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Virtual Screening and Molecular Docking Studies for Discovery of Potential RNA-Dependent RNA Polymerase Inhibitors. CRYSTALS 2021. [DOI: 10.3390/cryst11050471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The current COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Globally, this pandemic has affected over 111 million individuals and posed many health and economic challenges. Much research effort is dedicated to discovering new treatments to address the associated challenges and restrict the spread of SARS-CoV-2. Since SARS-CoV-2 is a positive-strand RNA virus, its replication requires the viral RNA-dependent RNA polymerase (RdRp) enzyme. In this study, we report the discovery of new potential RdRp enzyme inhibitors based on computer modeling and simulation methodologies. The antiviral ZINC database was utilized for covalent docking virtual screening followed by molecular inter-action analyses based on reported hot spots within the RdRp binding pocket (PDB: 7BV2). Eleven molecules, ZINC000014944915, ZINC000027556215, ZINC000013556344, ZINC000003589958, ZINC000003833965, ZINC000001642252, ZINC000028525778, ZINC000027557701, ZINC000013781295, ZINC000001651128 and ZINC000013473324, were shown to have the highest binding interactions. These molecules were further assessed by molecular dynamics (MD) simu-lations and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies. The results showed that all 11 molecules except ZINC000027557701 formed stable complexes with the viral RdRp and fell within the accepted ADMET parameters. The identified molecules can be used to design future potential RdRp inhibitors.
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Xu Z, Chen Q, Zhang Y, Liang C. Coumarin-based derivatives with potential anti-HIV activity. Fitoterapia 2021; 150:104863. [PMID: 33582266 DOI: 10.1016/j.fitote.2021.104863] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/11/2021] [Accepted: 01/31/2021] [Indexed: 02/06/2023]
Abstract
Acquired immunodeficiency syndrome (AIDS), as a result of human immunodeficiency virus (HIV) infection which leads to severe suppression of immune functions, is an enormous world-wide health threat. The anti-HIV agents are critical for the HIV/AIDS therapy, but the generation of viral mutants and the severe side effects of the anti-HIV agents pose serious hurdles in the treatment of HIV infection, and creat an urgent need to develop novel anti-HIV agents. The plant-derived compounds possess structural and mechanistic diversity, and among them, coumarin-based derivatives have the potential to inhibit different stages in the HIV replication cycle, inclusive of virus-host cell attachment, cell membrane fusion, integration, assembly besides the conventional target like inhibition of the reverse transcriptase, protease, and integrase. Moreover, (+)-calanolide A, a coumarin-based natural product, is a potential anti-HIV agent. Thus, coumarin-based derivatives are useful scaffolds for the development of anti-HIV agents. This review article describes the recent progress in the discovery, structural modification, and structure-activity relationship studies of potent anti-HIV coumarin-based derivatives including natural coumarin compounds, synthetic hybrids, dimers, and other synthetic derivatives covering articles published between 2000 and 2020.
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Affiliation(s)
- Zhi Xu
- Huanghuai University Industry Innovation & Research and Development Institute of Zhumadian, Zhumadian, People's Republic of China.
| | - Qingtai Chen
- Huanghuai University Industry Innovation & Research and Development Institute of Zhumadian, Zhumadian, People's Republic of China
| | - Yan Zhang
- Huanghuai University Industry Innovation & Research and Development Institute of Zhumadian, Zhumadian, People's Republic of China
| | - Changli Liang
- Huanghuai University Industry Innovation & Research and Development Institute of Zhumadian, Zhumadian, People's Republic of China.
