1
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Mbhele N, Gordon M. Structural effects of HIV-1 subtype C integrase mutations on the activity of integrase strand transfer inhibitors in South African patients. J Biomol Struct Dyn 2022; 40:12546-12556. [PMID: 34488561 DOI: 10.1080/07391102.2021.1972840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
HIV-1 integrase enzyme is responsible for the integration of viral DNA into the host genomic DNA. Integrase strand transfer inhibitors (INSTIs) are highly potent antiretroviral agents that inhibit this process, and are internationally approved for the treatment of both naïve and treated HIV-1 patients. However, their long-term efficacy is threatened by development of drug resistance strains resulting in resistance mutations. This work aimed to examine the effect of INSTI resistance-associated mutations (RAMs) and polymorphisms on the structure of HIV-1 subtype C (HIV-1C) integrase. Genetic analysis was performed on seven HIV-1C infected individuals with virologic failure after at least 6 months of INSTI-based antiretroviral therapy, presenting at the King Edward VIII hospital in Durban, South Africa. These were compared with sequences from 41 INSTI-naïve isolates. Integrase structures of selected isolates were modeled on the SWISS model online server. Molecular docking and dynamics simulations were also conducted using AutoDock-Vina and AMBER 18 force fields, respectively. Only one INSTI-treated isolate (14.28%) harboured major mutations (G140A + Q148R) as well as the E157Q minor mutation. Interestingly, S119T and V151I were only found in patients failing raltegravir (an INSTI drug). Molecular modeling and docking showed that RAMs and polymorphisms associated with INSTI-based therapy affect protein stability and this is supported by their weakened hydrogen-bond interactions compared to the wild-type. To the best of our knowledge, this is the first study to identify a double mutant in the 140's loop region from South African HIV-1C isolates and study its effects on Raltegravir, Elvitegravir, and Dolutegravir binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nokuzola Mbhele
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Michelle Gordon
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
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2
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Goodsell DS, Sanner MF, Olson AJ, Forli S. The AutoDock suite at 30. Protein Sci 2020; 30:31-43. [PMID: 32808340 DOI: 10.1002/pro.3934] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022]
Abstract
The AutoDock suite provides a comprehensive toolset for computational ligand docking and drug design and development. The suite builds on 30 years of methods development, including empirical free energy force fields, docking engines, methods for site prediction, and interactive tools for visualization and analysis. Specialized tools are available for challenging systems, including covalent inhibitors, peptides, compounds with macrocycles, systems where ordered hydration plays a key role, and systems with substantial receptor flexibility. All methods in the AutoDock suite are freely available for use and reuse, which has engendered the continued growth of a diverse community of primary users and third-party developers.
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Affiliation(s)
- David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.,Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Michel F Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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3
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Ercan S, Şenyiğit B, Şenses Y. Dual inhibitor design for HIV-1 reverse transcriptase and integrase enzymes: a molecular docking study. J Biomol Struct Dyn 2019; 38:573-580. [DOI: 10.1080/07391102.2019.1700166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Selami Ercan
- School of Health Sciences, Department of Nursing, Batman University, Batman, Turkey
| | | | - Yusuf Şenses
- Institute of Science, Batman University, Batman, Turkey
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4
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Singer CM, Joy D, Jacobs DJ, Nesmelova IV. Rigidity and flexibility characteristics of DD[E/D]-transposases Mos1 and Sleeping Beauty. Proteins 2018; 87:313-325. [PMID: 30582767 DOI: 10.1002/prot.25653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/06/2018] [Accepted: 12/19/2018] [Indexed: 11/05/2022]
Abstract
DD[E/D]-transposases catalyze the multistep reaction of cut-and-paste DNA transposition. Structurally, several DD[E/D]-transposases have been characterized, revealing a multi-domain structure with the catalytic domain possessing the RNase H-like structural motif that brings three catalytic residues (D, D, and E or D) into close proximity for the catalysis. However, the dynamic behavior of DD[E/D]-transposases during transposition remains poorly understood. Here, we analyze the rigidity and flexibility characteristics of two representative DD[E/D]-transposases Mos1 and Sleeping Beauty (SB) using the minimal distance constraint model (mDCM). We find that the catalytic domain of both transposases is globally rigid, with the notable exception of the clamp loop being flexible in the DNA-unbound form. Within this globally rigid structure, the central β-sheet of the RNase H-like motif is much less rigid in comparison to its surrounding α-helices, forming a cage-like structure. The comparison of the original SB transposase to its hyperactive version SB100X reveals the region where the change in flexibility/rigidity correlates with increased activity. This region is found to be within the RNase H-like structural motif and comprise the loop leading from beta-strand B3 to helix H1, helices H1 and H2, which are located on the same side of the central beta-sheet, and the loop between helix H3 and beta-strand B5. We further identify the RKEN214-217DAVQ mutations of the set of hyperactive mutations within the catalytic domain of SB transposase to be the driving factor that induces change in residue-pair rigidity correlations within SB transposase. Given that a signature RNase H-like structural motif is found in DD[E/D]-transposases and, more broadly, in a large superfamily of polynucleotidyl transferases, our results are relevant to these proteins as well.
