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Parvez MK, Al-Dosari MS, Sinha GP. Machine learning-based predictive models for identifying high active compounds against HIV-1 integrase. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:387-402. [PMID: 35410555 DOI: 10.1080/1062936x.2022.2057588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
HIV-integrase is an important drug target because it catalyzes chromosomal integration of proviral DNA towards establishing latent infection. Computer-aided drug design has immensely contributed to identifying and developing novel antiviral drugs. We have developed various machine learning-based predictive models for identifying high activity compounds against HIV-integrase. Multiclass models were built using support vector machine with reasonable accuracy on the test and evaluation sets. The developed models were evaluated by rigorous validation approaches and the best features were selected by Boruta method. As compared to the model developed from all descriptors set, a slight improvement was observed among the selected descriptors. Validated models were further used for virtual screening of potential compounds from ChemBridge library. Of the six high active compounds predicted from selected models, compounds 9103124, 6642917 and 9082952 showed the most reasonable binding-affinity and stable-interaction with HIV-integrase active-site residues Asp64, Glu152 and Asn155. This was in agreement with previous reports on the essentiality of these residues against a wide range of inhibitors. We therefore highlight the rigorosity of validated classification models for accurate prediction and ranking of high active lead drugs against HIV-integrase.
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Affiliation(s)
- M K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - M S Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - G P Sinha
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Safakish M, Hajimahdi Z, Aghasadeghi MR, Vahabpour R, Zarghi A. Design, Synthesis, Molecular Modeling and Anti-HIV Assay of Novel Quinazolinone Incorporated Coumarin Derivatives. Curr HIV Res 2021; 18:41-51. [PMID: 31820700 DOI: 10.2174/1570162x17666191210105809] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND The emergence of drug-resistant viral strains has created the need for the development of novel anti-HIV agents with a diverse structure that targets key enzymes in the HIV lifecycle. OBJECTIVE Considering the pharmacophore of integrase inhibitors, one of the validated targets for anti-HIV therapy, we designed a quinazolinone incorporated coumarin scaffold to affect HIV. METHODS Coumarin is a beta enol ester and also a well-known drug scaffold. Designed structures were prepared using a one-pot three-component reaction from 3-amino-4-hydroxycoumarin, isatoic anhydride and benzaldehyde derivatives. RESULTS In vitro anti-HIV and cytotoxicity assay indicated that more than half of the compounds had EC50 values lower than 50 µM. Unsubstituted phenyl derivative showed the highest activity and selectivity with an EC50 value of 5 µM and a therapeutic index of 7. Compounds were docked into the integrase active site to investigate the probable mechanism of action. Accordingly, the hydroxyl moiety of coumarin along with the carbonyl of the quinazolinone ring could function as the metal chelating group. Quinazolinone and phenyl groups interact with side chains of IN residues, as well. CONCLUSION Here, a novel anti-HIV scaffold is represented for further modification and in-vivo studies.
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Affiliation(s)
- Mahdieh Safakish
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Hajimahdi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Rouhollah Vahabpour
- Medical Lab Technology Department, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Zarghi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Synthesis of Novel Tetrahydropyrimido[4,5-B][1,6]Naphthyridines via Condensation of 1-benzyl-3,5-bis[(E)-arylmethylidene]tetrahydropyridin-4(1H)-ones with 6-aminouracils. Chem Heterocycl Compd (N Y) 2020. [DOI: 10.1007/s10593-020-02840-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Akher FB, Farrokhzadeh A, Honarparvar B. Effect of substituent and π-stacking interaction on the metal chelation ability of 7-subestituted 2-oxyisoquinoline-1,3(2H,4H)-diones as an HIV integrase inhibitor: A DFT study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase. Future Sci OA 2018; 4:FSO338. [PMID: 30416746 PMCID: PMC6222271 DOI: 10.4155/fsoa-2018-0060] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022] Open
Abstract
AIDS caused by the infection of HIV is a prevalent problem today. Rapid development of drug resistance to existing drug classes has called for the discovery of new targets. Within the three major enzymes (i.e., HIV-1 protease, HIV-1 reverse transcriptase and HIV-1 integrase [IN]) of the viral replication cycle, HIV-1 IN has been of particular interest due to the absence of human cellular homolog. HIV-1 IN catalyzes the integration of viral genetic material with the host genome, a key step in the viral replication process. Several novel classes of HIV IN inhibitors have been explored by targeting different sites on the enzyme. This review strives to provide readers with updates on the recent developments of HIV-1 IN inhibitors. AIDS is an epidemic disease that endangers the lives of millions of people across the world. The AIDS virus, also known as HIV, has developed resistance to the majority of available drugs on the market, thus requiring the need for new drugs. HIV integrase is one of the key viral enzymes required for viral cell proliferation. Since there is no similar enzyme in the human body, major emphasis is being made to develop therapeutics for this novel target. The drugs that are at various stages of development for this target are reviewed here.