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3
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Kharrngi B, Dhar ED, Basumatary G, Das D, Deka RC, Yadav AK, Bez G. Developing a highly potent anthelmintic: study of catalytic application of l-proline derived aminothiourea in rapid synthesis of biscoumarins and their in vitro anthelmintic essay. J CHEM SCI 2021. [DOI: 10.1007/s12039-020-01881-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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4
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Kaur G, Singh D, Singh A, Banerjee B. Camphor sulfonic acid catalyzed facile and general method for the synthesis of 3,3'-(arylmethylene)bis(4-hydroxy-2H-chromen-2-ones), 3,3'-(arylmethylene)bis(2-hydroxynaphthalene-1,4-diones) and 3,3'-(2-oxoindoline-3,3-diyl)bis(2-hydroxynaphthalene-1,4-dione) derivatives at room temperature. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1856877] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Gurpreet Kaur
- Department of Chemistry, Indus International University, Bathu, Himachal Pradesh, India
| | - Diksha Singh
- Department of Chemistry, Indus International University, Bathu, Himachal Pradesh, India
| | - Arvind Singh
- Department of Chemistry, Indus International University, Bathu, Himachal Pradesh, India
| | - Bubun Banerjee
- Department of Chemistry, Indus International University, Bathu, Himachal Pradesh, India
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Brahmachari G, Begam S. Ceric Ammonium Nitrate (CAN): An Efficient and Eco‐Friendly Catalyst for One‐Pot Synthesis of Diversely Functionalized Biscoumarins in Aqueous Medium under Ambient Conditions. ChemistrySelect 2019. [DOI: 10.1002/slct.201900961] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Goutam Brahmachari
- Laboratory of Natural Products & Organic SynthesisDepartment of ChemistryVisva-Bharati (a Central University), Santiniketan- 731 235 West Bengal India
| | - Sanchari Begam
- Laboratory of Natural Products & Organic SynthesisDepartment of ChemistryVisva-Bharati (a Central University), Santiniketan- 731 235 West Bengal India
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Banerjee B. Recent developments on ultrasound assisted catalyst-free organic synthesis. ULTRASONICS SONOCHEMISTRY 2017; 35:1-14. [PMID: 27771266 DOI: 10.1016/j.ultsonch.2016.09.023] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/23/2016] [Accepted: 09/27/2016] [Indexed: 05/04/2023]
Abstract
Mother Nature needs to be protected from ever increasing chemical pollutions associated with synthetic organic processes. The fundamental challenge for today's methodologists is to make their protocols more environmentally benign and sustainable by avoiding the extensive use of hazardous reagents and solvents, harsh reaction conditions, and toxic metal catalysts. However, the people of the twenty-first century are well aware about the side effects of those hazardous substances used and generated by the chemical processes. As a result, the last decade has seen a tremendous outburst in modifying chemical processes to make them 'sustainable' for the betterment of our environment. Catalysts play a crucial role in organic synthesis and thus they find huge applications and uses. Scientists' continuously trying to modify the catalysts to reduce their toxicity level, but the most benign way is to design an organic reaction without catalyst(s), if possible. It is worthy to mention that the involvement of ultrasound in organic synthesis is sometimes fulfilling this goal. In many occasions the applications of ultrasound can avoid the use of catalysts in organic reactions. Such beneficial features as a whole have motivated the organic chemists to apply ultrasonic irradiation in more heights and as a results, in recent past, there were immense applications of ultrasound in organic reactions for the synthesis of diverse organic scaffolds under catalyst-free condition. The present review summarizes the latest developments on ultrasound assisted catalyst-free organic synthesis reported so far.
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Affiliation(s)
- Bubun Banerjee
- Department of Chemistry, Indus International University, V.P.O. Bathu, Distt. Una, Himachal Pradesh 174301, India.
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7
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Wang Y, Klock H, Yin H, Wolff K, Bieza K, Niswonger K, Matzen J, Gunderson D, Hale J, Lesley S, Kuhen K, Caldwell J, Brinker A. Homogeneous High-Throughput Screening Assays for HIV-1 Integrase 3β-Processing and Strand Transfer Activities. ACTA ACUST UNITED AC 2016; 10:456-62. [PMID: 16093555 DOI: 10.1177/1087057105275212] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
HIV-1 integrase (HIV-IN) is a well-validated antiviral drug target catalyzing a multistep reaction to incorporate the HIV-1 provirus into the genome of the host cell. Smallmolecule inhibitors of HIV-1 integrase that specifically target the strand transfer step have demonstrated efficacy in the suppression of virus propagation. However, only fewspecific strand transfer inhibitors have been identified to date, and the need to screen for novel compound scaffolds persists. Here, the authors describe 2 homogeneous time-resolved fluorescent resonance energy transfer-based assays for the measurement of HIV-1 integrase 3'-processing and strand transfer activities. Both assayswere optimized for high-throughput screening formats, and a diverse library containingmore than 1million compoundswas screened in 1536-well plates for HIV-IN strand transfer inhibitors. As a result, compounds were found that selectively affect the enzymatic strand transfer reaction over 3β processing. Moreover, several bioactivemoleculeswere identified that inhibited HIV-1 reporter virus infection in cellularmodel systems. In conclusion, the assays presented herein have proven their utility for the identification ofmechanistically interesting and biologically active inhibitors of HIV-1 integrase that hold potential for further development into potent antiviral drugs.