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Affiliation(s)
- Christopher M Singer
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Diana Joy
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Donald J Jacobs
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.,Center for Biomedical Engineering, University of North Carolina, Charlotte, North Carolina
| | - Irina V Nesmelova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.,Center for Biomedical Engineering, University of North Carolina, Charlotte, North Carolina
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5
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Jesumoroti OJ, Faridoon, Mnkandhla D, Isaacs M, Hoppe HC, Klein R. Evaluation of novel N'-(3-hydroxybenzoyl)-2-oxo-2 H-chromene-3-carbohydrazide derivatives as potential HIV-1 integrase inhibitors. MEDCHEMCOMM 2018; 10:80-88. [PMID: 30774857 DOI: 10.1039/c8md00328a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/01/2018] [Indexed: 12/11/2022]
Abstract
In an attempt to identify potential new agents that are active against HIV-1 IN, a series of novel coumarin-3-carbohydrazide derivatives were designed and synthesised. The toxicity profiles of these compounds showed that they were non-toxic to human cells and they exhibited promising anti-HIV-1 IN activities with IC50 values in nM range. Also, an accompanying molecular modeling study showed that the compounds bind to the active pocket of the enzyme.
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Affiliation(s)
| | - Faridoon
- Department of Chemistry , Rhodes University , Grahamstown , 6140 , South Africa .
| | - Dumisani Mnkandhla
- Department of Biochemistry and Microbiology , Rhodes University , Grahamstown , 6140 , South Africa.,Centre for Chemico- and Biomedicinal Research , Rhodes University , Grahamstown , 6140 , South Africa
| | - Michelle Isaacs
- Department of Biochemistry and Microbiology , Rhodes University , Grahamstown , 6140 , South Africa.,Centre for Chemico- and Biomedicinal Research , Rhodes University , Grahamstown , 6140 , South Africa
| | - Heinrich C Hoppe
- Department of Biochemistry and Microbiology , Rhodes University , Grahamstown , 6140 , South Africa.,Centre for Chemico- and Biomedicinal Research , Rhodes University , Grahamstown , 6140 , South Africa
| | - Rosalyn Klein
- Department of Chemistry , Rhodes University , Grahamstown , 6140 , South Africa . .,Centre for Chemico- and Biomedicinal Research , Rhodes University , Grahamstown , 6140 , South Africa
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6
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Musyoka T, Tastan Bishop Ö, Lobb K, Moses V. The determination of CHARMM force field parameters for the Mg2+ containing HIV-1 integrase. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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7
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A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.11.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Mortensen OV, Kortagere S. Designing modulators of monoamine transporters using virtual screening techniques. Front Pharmacol 2015; 6:223. [PMID: 26483692 PMCID: PMC4586420 DOI: 10.3389/fphar.2015.00223] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/17/2015] [Indexed: 12/15/2022] Open
Abstract
The plasma-membrane monoamine transporters (MATs), including the serotonin (SERT), norepinephrine (NET) and dopamine (DAT) transporters, serve a pivotal role in limiting monoamine-mediated neurotransmission through the reuptake of their respective monoamine neurotransmitters. The transporters are the main target of clinically used psychostimulants and antidepressants. Despite the availability of several potent and selective MAT substrates and inhibitors the continuing need for therapeutic drugs to treat brain disorders involving aberrant monoamine signaling provides a compelling reason to identify novel ways of targeting and modulating the MATs. Designing novel modulators of MAT function have been limited by the lack of three dimensional structure information of the individual MATs. However, crystal structures of LeuT, a bacterial homolog of MATs, in a substrate-bound occluded, substrate-free outward-open, and an apo inward-open state and also with competitive and non-competitive inhibitors have been determined. In addition, several structures of the Drosophila DAT have also been resolved. Together with computational modeling and experimental data gathered over the past decade, these structures have dramatically advanced our understanding of several aspects of SERT, NET, and DAT transporter function, including some of the molecular determinants of ligand interaction at orthosteric substrate and inhibitor binding pockets. In addition progress has been made in the understanding of how allosteric modulation of MAT function can be achieved. Here we will review all the efforts up to date that has been made through computational approaches employing structural models of MATs to design small molecule modulators to the orthosteric and allosteric sites using virtual screening techniques.