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Suneel Kumar Y, Nawaz Khan FR. Chemo-selective Suzuki–Miyaura reactions: Synthesis of highly substituted [1,6]-naphthyridines. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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7
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Wang T, Yuan XS, Wu MB, Lin JP, Yang LR. The advancement of multidimensional QSAR for novel drug discovery - where are we headed? Expert Opin Drug Discov 2017; 12:769-784. [PMID: 28562095 DOI: 10.1080/17460441.2017.1336157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION The Multidimensional quantitative structure-activity relationship (multidimensional-QSAR) method is one of the most popular computational methods employed to predict interesting biochemical properties of existing or hypothetical molecules. With continuous progress, the QSAR method has made remarkable success in various fields, such as medicinal chemistry, material science and predictive toxicology. Areas covered: In this review, the authors cover the basic elements of multidimensional -QSAR including model construction, validation and application. It includes and emphasizes the very recent developments of multidimensional -QSAR such as: HQSAR, G-QSAR, MIA-QSAR, multi-target QSAR. The advantages and disadvantages of each method are also discussed and typical examples of their application are detailed. Expert opinion: Although there are defects in multidimensional-QSAR modeling, it is still of enormous help to chemists, biologists and other researchers in various fields. In the authors' opinion, the latest more precise and feasible QSAR models should be further developed by integrating new descriptors, algorithms and other relevant computational techniques. Apart from being applied in traditional fields (e.g. lead optimization and predictive risk assessment), QSAR should be used more widely as a routine method in other emerging research fields including the modeling of nanoparticles(NPs), mixture toxicity and peptides.
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Affiliation(s)
- Tao Wang
- a School of biological science , Jining Medical University , Jining , China.,b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Xin-Song Yuan
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Mian-Bin Wu
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Jian-Ping Lin
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Li-Rong Yang
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
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8
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Li Y, Xuan S, Feng Y, Yan A. Targeting HIV-1 integrase with strand transfer inhibitors. Drug Discov Today 2014; 20:435-49. [PMID: 25486307 DOI: 10.1016/j.drudis.2014.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 11/14/2014] [Accepted: 12/01/2014] [Indexed: 01/03/2023]
Abstract
HIV-1 integrase (IN) is a retroviral enzyme essential for integration of genetic material into the DNA of the host cell and hence for viral replication. The absence of an equivalent enzyme in humans makes IN an interesting target for anti-HIV drug design. This review briefly overviews the structural and functional properties of HIV-1 IN. We analyze the binding modes of the established drugs, clinical candidates and a comprehensive library of leads based on innovative chemical scaffolds of HIV-1 IN strand transfer inhibitors (INSTIs). Computational clustering techniques are applied for identifying structural features relating to bioactivity. From bio- and chemo-informatics analyses, we provide novel insights into structure-activity relationships of INSTIs and elaborate new strategies for design of innovative inhibitors.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, P.O. Box 53, Beijing 100029, PR China
| | - Shouyi Xuan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, P.O. Box 53, Beijing 100029, PR China
| | - Yue Feng
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, P.O. Box 53, Beijing 100029, PR China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, P.O. Box 53, Beijing 100029, PR China.