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Affiliation(s)
- Yu Wang
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
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8
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Wu B, Tang J, Wilson DJ, Huber AD, Casey MC, Ji J, Kankanala J, Xie J, Sarafianos SG, Wang Z. 3-Hydroxypyrimidine-2,4-dione-5-N-benzylcarboxamides Potently Inhibit HIV-1 Integrase and RNase H. J Med Chem 2016; 59:6136-48. [PMID: 27283261 DOI: 10.1021/acs.jmedchem.6b00040] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Resistance selection by human immunodeficiency virus (HIV) toward known drug regimens necessitates the discovery of structurally novel antivirals with a distinct resistance profile. On the basis of our previously reported 3-hydroxypyrimidine-2,4-dione (HPD) core, we have designed and synthesized a new integrase strand transfer (INST) inhibitor type featuring a 5-N-benzylcarboxamide moiety. Significantly, the 6-alkylamino variant of this new chemotype consistently conferred low nanomolar inhibitory activity against HIV-1. Extended antiviral testing against a few raltegravir-resistant HIV-1 clones revealed a resistance profile similar to that of the second generation INST inhibitor (INSTI) dolutegravir. Although biochemical testing and molecular modeling also strongly corroborate the inhibition of INST as the antiviral mechanism of action, selected antiviral analogues also potently inhibited reverse transcriptase (RT) associated RNase H, implying potential dual target inhibition. In vitro ADME assays demonstrated that this novel chemotype possesses largely favorable physicochemical properties suitable for further development.
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Affiliation(s)
- Bulan Wu
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Andrew D Huber
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia, Missouri 65211, United States
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia, Missouri 65211, United States
| | - Juan Ji
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia, Missouri 65211, United States
| | - Jayakanth Kankanala
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia, Missouri 65211, United States
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
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Domingo A, Specklin D, Rosa V, Mameri S, Robert V, Welter R. Probing the Influence of the Ligands on the Magnetism of Dinuclear Manganese, Iron, and Chromium Complexes Supported by Aroylhydrazone. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Kumar SP, Jasrai YT, Mehta VP, Pandya HA. Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors. J Biomol Struct Dyn 2014; 33:706-22. [PMID: 24735019 DOI: 10.1080/07391102.2014.908142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantitative pharmacophore hypothesis combines the 3D spatial arrangement of pharmacophore features with biological activities of the ligand data-set and predicts the activities of geometrically and/or pharmacophoric similar ligands. Most pharmacophore discovery programs face difficulties in conformational flexibility, molecular alignment, pharmacophore features sampling, and feature selection to score models if the data-set constitutes diverse ligands. Towards this focus, we describe a ligand-based computational procedure to introduce flexibility in aligning the small molecules and generating a pharmacophore hypothesis without geometrical constraints to define pharmacophore space, enriched with chemical features necessary to elucidate common pharmacophore hypotheses (CPHs). Maximal common substructure (MCS)-based alignment method was adopted to guide the alignment of carbon molecules, deciphered the MCS atom connectivity to cluster molecules in bins and subsequently, calculated the pharmacophore similarity matrix with the bin-specific reference molecules. After alignment, the carbon molecules were enriched with original atoms in their respective positions and conventional pharmacophore features were perceived. Distance-based pharmacophoric descriptors were enumerated by computing the interdistance between perceived features and MCS-aligned 'centroid' position. The descriptor set and biological activities were used to develop support vector machine models to predict the activities of the external test set. Finally, fitness score was estimated based on pharmacophore similarity with its bin-specific reference molecules to recognize the best and poor alignments and, also with each reference molecule to predict outliers of the quantitative hypothesis model. We applied this procedure to a diverse data-set of 40 HIV-1 integrase inhibitors and discussed its effectiveness with the reported CPH model.