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Affiliation(s)
- Ole V Mortensen
- Department of Pharmacology and Physiology, Drexel University College of Medicine , Philadelphia, PA, USA
| | - Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine , Philadelphia, PA, USA
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9
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Kasprzak MM, Erxleben A, Ochocki J. Properties and applications of flavonoid metal complexes. RSC Adv 2015. [DOI: 10.1039/c5ra05069c] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Flavonoid metal complexes have a wide spectrum of activities as well as potential and actual applications.
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Affiliation(s)
- Maria M. Kasprzak
- Department of Bioinorganic Chemistry
- Medical University of Lodz
- Lodz
- Poland
| | - Andrea Erxleben
- School of Chemistry
- National University of Ireland
- Galway
- Ireland
| | - Justyn Ochocki
- Department of Bioinorganic Chemistry
- Medical University of Lodz
- Lodz
- Poland
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10
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Abstract
Virtual molecular screening is used to dock small-molecule libraries to a macromolecule in order to find lead compounds with desired biological function. This in silico method is well known for its application in computer-aided drug design. This chapter describes how to perform small-molecule virtual screening by docking with PyRx, which is open-source software with an intuitive user interface that runs on all major operating systems (Linux, Windows, and Mac OS). Specific steps for using PyRx, as well as considerations for data preparation, docking, and data analysis, are also described.
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Affiliation(s)
- Sargis Dallakyan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037-1000, USA,
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11
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Forli S, Olson AJ. Computational challenges of structure-based approaches applied to HIV. Curr Top Microbiol Immunol 2015; 389:31-51. [PMID: 25711462 DOI: 10.1007/82_2015_432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Here, we review some of the opportunities and challenges that we face in computational modeling of HIV therapeutic targets and structural biology, both in terms of methodology development and structure-based drug design (SBDD). Computational methods have provided fundamental support to HIV research since the initial structural studies, helping to unravel details of HIV biology. Computational models have proved to be a powerful tool to analyze and understand the impact of mutations and to overcome their structural and functional influence in drug resistance. With the availability of structural data, in silico experiments have been instrumental in exploiting and improving interactions between drugs and viral targets, such as HIV protease, reverse transcriptase, and integrase. Issues such as viral target dynamics and mutational variability, as well as the role of water and estimates of binding free energy in characterizing ligand interactions, are areas of active computational research. Ever-increasing computational resources and theoretical and algorithmic advances have played a significant role in progress to date, and we envision a continually expanding role for computational methods in our understanding of HIV biology and SBDD in the future.