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9
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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Bondock S, Tarhoni AEG, Fadda AA. A Convenient Synthesis of 2H-Pyran-2-ones, Fused Pyran-2-ones, and Pyridones Bearing a Thiazole Moiety. J Heterocycl Chem 2013. [DOI: 10.1002/jhet.1677] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Samir Bondock
- Chemistry Department, Faculty of Science; Mansoura University; ET-35516 Mansoura Egypt
- Chemistry Department, Faculty of Science; King Khalid University; 9004 Abha Saudi Arabia
| | - Abd El-Gaber Tarhoni
- Chemistry Department, Faculty of Science; Mansoura University; ET-35516 Mansoura Egypt
| | - Ahmed A. Fadda
- Chemistry Department, Faculty of Science; Mansoura University; ET-35516 Mansoura Egypt
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11
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Yu S, Wang P, Li Y, Liu Y, Zhao G. Docking-based CoMFA and CoMSIA study of azaindole carboxylic acid derivatives as promising HIV-1 integrase inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:819-839. [PMID: 23988186 DOI: 10.1080/1062936x.2013.820792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed based on a series of azaindole carboxylic acid derivatives that had previously been reported as promising HIV-1 integrase inhibitors. Docking studies to explore the binding mode were performed based on the highly active molecule 36. The best docked conformation of molecule 36 was used as template for alignment. The comparative molecular field analysis (CoMFA) model (including steric and electrostatic fields) yielded the cross validation q (2) = 0.655, non-cross validation r (2) = 0.989 and predictive r (2) pred = 0.979. The best comparative molecular similarity indices analysis (CoMSIA) model (including steric, electrostatic, hydrophobic and hydrogen-bond acceptor fields) yielded the cross validation q (2) = 0.719, non-cross validation r (2) = 0.992 and predictive r (2) pred = 0.953. A series of new azaindole carboxylic acid derivatives were designed and the HIV-1 integrase inhibitory activities of these designed compounds were predicted based on the CoMFA and CoMSIA models.
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Affiliation(s)
- S Yu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Shandong , China
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12
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Yu S, Sanchez TW, Liu Y, Yin Y, Neamati N, Zhao G. Design and synthesis of novel pyrimidone analogues as HIV-1 integrase inhibitors. Bioorg Med Chem Lett 2013; 23:6134-7. [PMID: 24084160 DOI: 10.1016/j.bmcl.2013.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 08/14/2013] [Accepted: 09/05/2013] [Indexed: 01/22/2023]
Abstract
A series of novel pyrimidone analogues have been designed and synthesized as HIV-1 integrase (IN) inhibitors. This study demonstrated that introducing a substituent in the N1-position of the pyrimidone scaffold does not significantly influence IN inhibitory activity. Molecular docking studies showed these compounds could occupy the IN active site and form pi-pi interactions with viral DNA nucleotides DC16 and DA17 to displace reactive viral DNA 3'OH and block intasome activity.
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Affiliation(s)
- Shenghui Yu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
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13
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De Luca L, Morreale F, Christ F, Debyser Z, Ferro S, Gitto R. New scaffolds of natural origin as Integrase-LEDGF/p75 interaction inhibitors: virtual screening and activity assays. Eur J Med Chem 2013; 68:405-11. [PMID: 23994868 DOI: 10.1016/j.ejmech.2013.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 01/08/2023]
Abstract
The disruption of crucial interactions between HIV-1 Integrase and cellular cofactor LEDGF/p75 represents an emerging approach for the design and development of new antiretroviral agents. In this study we report the successful application of a structure-based virtual screening strategy for the discovery of natural hit structures able to inhibit Integrase-LEDGF/p75 interaction. The application of sequential filters (drug-likeness, 3D-pharmacophore mapping, docking, molecular dynamics simulations) yielded a hit list of compounds, out of which 9 were tested in the in vitro AlphaScreen assays and 8 exhibited a detectable inhibition of the interaction between the two proteins. The best inhibitors belong to different chemical classes and could be represent a good starting point for further optimization and structure-activity relationship studies.
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Affiliation(s)
- Laura De Luca
- Dipartimento di Scienze del Farmaco e Prodotti per la Salute, Università di Messina, Viale Annunziata, I-98168 Messina, Italy.