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Affiliation(s)
- Sivakumar Prasanth Kumar
- a Department of Bioinformatics, Applied Botany Centre (ABC) , Gujarat University , Ahmedabad 380009 , Gujarat , India
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11
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Bhatt H, Patel P, Pannecouque C. Discovery of HIV-1 Integrase Inhibitors: Pharmacophore Mapping, Virtual Screening, Molecular Docking, Synthesis, and Biological Evaluation. Chem Biol Drug Des 2013; 83:154-66. [DOI: 10.1111/cbdd.12207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 07/18/2013] [Accepted: 08/12/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Hardik Bhatt
- Department of Pharmaceutical Chemistry; Institute of Pharmacy; Nirma University; Ahmedabad 382 481 India
| | - Paresh Patel
- Department of Pharmaceutical Chemistry; L.J. Institute of Pharmacy; L.J. Campus, S.G. Highway Ahmedabad 382 210 India
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12
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Lee S, Lee Y, Briggs JM, Lee KW. Pharmacophore Models of Paclitaxel- and Epothilone-Based Microtubule Stabilizing Agents. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.7.1972] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Cheaib K, Martel D, Clément N, Eckes F, Kouaho S, Rogez G, Dagorne S, Kurmoo M, Choua S, Welter R. Structural, magnetic and optical properties of an FeIIIdimer bridged by the meridional planar divergent N,N′-bis(salicyl)hydrazide and its photo- and electro-chemistry in solution. Dalton Trans 2013; 42:1406-16. [DOI: 10.1039/c2dt32310a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Gupta P, Garg P, Roy N. Identification of Novel HIV-1 Integrase Inhibitors Using Shape-Based Screening, QSAR, and Docking Approach. Chem Biol Drug Des 2012; 79:835-49. [DOI: 10.1111/j.1747-0285.2012.01326.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Scaffold hopping for identification of novel D(2) antagonist based on 3D pharmacophore modelling of illoperidone analogs. Mol Divers 2011; 16:367-75. [PMID: 22161148 DOI: 10.1007/s11030-011-9349-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
Abstract
The dopamine D(2) receptor is involved in the etiology of a number of disorders, such as Parkinson's disease, Huntington's Chorea, tardive dyskinesia and schizophrenia. Antagonism of D(2) receptors is implicated in the treatment of various psychiatric disorders. In order to understand essential structural features required for D(2) antagonism, this research article elaborates on the generation of a four-point 3D pharmacophore model which was extracted from a series of 45 novel 3-[[(aryloxy)alkyl]piperidinyl]-1,2-benzisoxazole derivatives. The best pharmacophore model generated consisted of four PRRR features: a positively charged group (P), and three aromatic rings (R). Based on the model generated, a statistically valid 3D-QSAR with good predictability (Q(2) = 0.756) was derived. For the validation of the pharmacophore hypothesis, active compounds were docked against the 3D structure of the D(2) receptor which was constructed through homology modeling. Further, the derived pharmacophore was used as a query to search the Zinc 'clean drug-like' database. Hits retrieved were passed progressively through filters, such as fitness score, predicted activity and docking scores. The resulting hits present new scaffolds with a strong potential for D(2) antagonist.
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Sun HP, Zhu J, Chen FH, Zhang SL, Zhang Y, You QD. Combination of pharmacophore model development and binding mode analyses: Identification of ligand features essential for IκB kinase-beta (IKKβ) inhibitors and virtual screening based on it. Eur J Med Chem 2011; 46:3942-52. [DOI: 10.1016/j.ejmech.2011.05.066] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 04/02/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
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Telvekar VN, Patel KN. Pharmacophore development and docking studies of the hiv-1 integrase inhibitors derived from N-methylpyrimidones, Dihydroxypyrimidines, and bicyclic pyrimidinones. Chem Biol Drug Des 2011; 78:150-60. [PMID: 21518263 DOI: 10.1111/j.1747-0285.2011.01130.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To elucidate the crucial structural features for the HIV-1 integrase inhibitors, a three-dimensional pharmacophore model was developed based on N-methyl pyrimidones, dihydroxypyrimidines, and bicyclic pyrimidinones derivatives using Phase. N-methyl pyrimidone derivative raltegravir, the first US-FDA approved drug by Merck, belongs to this series. The best-fitted common pharmacophore hypothesis was characterized by two acceptor, two hydrophobic, and two ring features having a correlation coefficient of 0.895, cross-validated Q(2) value of 0.631, and survival score of 8.862, suggesting that a highly predictive pharmacophore model was developed. The cross-validation studies using 23 test set molecules and fifteen structurally diverse HIV-integrase inhibitors give extra confidence about the correctness of the pharmacophore model. The cross-validation studies proved that our developed model can successfully differentiate between active and inactive HIV-integrase inhibitors. The docking studies were also carried out wherein the molecules were docked against the active site of HIV integrase to analyze the binding mode and the necessary structural requirement for their respective enzymatic inhibition. The results obtained from our studies provide a valuable tool for designing of new lead molecules with potent activity.
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Affiliation(s)
- Vikas N Telvekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga (E), Mumbai, India.