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Affiliation(s)
- Stefano Forli
- MGL, Department of Integrative Structural and Computational Biology and HIV Interaction and Viral Evolution Center, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
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12
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Chen Q, Cheng X, Wei D, Xu Q. Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase. Interdiscip Sci 2014; 7:36-42. [PMID: 25519157 DOI: 10.1007/s12539-014-0235-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/16/2013] [Accepted: 03/24/2014] [Indexed: 10/24/2022]
Abstract
Although Elvitegravir (EVG) is a newly developed antiretrovirals drug to treat the acquired immunodeficiency syndrome (AIDS), drug resistance has already been found in clinic, such as E92Q/N155H and Q148H/G140S. Several structural investigations have already been reported to reveal the molecular mechanism of the drug resistance. As full length crystal structure for HIV-1 integrase is still unsolved, we herein use the crystal structure of the full length prototype foamy virus (PFV) in complex with virus DNA and inhibitor Elvitegravir as a template to construct the wild type and E92Q/N155H mutant system of HIV-1 integrase. Molecular dynamic simulations was used to revel the binding mode and the drug resistance of the EVG ligand in E92Q/N155H. Several important interactions were discovered between the mutated residues and the residues in the active site of the E92Q/N155H double mutant pattern, and cross correlation and clustering methods were used for detailed analysis. The results from the MD simulation studies will be used to guide the experimental efforts of developing novel inhibitors against drug-resistant HIV integrase mutants.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Microbial Metabolism and College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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13
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Chen Q, Cheng X, Wei D, Xu Q. Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase. Interdiscip Sci 2014. [PMID: 25373632 DOI: 10.1007/s12539-013-0215-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/16/2013] [Accepted: 03/24/2014] [Indexed: 06/04/2023]
Abstract
Although Elvitegravir (EVG) is a newly developed antiretrovirals drug to treat the acquired immunodeficiency syndrome (AIDS), drug resistance has already been found in clinic, such as E92Q/N155H and Q148H/G140S. Several structural investigations have already been reported to reveal the molecular mechanism of the drug resistance. As full length crystal structure for HIV-1 integrase is still unsolved, we herein use the crystal structure of the full length prototype foamy virus (PFV) in complex with virus DNA and inhibitor Elvitegravir as a template to construct the wild type and E92Q/N155H mutant system of HIV-1 integrase. Molecular dynamic simulations was used to revel the binding mode and the drug resistance of the EVG ligand in E92Q/N155H. Several important interactions were discovered between the mutated residues and the residues in the active site of the E92Q/N155H double mutant pattern, and cross correlation and clustering methods were used for detailed analysis. The results from the MD simulation studies will be used to guide the experimental efforts of developing novel inhibitors against drug-resistant HIV integrase mutants.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Microbial Metabolism and College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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14
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Wang J, Qiu J, Tan W, Zhang Y, Wang H, Zhou X, Liu S, Feng H, Li W, Niu X, Deng X. Fisetin inhibits Listeria monocytogenes virulence by interfering with the oligomerization of listeriolysin O. J Infect Dis 2014; 211:1376-87. [PMID: 25231018 DOI: 10.1093/infdis/jiu520] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/04/2014] [Indexed: 11/14/2022] Open
Abstract
Listeriolysin O (LLO), an essential virulence determinant of Listeria monocytogenes, is a pore-forming toxin whose primary function is to facilitate cytosolic bacterial replication by breaching the phagosomal membranes, which is critical for the pathogen to evade host immune recognition. The critical role of LLO in the virulence of L. monocytogenes renders it an ideal target for designing novel antivirulence therapeutics. We found that fisetin, a natural flavonoid without antimicrobial activity, is a potent antagonist of LLO-mediated hemolysis. Fisetin effectively inhibits L. monocytogenes infection in both tissue culture and animal infection models. Molecular modeling and mutational analysis revealed that fisetin directly engages loop 2 and loop 3 of LLO, leading to the blockage of cholesterol binding and the reduction of its oligomerization, thus inhibiting its hemolytic activity. Our results establish fisetin as an effective antitoxin agent for LLO, which can be further developed into novel therapeutics against infections caused by L. monocytogenes.
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Affiliation(s)
- Jianfeng Wang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Wei Tan
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Yu Zhang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Hongshu Wang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Xuan Zhou
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Shui Liu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Haihua Feng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Wenhua Li
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Xiaodi Niu
- Department of Food Quality and Safety, Jilin University, Changchun, China
| | - Xuming Deng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
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15
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Wolkowicz U, Morris ER, Robson M, Trubitsyna M, Richardson JM. Structural basis of Mos1 transposase inhibition by the anti-retroviral drug Raltegravir. ACS Chem Biol 2014; 9:743-51. [PMID: 24397848 PMCID: PMC3977574 DOI: 10.1021/cb400791u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/07/2014] [Indexed: 11/28/2022]
Abstract
DNA transposases catalyze the movement of transposons around genomes by a cut-and-paste mechanism related to retroviral integration. Transposases and retroviral integrases share a common RNaseH-like domain with a catalytic DDE/D triad that coordinates the divalent cations required for DNA cleavage and integration. The anti-retroviral drugs Raltegravir and Elvitegravir inhibit integrases by displacing viral DNA ends from the catalytic metal ions. We demonstrate that Raltegravir, but not Elvitegravir, binds to Mos1 transposase in the presence of Mg(2+) or Mn(2+), without the requirement for transposon DNA, and inhibits transposon cleavage and DNA integration in biochemical assays. Crystal structures at 1.7 Å resolution show Raltegravir, in common with integrases, coordinating two Mg(2+) or Mn(2+) ions in the Mos1 active site. However, in the absence of transposon ends, the drug adopts an unusual, compact binding mode distinct from that observed in the active site of the prototype foamy virus integrase.