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14
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Billamboz M, Suchaud V, Bailly F, Lion C, Demeulemeester J, Calmels C, Andréola ML, Christ F, Debyser Z, Cotelle P. 4-Substituted 2-Hydroxyisoquinoline-1,3(2H,4H)-diones as a Novel Class of HIV-1 Integrase Inhibitors. ACS Med Chem Lett 2013; 4:606-11. [PMID: 24900718 DOI: 10.1021/ml400009t] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/17/2013] [Indexed: 12/25/2022] Open
Abstract
A series of 2-hydroxy-1,3-dioxoisoquinoline-4-carboxamides featuring an N-hydroxyimide chelating functionality was evaluated for their inhibitory properties against human immunodeficiency virus type 1 integrase (HIV-1 IN). Several derivatives displayed low nanomolar IC50 values comparable to that of the clinically used raltegravir. A marked effect of one compound on both primary IN-catalyzed reactions, strand transfer (ST), and 3' processing (3'-P), emphasizes a novel IN inhibition mechanism establishing it as a potential new generation IN inhibitor. Substitution of the 2-hydroxyisoquinoline-1,3-dione scaffold at position 4 by carboxamido chains was beneficial for antiviral activity since reproducible low micromolar anti-HIV activities were obtained for the first time within this scaffold.
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Affiliation(s)
- Muriel Billamboz
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Virginie Suchaud
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Fabrice Bailly
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Cedric Lion
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Jonas Demeulemeester
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Christina Calmels
- UMR 5234 CNRS, Université Bordeaux Segalen, 146 Rue Léo Saignat, F-33076 Bordeaux, France
| | - Marie-Line Andréola
- UMR 5234 CNRS, Université Bordeaux Segalen, 146 Rue Léo Saignat, F-33076 Bordeaux, France
| | - Frauke Christ
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Zeger Debyser
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Philippe Cotelle
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
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Reddy KK, Singh SK, Tripathi SK, Selvaraj C. Identification of potential HIV-1 integrase strand transfer inhibitors: in silico virtual screening and QM/MM docking studies. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:581-595. [PMID: 23521430 DOI: 10.1080/1062936x.2013.772919] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
HIV-1 integrase (IN) is a retroviral enzyme that catalyses integration of the reverse-transcribed viral DNA into the host genome, which is necessary for efficient viral replication. In this study, we have performed an in silico virtual screening for the identification of potential HIV-1 IN strand transfer (ST) inhibitors. Pharmacophore modelling and atom-based 3D-QSAR studies were carried out for a series of compounds belonging to 3-Hydroxypyrimidine-2,4-diones. Based on the ligand-based pharmacophore model, we obtained a five-point pharmacophore with two hydrogen bond acceptors (A), one hydrogen bond donor (D), one hydrophobic group (H) and one aromatic ring (R) as pharmacophoric features. The pharmacophore hypothesis AADHR was used as a 3D query in a sequential virtual screening study to filter small molecule databases Maybridge, ChemBridge and Asinex. Hits matching with pharmacophore hypothesis AADHR were retrieved and passed progressively through Lipinski's rule of five filtering, molecular docking and hierarchical clustering. The five compounds with best hits with novel and diverse chemotypes were subjected to QM/MM docking, which showed improved docking accuracy. We further performed molecular dynamics simulation and found three compounds that form stable interactions with key residues. These compounds could be used as a leads for further drug development and rational design of HIV-1 IN inhibitors.