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18
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Tang J, Maddali K, Dreis CD, Sham YY, Vince R, Pommier Y, Wang Z. 6-Benzoyl-3-hydroxypyrimidine-2,4-diones as dual inhibitors of HIV reverse transcriptase and integrase. Bioorg Med Chem Lett 2011; 21:2400-2. [PMID: 21392991 PMCID: PMC3070847 DOI: 10.1016/j.bmcl.2011.02.069] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 02/14/2011] [Accepted: 02/16/2011] [Indexed: 01/21/2023]
Abstract
N-3-hydroxylation of pyrimidine-2,4-diones was recently found to yield inhibitors of both HIV-1 reverse transcriptase (RT) and integrase (IN). An extended series of analogues featuring a benzoyl group at the C-6 position of the pyrimidine ring was synthesized. Through biochemical studies it was found that these new analogues are dually active against both RT and IN in low micromolar range. Antiviral assays confirmed that these new inhibitors are active against HIV-1 in cell culture at nanomolar to low micromolar range, further validating 3-hydroxypyrimidine-2,4-diones as a viable scaffold for antiviral development.
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Affiliation(s)
- Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St SE, Minneapolis, MN 55455
| | - Kasthuraiah Maddali
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Christine D. Dreis
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St SE, Minneapolis, MN 55455
| | - Yuk Y. Sham
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St SE, Minneapolis, MN 55455
| | - Robert Vince
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St SE, Minneapolis, MN 55455
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St SE, Minneapolis, MN 55455
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Tang J, Maddali K, Metifiot M, Sham YY, Vince R, Pommier Y, Wang Z. 3-Hydroxypyrimidine-2,4-diones as an inhibitor scaffold of HIV integrase. J Med Chem 2011; 54:2282-92. [PMID: 21381765 DOI: 10.1021/jm1014378] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Integrase (IN) represents a clinically validated target for the development of antivirals against human immunodeficiency virus (HIV). Inhibitors with a novel structure core are essential for combating resistance associated with known IN inhibitors (INIs). We have previously disclosed a novel dual inhibitor scaffold of HIV IN and reverse transcriptase (RT). Here we report the complete structure-activity relationship (SAR), molecular modeling, and resistance profile of this inhibitor type on IN inhibition. These studies support an antiviral mechanism of dual inhibition against both IN and RT and validate 3-hydroxypyrimidine-2,4-diones as an IN inhibitor scaffold.
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Affiliation(s)
- Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Abstract
Computer-aided drug design (CADD) methodologies have made great advances and contributed significantly to the discovery and/or optimization of many clinically used drugs in recent years. CADD tools have likewise been applied to the discovery of inhibitors of HIV-1 integrase, a difficult and worthwhile target for the development of efficient anti-HIV drugs. This article reviews the application of CADD tools, including pharmacophore search, quantitative structure-activity relationships, model building of integrase complexed with viral DNA and quantum-chemical studies in the discovery of HIV-1 integrase inhibitors. Different structurally diverse integrase inhibitors have been identified by, or with significant help from, various CADD tools.
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Affiliation(s)
- Chenzhong Liao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles Street, Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles Street, Frederick, MD 21702, USA
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Shi W, Duan Y, Qian Y, Li M, Yang L, Hu W. Design, synthesis, and antibacterial activity of 2,5-dihydropyrrole formyl hydroxyamino derivatives as novel peptide deformylase inhibitors. Bioorg Med Chem Lett 2010; 20:3592-5. [DOI: 10.1016/j.bmcl.2010.04.123] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 04/23/2010] [Accepted: 04/27/2010] [Indexed: 10/19/2022]
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Scaffold rearrangement of dihydroxypyrimidine inhibitors of HIV integrase: Docking model revisited. Bioorg Med Chem Lett 2010; 20:3275-9. [PMID: 20457521 DOI: 10.1016/j.bmcl.2010.04.048] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 04/09/2010] [Accepted: 04/12/2010] [Indexed: 12/12/2022]
Abstract
A series of dihydroxypyrimidine (DHP) derivatives were designed as inhibitors of HIV integrase (IN) based on known homology models. Through chemical synthesis and biochemical assays it was found that the activity profile of these compounds largely deviates from predictions with existing models. With the recently disclosed IN crystal structure of prototype foamy virus (PFV), a new HIV IN homology model was constructed featuring a critical IN/DNA interface previously lacking. With this new model, docking results completely corroborated observed biological activities. This new model should provide a more accurate and improved platform for the design of new inhibitors of HIV IN.
