drugs including both nucleoside inhibitor (NRTI) and non-nucleosides (NNRTI). The many available crystal structures of RT reveal that, generally, in relation to their binding sites NRTI resistance mutations are generally more distally positioned, whilst for NNRTIs mutations are clustered. Such clustering implies a direct stereochemical basis for NNRTI resistance mechanisms, which is indeed observed in many cases such as the loss of key ring stacking interactions with inhibitors via mutations at Tyr181 and Tyr188. However, there are also indirect resistance mechanisms observed, e.g. V108I (via perturbation of Tyr188 and Tyr181) and K103N (apo-enzyme stabilisation). The resistance mechanism can be NNRTI-dependent as is the case for K101E where either indirect (nevirapine) or direct effects (efavirenz) apply. Structural studies have contributed to the design of newer generation NNRTIs and identified a number of features which may contribute to their much improved resistance profiles. Such factors include reduced interactions with Tyr181, the presence of inhibitor/main-chain H-bonds and ability to undergo conformational flexing and rearrangement within the mutated drug site.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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Vargas G, Escalona IS, Salas M, Gordillo B, Sierra A. Synthesis and RT inhibitory activity evaluation of new pyrimidine-based seco-nucleosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 25:243-57. [PMID: 16629118 DOI: 10.1080/15257770500446931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Eleven new 3',4'-seco acyclic nucleosides (4-14) were prepared by nucleophilic substitution of protected pyrimidine bases on ethyl 3,3-diethoxypropanoate (3). Structures were characterized spectroscopically and a brief analysis of their conformation in solution was performed by the vicinal coupling constants (3)JH2'aH3' and (3)JH2'bH3'. In solid state, compound 6 forms a homodimer linked by hydrogen bonding. In preliminary tests all compounds show low toxicity and gentle activity against HIV-1 RT in vitro.
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Affiliation(s)
- Genaro Vargas
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México, DF México
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Wang Y, Chen FE, Balzarini J, De Clercq E, Pannecouque C. Non-Nucleoside HIV-1 Reverse-Transcriptase Inhibitors. Part 10. Chem Biodivers 2008; 5:168-76. [DOI: 10.1002/cbdv.200890008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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