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Affiliation(s)
- K K Reddy
- Computer-Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Insuasty B, Becerra D, Quiroga J, Abonia R, Nogueras M, Cobo J. Microwave-assisted synthesis of pyrimido[4,5-b][1,6]naphthyridin-4(3H)-ones with potential antitumor activity. Eur J Med Chem 2013; 60:1-9. [DOI: 10.1016/j.ejmech.2012.11.037] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/15/2012] [Accepted: 11/26/2012] [Indexed: 11/16/2022]
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17
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De Luca L, Morreale F, Chimirri A. Insight into the Fundamental Interactions between LEDGF Binding Site Inhibitors and Integrase Combining Docking and Molecular Dynamics Simulations. J Chem Inf Model 2012. [DOI: 10.1021/ci300361e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura De Luca
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Francesca Morreale
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Alba Chimirri
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
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18
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Serrao E, Thys W, Demeulemeester J, Al-Mawsawi LQ, Christ F, Debyser Z, Neamati N. A symmetric region of the HIV-1 integrase dimerization interface is essential for viral replication. PLoS One 2012; 7:e45177. [PMID: 23028829 PMCID: PMC3445459 DOI: 10.1371/journal.pone.0045177] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/17/2012] [Indexed: 01/06/2023] Open
Abstract
HIV-1 integrase (IN) is an important target for contemporary antiretroviral drug design research. Historically, efforts at inactivating the enzyme have focused upon blocking its active site. However, it has become apparent that new classes of allosteric inhibitors will be necessary to advance the antiretroviral field in light of the emergence of viral strains resistant to contemporary clinically used IN drugs. In this study we have characterized the importance of a close network of IN residues, distant from the active site, as important for the obligatory multimerization of the enzyme and viral replication as a whole. Specifically, we have determined that the configuration of six residues within a highly symmetrical region at the IN dimerization interface, composed of a four-tiered aromatic interaction flanked by two salt bridges, significantly contributes to proper HIV-1 replication. Additionally, we have utilized a quantitative luminescence assay to examine IN oligomerization and have determined that there is a very low tolerance for amino acid substitutions along this region. Even conservative residue substitutions negatively impacted IN multimerization, resulting in an inactive viral enzyme and a non-replicative virus. We have shown that there is a very low tolerance for amino acid variation at the symmetrical dimeric interface region characterized in this study, and therefore drugs designed to target the amino acid network detailed here could be expected to yield a significantly reduced number of drug-resistant escape mutations compared to contemporary clinically-evaluated antiretrovirals.
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Affiliation(s)
- Erik Serrao
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Wannes Thys
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven, Flanders, Belgium
| | - Jonas Demeulemeester
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven, Flanders, Belgium
| | - Laith Q. Al-Mawsawi
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven, Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven, Flanders, Belgium
| | - Nouri Neamati
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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Abstract
Integrase (IN) is a clinically validated target for the treatment of human immunodeficiency virus infections and raltegravir exhibits remarkable clinical activity. The next most advanced IN inhibitor is elvitegravir. However, mutant viruses lead to treatment failure and mutations within the IN coding sequence appear to confer cross-resistance. The characterization of those mutations is critical for the development of second generation IN inhibitors to overcome resistance. This review focuses on IN resistance based on structural and biochemical data, and on the role of the IN flexible loop i.e., between residues G140-G149 in drug action and resistance.
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Affiliation(s)
| | | | | | - Yves Pommier
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-301-496-5944; Fax: +1-301-402-0752
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Bernardino AMR, Azevedo AR, Pinheiro LCS, Borges JC, Paixão ICP, Mesquita M, Souza TML, dos Santos MS. Synthesis and anti-HSV-1 evaluation of new 3H-benzo[b]pyrazolo[3,4-h]-1,6-naphthyridines and 3H-pyrido[2,3-b]pyrazolo[3,4-h]-1,6-naphthyridines. Org Med Chem Lett 2012; 2:3. [PMID: 22373524 PMCID: PMC3342845 DOI: 10.1186/2191-2858-2-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 02/01/2012] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Herpes simplex virus type-1 (HSV-1) is the primary cause of facial lesions (mouth, lips, and eyes) in humans. The widespread use of acyclovir and nucleoside analogues has led to emergence of HSV strains that are resistant to these drugs. Recently, non-nucleoside anti-HSV compounds have received considerable attention. 1,6-Naphthyridines are a class of heterocyclic compounds that exhibit a broad spectrum of biological activities such as inhibitor of HIV-1 integrase, HCMV, FGF receptor-1 tyrosine kinase, and the enzyme acetylcholinesterase. We previously reported the synthesis, SAR studies, and evaluation anti-HSV-1 activity of 3H-benzo[b]pyrazolo[3,4-h]-1,6-naphthyridines. In the course of our search for new 1,6-naphthyridines derivatives with potential activity against HSV-1, we have synthesized and evaluated new 3H-benzo[b]pyrazolo[3,4-h]-1,6-naphthyridines (1a-k) and 3H-pyrido[2,3-b]pyrazolo[3,4-h]-1,6-naphthyridines (2a-c). RESULTS A known synthetic approach was used for preparing new 3H-benzo[b]pyrazolo[3,4-h]-1,6-naphthyridines (1a-k) and 3H-pyrido[2,3-b]pyrazolo[3,4-h]-1,6-naphthyridines (2a-c), starting from ethyl 4-chloro-1-phenyl-1H-pyrazolo[3,4-b]pyridine-5-carboxylate (7). All compounds were identified by FTIR, 1H NMR, and mass spectrometry. The antiviral effect on HSV-1 virus replication was determined. CONCLUSIONS The compounds 1d, 1f, 1g, and 1h exhibited the highest anti-HSV-1 activity. In general, 3H-benzo[b]pyrazolo[3,4-h]-1,6-naphthyridines were more effective inhibitors than their corresponding 3H-pyrido[2,3-b]pyrazolo[3,4-h]-1,6-naphthyridines. The compound 1h reduced the virus yield in 91% at 50 μM and exhibited a low cytotoxicity (CC50 600 μM).