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23
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Murumkar PR, Zambre VP, Yadav MR. Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors. J Comput Aided Mol Des 2010; 24:143-56. [DOI: 10.1007/s10822-010-9322-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 02/09/2010] [Indexed: 11/25/2022]
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Kim KH, Kim ND, Seong BL. Pharmacophore-based virtual screening: a review of recent applications. Expert Opin Drug Discov 2010; 5:205-22. [DOI: 10.1517/17460441003592072] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA). J Mol Model 2008; 15:233-45. [DOI: 10.1007/s00894-008-0399-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 09/06/2008] [Indexed: 11/26/2022]
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26
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Vadivelan S, Sinha BN, Rambabu G, Boppana K, Jagarlapudi SARP. Pharmacophore modeling and virtual screening studies to design some potential histone deacetylase inhibitors as new leads. J Mol Graph Model 2008; 26:935-46. [PMID: 17707666 DOI: 10.1016/j.jmgm.2007.07.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 07/07/2007] [Accepted: 07/08/2007] [Indexed: 11/26/2022]
Abstract
Histone deacetylase is one of the important targets in the treatment of solid tumors and hematological cancers. A total of 20 well-defined inhibitors were used to generate Pharmacophore models using and HypoGen module of Catalyst. These 20 molecules broadly represent 3 different chemotypes. The best HypoGen model consists of four-pharmacophore features--one hydrogen bond acceptor, one hydrophobic aliphatic and two ring aromatic centers. This model was validated against 378 known HDAC inhibitors with a correlation of 0.897 as well as enrichment factor of 2.68 against a maximum value of 3. This model was further used to retrieve molecules from NCI database with 238,819 molecules. A total of 4638 molecules from a pool of 238,819 molecules were identified as hits while 297 molecules were indicated as highly active. Also, a Similarity analysis has been carried out for set of 4638 hits with respect to most active molecule of each chemotypes which validated not only the Virtual Screening potential of the model but also identified the possible new Chemotypes. This type of Similarity analysis would prove to be efficient not only for lead generation but also for lead optimization.
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Affiliation(s)
- S Vadivelan
- GVK Biosciences Pvt. Ltd., S-1, Phase-1, TIE Balanagar, Hyderabad 500037, India.
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27
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Bandyopadhyay D, Agrafiotis DK. A self-organizing algorithm for molecular alignment and pharmacophore development. J Comput Chem 2008; 29:965-82. [DOI: 10.1002/jcc.20854] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Tymoshenko D. Chapter 1 Benzoheteropines with Fused Pyrrole, Furan and Thiophene Rings. ADVANCES IN HETEROCYCLIC CHEMISTRY 2008. [DOI: 10.1016/s0065-2725(07)00001-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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29
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Mugnaini C, Rajamaki S, Tintori C, Corelli F, Massa S, Witvrouw M, Debyser Z, Veljkovic V, Botta M. Toward novel HIV-1 integrase binding inhibitors: Molecular modeling, synthesis, and biological studies. Bioorg Med Chem Lett 2007; 17:5370-3. [PMID: 17716893 DOI: 10.1016/j.bmcl.2007.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 11/17/2022]
Abstract
The identification of a novel hit compound as integrase binding inhibitor has been accomplished by means of virtual screening techniques. A small family of structurally related molecules has been synthesized and biologically evaluated with one of the compounds showing an IC(50)=12 microM.
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Affiliation(s)
- Claudia Mugnaini
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
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30
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Nunthaboot N, Pianwanit S, Parasuk V, Ebalunode JO, Briggs JM, Kokpol S. Hybrid quantum mechanical/molecular mechanical molecular dynamics simulations of HIV-1 integrase/inhibitor complexes. Biophys J 2007; 93:3613-26. [PMID: 17693479 PMCID: PMC2072063 DOI: 10.1529/biophysj.107.108464] [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: 11/18/2022] Open
Abstract
Human immunodeficiency virus (HIV)-1 integrase (IN) is an attractive target for development of acquired immunodeficiency syndrome chemotherapy. In this study, conventional and coupled quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations of HIV-1 IN complexed with 5CITEP (IN-5CITEP) were carried out. In addition to differences in the bound position of 5CITEP, significant differences at the two levels of theory were observed in the metal coordination geometry and the areas involving residues 116-119 and 140-166. In the conventional MD simulation, the coordination of Mg(2+) was found to be a near-perfect octahedral geometry whereas a distorted octahedral complex was observed in QM/MM. All of the above reasons lead to a different pattern of protein-ligand salt link formation that was not observed in the classical MD simulation. Furthermore to provide a theoretical understanding of inhibition mechanisms of 5CITEP and its derivative (DKA), hybrid QM/MM MD simulations of the two complexes (IN-5CITEP and IN-DKA) have been performed. The results reveal that areas involving residues 60-68, 116-119, and 140-149 were substantially different among the two systems. The two systems show similar pattern of metal coordination geometry, i.e., a distorted octahedron. In IN-DKA, both OD1 and OD2 of Asp-64 coordinate the Mg(2+) in a monodentate fashion whereas only OD1 is chelated to the metal as observed in IN-5CITEP. The high potency of DKA as compared to 5CITEP is supported by a strong salt link formed between its carboxylate moiety and the ammonium group of Lys-159. Detailed comparisons between HIV-1 IN complexed with DKA and with 5CITEP provide information about ligand structure effects on protein-ligand interactions in particular with the Lys-159. This is useful for the design of new selective HIV-1 IN inhibitors.