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Affiliation(s)
- Urszula
M. Wolkowicz
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
| | - Elizabeth R. Morris
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
| | - Michael Robson
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
| | - Maryia Trubitsyna
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
| | - Julia M. Richardson
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
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16
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Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ. Blind prediction of HIV integrase binding from the SAMPL4 challenge. J Comput Aided Mol Des 2014; 28:327-45. [PMID: 24595873 DOI: 10.1007/s10822-014-9723-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 12/11/2022]
Abstract
Here, we give an overview of the protein-ligand binding portion of the Statistical Assessment of Modeling of Proteins and Ligands 4 (SAMPL4) challenge, which focused on predicting binding of HIV integrase inhibitors in the catalytic core domain. The challenge encompassed three components--a small "virtual screening" challenge, a binding mode prediction component, and a small affinity prediction component. Here, we give summary results and statistics concerning the performance of all submissions at each of these challenges. Virtual screening was particularly challenging here in part because, in contrast to more typical virtual screening test sets, the inactive compounds were tested because they were thought to be likely binders, so only the very top predictions performed significantly better than random. Pose prediction was also quite challenging, in part because inhibitors in the set bind to three different sites, so even identifying the correct binding site was challenging. Still, the best methods managed low root mean squared deviation predictions in many cases. Here, we give an overview of results, highlight some features of methods which worked particularly well, and refer the interested reader to papers in this issue which describe specific submissions for additional details.
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Affiliation(s)
- David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA,
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17
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Zhao XZ, Smith SJ, Métifiot M, Johnson BC, Marchand C, Pommier Y, Hughes SH, Burke TR. Bicyclic 1-hydroxy-2-oxo-1,2-dihydropyridine-3-carboxamide-containing HIV-1 integrase inhibitors having high antiviral potency against cells harboring raltegravir-resistant integrase mutants. J Med Chem 2014; 57:1573-82. [PMID: 24471816 PMCID: PMC3983366 DOI: 10.1021/jm401902n] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Integrase
(IN) inhibitors are the newest class of antiretroviral
agents developed for the treatment of HIV-1 infections. Merck’s
Raltegravir (RAL) (October 2007) and Gilead’s Elvitegravir
(EVG) (August 2012), which act as IN strand transfer inhibitors (INSTIs),
were the first anti-IN drugs to be approved by the FDA. However, the
virus develops resistance to both RAL and EVG, and there is extensive
cross-resistance to these two drugs. New “2nd-generation”
INSTIs are needed that will have greater efficacy against RAL- and
EVG-resistant strains of IN. The FDA has recently approved the first
second generation INSTI, GSK’s Dolutegravir (DTG) (August 2013).
Our current article describes the design, synthesis, and evaluation
of a series of 1,8-dihydroxy-2-oxo-1,2-dihydroquinoline-3-carboxamides,
1,4-dihydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides,
and 1-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides.
This resulted in the identification of noncytotoxic inhibitors that
exhibited single digit nanomolar EC50 values against HIV-1
vectors harboring wild-type IN in cell-based assays. Importantly,
some of these new inhibitors retain greater antiviral efficacy compared
to that of RAL when tested against a panel of IN mutants that included
Y143R, N155H, G140S/Q148H, G118R, and E138K/Q148K.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health , Frederick, Maryland 21702, United States
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18
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Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J Comput Aided Mol Des 2014; 28:475-90. [PMID: 24504704 DOI: 10.1007/s10822-014-9711-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Abstract
As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein. The computational protocol leveraged docking and high level atomistic models to improve enrichment. The enrichment factor of our blind predictions ranked best among all of the computational submissions, and second best overall. This work represents to our knowledge the first example of the application of an all-atom physics-based binding free energy model to large scale virtual screening. A total of 285 parallel Hamiltonian replica exchange molecular dynamics absolute protein-ligand binding free energy simulations were conducted starting from docked poses. The setup of the simulations was fully automated, calculations were distributed on multiple computing resources and were completed in a 6-weeks period. The accuracy of the docked poses and the inclusion of intramolecular strain and entropic losses in the binding free energy estimates were the major factors behind the success of the method. Lack of sufficient time and computing resources to investigate additional protonation states of the ligands was a major cause of mispredictions. The experiment demonstrated the applicability of binding free energy modeling to improve hit rates in challenging virtual screening of focused ligand libraries during lead optimization.