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Affiliation(s)
- Alice MR Bernardino
- Departamento de Química Orgânica, Instituto de Química, Programa de Pós-Graduação em Química, Universidade Federal Fluminense, Campus do Valonguinho, 24020-150, Niterói, RJ, Brazil
| | - Alexandre R Azevedo
- Departamento de Química Orgânica, Instituto de Química, Programa de Pós-Graduação em Química, Universidade Federal Fluminense, Campus do Valonguinho, 24020-150, Niterói, RJ, Brazil
| | - Luiz CS Pinheiro
- Departamento de Química Orgânica, Instituto de Química, Programa de Pós-Graduação em Química, Universidade Federal Fluminense, Campus do Valonguinho, 24020-150, Niterói, RJ, Brazil
| | - Júlio C Borges
- Departamento de Química Orgânica, Instituto de Química, Programa de Pós-Graduação em Química, Universidade Federal Fluminense, Campus do Valonguinho, 24020-150, Niterói, RJ, Brazil
| | - Izabel CP Paixão
- Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, 24020-150, Niterói, RJ, Brazil
| | - Milene Mesquita
- Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, 24020-150, Niterói, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, 21040-900, Rio de Janeiro, RJ, Brazil
| | - Thiago ML Souza
- Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, 24020-150, Niterói, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, 21040-900, Rio de Janeiro, RJ, Brazil
| | - Maurício S dos Santos
- Departamento de Física e Química, Instituto de Ciências Exatas, Universidade Federal de Itajubá, 37500-903, Itajubá, MG, Brazil
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Hu L, Zhang S, He X, Luo Z, Wang X, Liu W, Qin X. Design and synthesis of novel β-diketo derivatives as HIV-1 integrase inhibitors. Bioorg Med Chem 2012; 20:177-82. [DOI: 10.1016/j.bmc.2011.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/08/2011] [Accepted: 11/08/2011] [Indexed: 10/15/2022]
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Sierra S, Walter H. Targets for Inhibition of HIV Replication: Entry, Enzyme Action, Release and Maturation. Intervirology 2012; 55:84-97. [DOI: 10.1159/000331995] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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4-[1-(4-Fluorobenzyl)-4-hydroxy-1H-indol-3-yl]-2-hydroxy-4-oxobut-2-enoic acid as a prototype to develop dual inhibitors of HIV-1 integration process. Antiviral Res 2011; 92:102-7. [DOI: 10.1016/j.antiviral.2011.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/16/2011] [Accepted: 07/05/2011] [Indexed: 01/22/2023]
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Fan X, Zhang FH, Al-Safi RI, Zeng LF, Shabaik Y, Debnath B, Sanchez TW, Odde S, Neamati N, Long YQ. Design of HIV-1 integrase inhibitors targeting the catalytic domain as well as its interaction with LEDGF/p75: a scaffold hopping approach using salicylate and catechol groups. Bioorg Med Chem 2011; 19:4935-52. [PMID: 21778063 DOI: 10.1016/j.bmc.2011.06.058] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 06/18/2011] [Accepted: 06/20/2011] [Indexed: 12/31/2022]
Abstract
HIV-1 integrase (IN) is a validated therapeutic target for antiviral drug design. However, the emergence of viral strains resistant to clinically studied IN inhibitors demands the discovery of novel inhibitors that are structurally as well mechanistically different. Herein, we describe the design and discovery of novel IN inhibitors targeting the catalytic domain as well as its interaction with LEDGF/p75, which is essential for the HIV-1 integration as an IN cofactor. By merging the pharmacophores of salicylate and catechol, the 2,3-dihydroxybenzamide (5a) was identified as a new scaffold to inhibit the strand transfer reaction efficiently. Further structural modifications on the 2,3-dihydroxybenzamide scaffold revealed that the heteroaromatic functionality attached on the carboxamide portion and the