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Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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31
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Tintori C, Manetti F, Veljkovic N, Perovic V, Vercammen J, Hayes S, Massa S, Witvrouw M, Debyser Z, Veljkovic V, Botta M. Novel virtual screening protocol based on the combined use of molecular modeling and electron-ion interaction potential techniques to design HIV-1 integrase inhibitors. J Chem Inf Model 2007; 47:1536-44. [PMID: 17608406 DOI: 10.1021/ci700078n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 integrase (IN) is an essential enzyme for viral replication and represents an intriguing target for the development of new drugs. Although a large number of compounds have been reported to inhibit IN in biochemical assays, no drug active against this enzyme has been approved by the FDA so far. In this study, we report, for the first time, the use of the electron-ion interaction potential (EIIP) technique in combination with molecular modeling approaches for the identification of new IN inhibitors. An innovative virtual screening approach, based on the determination of both short- and long-range interactions between interacting molecules, was employed with the aim of identifying molecules able to inhibit the binding of IN to viral DNA. Moreover, results from a database screening on the commercial Asinex Gold Collection led to the selection of several compounds. One of them showed a significant inhibitory potency toward IN in the overall integration assay. Biological investigations also showed, in agreement with modeling studies, that these compounds prevent recognition of DNA by IN in a fluorescence fluctuation assay, probably by interacting with the DNA binding domain of IN.
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Affiliation(s)
- Cristina Tintori
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy
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32
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Nunthaboot N, Tonmunphean S, Parasuk V, Wolschann P, Kokpol S. Three-dimensional quantitative structure–activity relationship studies on diverse structural classes of HIV-1 integrase inhibitors using CoMFA and CoMSIA. Eur J Med Chem 2006; 41:1359-72. [PMID: 17002889 DOI: 10.1016/j.ejmech.2006.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Revised: 03/10/2006] [Accepted: 06/01/2006] [Indexed: 11/19/2022]
Abstract
Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), three-dimensional quantitative structure-activity relationship (3D-QSAR) techniques, were applied to a set of 89 HIV-1 integrase (IN) inhibitors (training set=61, test set=28), belonging to 11 structurally different classes. The biological data for 3' processing mechanism were used. For CoMFA calculations, three different fitting methods for alignment process were investigated. The best CoMFA model yielded the cross-validated r(2) r(2)(cv) =0.698 and the non-cross-validated r(2) (r(2))=0.947. The derived model indicated the importance of steric (60.8%) as well as electrostatic (39.2%) contributions. For CoMSIA calculations, different combinations of the fields were tested. The best CoMSIA model gave r(2)(cv) =0.724 and r(2)=0.864. This model showed that steric (30.3%), hydrogen bond donor (43.4%) and hydrogen bond acceptor (26.3%) properties played major roles in HIV-1 IN inhibition. The mapping of hydrogen bond interaction fields with the HIV-1 IN active site gave details on hydrogen bond forming between ligands and enzyme. These obtained results agree well with the experimental observations that there should be hydrogen bond interactions between ligands and Glu152, Lys156 and Lys159 residues. The results not only lead to a better understanding of structural requirements of HIV-1 IN inhibitors but also can help in the design of new IN inhibitors.
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Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Manolov I, Maichle-Moessmer C, Nicolova I, Danchev N. Synthesis and anticoagulant activities of substituted 2,4-diketochromans, biscoumarins, and chromanocoumarins. Arch Pharm (Weinheim) 2006; 339:319-26. [PMID: 16649158 DOI: 10.1002/ardp.200500149] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Different substituted 2,4-diketochromans, biscoumarins, and chromanocoumarins are the final products when 4-hydroxycoumarin and aromatic aldehydes containing hydroxyl group in o-, m,- or p-position condense in boiling ethanol. We synthesized 14 compounds. Three of them are described for the first time. The X-ray crystal structure analysis of 3-[6-oxo-(6H, 7H)-benzopyrano[4,3-b]benzopyran-7-yl]-4-hydroxy-2H-1-benzopyran-2-one 1 confirmed the structure of this compound. Acute toxicity studies of the compounds were performed on mice by oral and intraperitoneal administration. A comparative pharmacological study of the in vivo anticoagulant effect of the derivatives with respect to warfarin showed that the synthesized compounds have different anticoagulant activities. The most prospective compounds are 3-(3'-hydroxybenzylidene)-2,4-diketochroman 4 and 3,3'-(2-pyridylmethylene)-bis-4-hydroxy-2H-1-benzopyran-2-one 11 with low toxicity and dose-dependent anticoagulant activity in vivo.