piperidin-1-ylsulfonyl substituted at the phenyl ring are beneficial for the activity, resulting in a low micromolar IN inhibitor (5p, IC(50)=5 μM) with more than 40-fold selectivity for the strand transfer over the 3'-processing reaction. More significantly, this active scaffold remarkably inhibited the interaction between IN and LEDGF/p75 cofactor. The prototype example, N-(cyclohexylmethyl)-2,3-dihydroxy-5-(piperidin-1-ylsulfonyl) benzamide (5u) inhibited the IN-LEDGF/p75 interaction with an IC(50) value of 8 μM. Using molecular modeling, the mechanism of action was hypothesized to involve the chelation of the divalent metal ions inside the IN active site. Furthermore, the inhibitor of IN-LEDGF/p75 interaction was properly bound to the LEDGF/p75 binding site on IN. This work provides a new and efficient approach to evolve novel HIV-1 IN inhibitors from rational integration and optimization of previously reported inhibitors.
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Affiliation(s)
- Xing Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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Sharma H, Patil S, Sanchez TW, Neamati N, Schinazi RF, Buolamwini JK. Synthesis, biological evaluation and 3D-QSAR studies of 3-keto salicylic acid chalcones and related amides as novel HIV-1 integrase inhibitors. Bioorg Med Chem 2011; 19:2030-45. [PMID: 21371895 DOI: 10.1016/j.bmc.2011.01.047] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/16/2011] [Accepted: 01/24/2011] [Indexed: 11/26/2022]
Abstract
HIV-1 integrase is one of the three most important enzymes required for viral replication and is therefore an attractive target for anti retroviral therapy. We herein report the design and synthesis of 3-keto salicylic acid chalcone derivatives as novel HIV-1 integrase inhibitors. The most active compound, 5-bromo-2-hydroxy-3-[3-(2,3,6-trichlorophenyl)acryloyl]benzoic acid (25) was selectively active against integrase strand transfer, with an IC(50) of 3.7 μM. While most of the compounds exhibited strand transfer selectivity, a few were nonselective, such as 5-bromo-3-[3-(4-bromophenyl)acryloyl]-2-hydroxybenzoic acid (15), which was active against both 3'-processing and strand transfer with IC(50) values of 11±4 and 5±2 μM, respectively. The compounds also inhibited HIV replication with potencies comparable with their integrase inhibitory potencies. Thus, 5-bromo-2-hydroxy-3-[3-(2,3,6-trichlorophenyl)acryloyl]benzoic acid (25) and 5-bromo-3-[3-(4-bromophenyl)acryloyl]-2-hydroxybenzoic acid (15) inhibited HIV-1 replication with EC(50) values of 7.3 and 8.7 μM, respectively. A PHASE pharmacophore hypothesis was developed and validated by 3D-QSAR, which gave a predictive r(2) of 0.57 for an external test set of ten compounds. Phamacophore derived molecular alignments were used for CoMFA and CoMSIA 3D-QSAR modeling. CoMSIA afforded the best model with q(2) and r(2) values of 0.54 and 0.94, respectively. This model predicted all the ten compounds of the test set within 0.56 log units of the actual pIC(50) values; and can be used to guide the rational design of more potent novel 3-keto salicylic acid integrase inhibitors.
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Affiliation(s)
- Horrick Sharma
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 847 Monroe Avenue, Suite 327, TN 38163, USA
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Maurin C, Lion C, Bailly F, Touati N, Vezin H, Mbemba G, Mouscadet JF, Debyser Z, Witvrouw M, Cotelle P. New 2-arylnaphthalenediols and triol inhibitors of HIV-1 integrase—Discovery of a new polyhydroxylated antiviral agent. Bioorg Med Chem 2010; 18:5194-201. [DOI: 10.1016/j.bmc.2010.05.059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Revised: 05/20/2010] [Accepted: 05/21/2010] [Indexed: 11/26/2022]
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