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Affiliation(s)
- Ilia Manolov
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Sofia, Bulgaria.
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Barreca ML, Ferro S, Rao A, De Luca L, Zappalà M, Monforte AM, Debyser Z, Witvrouw M, Chimirri A. Pharmacophore-Based Design of HIV-1 Integrase Strand-Transfer Inhibitors. J Med Chem 2005; 48:7084-8. [PMID: 16250669 DOI: 10.1021/jm050549e] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Using a training set of diketo-like acid HIV-1 integrase (IN) strand-transfer inhibitors, a 3D pharmacophore model was derived having quantitative predictive ability in terms of activity. The best statistical hypothesis consisted of four features (one hydrophobic aromatic region, two hydrogen-bond acceptors, and one hydrogen-bond donor) with r of 0.96. The resulting pharmacophore model guided the rational design of benzylindoles as new potent IN inhibitors, whose microwave-assisted synthesis and biological evaluation are reported.
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Affiliation(s)
- Maria Letizia Barreca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy.
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35
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Zhang XW, Yap YL, Altmeyer RM. Generation of predictive pharmacophore model for SARS-coronavirus main proteinase. Eur J Med Chem 2005; 40:57-62. [PMID: 15642409 PMCID: PMC7115589 DOI: 10.1016/j.ejmech.2004.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Accepted: 09/15/2004] [Indexed: 11/30/2022]
Abstract
Pharmacophore-based virtual screening is an effective, inexpensive and fast approach to discovering useful starting points for drug discovery. In this study, we developed a pharmacophore model for the main proteinase of severe acute respiratory syndrome coronavirus (SARS-CoV). Then we used this pharmacophore model to search NCI 3D database including 250, 251 compounds and identified 30 existing drugs containing the pharmacophore query. Among them are six compounds that already exhibited anti-SARS-CoV activity experimentally. This means that our pharmacophore model can lead to the discovery of potent anti-SARS-CoV inhibitors or promising lead compounds for further SARS-CoV main proteinase inhibitor development.
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Affiliation(s)
- Xue Wu Zhang
- Department of Bioinformatics, HKU-Pasteur Research Center, 8 Sassoon Road, Pokfulam, Hong Kong.
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36
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Dayam R, Sanchez T, Clement O, Shoemaker R, Sei S, Neamati N. β-Diketo Acid Pharmacophore Hypothesis. 1. Discovery of a Novel Class of HIV-1 Integrase Inhibitors. J Med Chem 2004; 48:111-20. [PMID: 15634005 DOI: 10.1021/jm0496077] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HIV-1 Integrase (IN) is an essential enzyme for viral replication. The discovery of beta-diketo acids was crucial in the validation of IN as a legitimate target in drug discovery against HIV infection. In this study, we discovered a novel class of IN inhibitors using a 3D pharmacophore guided database search. We used S-1360 (1), the first IN inhibitor to undergo clinical trials, and three other analogues to develop a common feature pharmacophore hypothesis. Testing this four-featured pharmacophore against a multiconformational database of 150,000 structurally diverse small molecules yielded 1,700 compounds that satisfied the 3D query. Subsequently, all 1,700 compounds were docked into the active site of IN. On the basis of docking scores, Lipinski's rule-of-five, and structural novelty, 110 compounds were selected for biological screening. We found that compounds that contain both salicylic acid and a 2-thioxo-4-thiazolidinone (rhodanine) group (e.g. 5-13) showed significant inhibitory potency against IN, while the presence of either salicylic acid or a rhodanine group alone did not. Although some of the compounds containing only a salicylic acid showed inhibitory potency against IN, none of the compounds containing only rhodanine exhibited considerable potency. Of the 52 compounds reported in this study, 11 compounds (5, 6, 8, 10-13, 32-33, 51, and 53) inhibited 3'-processing or strand transfer activities of IN with IC(50) < or = 25 microM. This is the first reported use of S-1360 and its analogues as leads in developing a pharmacophore hypothesis for IN inhibition and for identification of new compounds with potent inhibition of this enzyme.
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Affiliation(s)
- Raveendra Dayam
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, USA
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