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Perryman AL, Santiago DN, Forli S, Martins DS, Olson AJ. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge. J Comput Aided Mol Des 2014; 28:429-441. [PMID: 24493410 DOI: 10.1007/s10822-014-9709-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/11/2014] [Indexed: 01/01/2023]
Abstract
To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational structure-based drug discovery tools and strategies that are being developed to advance the goals of the newly created, multi-institution, NIH-funded center called the "HIV Interaction and Viral Evolution Center".
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Affiliation(s)
- Alexander L Perryman
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel N Santiago
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stefano Forli
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Diogo Santos Martins
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Arthur J Olson
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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Lukman S, Verma CS, Fuentes G. Exploiting Protein Intrinsic Flexibility in Drug Design. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:245-69. [DOI: 10.1007/978-3-319-02970-2_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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21
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Poongavanam V, Narayana Moorthy NSH, Kongsted J. Dual mechanism of HIV-1 integrase and RNase H inhibition by diketo derivatives – a computational study. RSC Adv 2014. [DOI: 10.1039/c4ra05728g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Dual inhibition of HIV-1 integrase and RNase H by the diketo derivatives is investigated through ligand and structure based computational methods.
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Affiliation(s)
| | | | - Jacob Kongsted
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- Odense M, Denmark
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22
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Chen Q, Buolamwini JK, Smith JC, Li A, Xu Q, Cheng X, Wei D. Impact of resistance mutations on inhibitor binding to HIV-1 integrase. J Chem Inf Model 2013; 53:3297-307. [PMID: 24205814 DOI: 10.1021/ci400537n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
HIV-1 integrase (IN) is essential for HIV-1 replication, catalyzing two key reaction steps termed 3' processing and strand transfer. Therefore, IN has become an important target for antiviral drug discovery. However, mutants have emerged, such as E92Q/N155H and G140S/Q148H, which confer resistance to raltegravir (RAL), the first IN strand transfer inhibitor (INSTI) approved by the FDA, and to the recently approved elvitegravir (EVG). To gain insights into the molecular mechanisms of ligand binding and drug resistance, we performed molecular dynamics (MD) simulations of homology models of the HIV-1 IN and four relevant mutants complexed with viral DNA and RAL. The results show that the structure and dynamics of the 140s' loop, comprising residues 140 to 149, are strongly influenced by the IN mutations. In the simulation of the G140S/Q148H double mutant, we observe spontaneous dissociation of RAL from the active site, followed by an intrahelical swing-back of the 3'-OH group of nucleotide A17, consistent with the experimental observation that the G140S/Q148H mutant exhibits the highest resistance to RAL compared to other IN mutants. An important hydrogen bond between residues 145 and 148 is present in the wild-type IN but not in the G140S/Q148H mutant, accounting for the structural and dynamical differences of the 140s' loop and ultimately impairing RAL binding in the double mutant. End-point free energy calculations that broadly capture the experimentally known RAL binding profiles elucidate the contributions of the 140s' loop to RAL binding free energies and suggest possible approaches to overcoming drug resistance.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Microbial Metabolism and College of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
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Miri L, Bouvier G, Kettani A, Mikou A, Wakrim L, Nilges M, Malliavin TE. Stabilization of the integrase-DNA complex by Mg2+ions and prediction of key residues for binding HIV-1 integrase inhibitors. Proteins 2013; 82:466-78. [DOI: 10.1002/prot.24412] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 07/18/2013] [Accepted: 08/14/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Lamia Miri
- Laboratoire de Virologie; Institut Pasteur du Maroc; Casablanca 20360 Morocco
- Unité de modélisation moléculaire et d'ingénierie des biomolécules, Laboratoire de recherche sur les lipoprotéines et l'athérosclérose; Unité Associée au CNRST-URAC34, Faculté des Sciences Ben M'Sik; Casablanca Morocco
| | - Guillaume Bouvier
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
| | - Anass Kettani
- Unité de modélisation moléculaire et d'ingénierie des biomolécules, Laboratoire de recherche sur les lipoprotéines et l'athérosclérose; Unité Associée au CNRST-URAC34, Faculté des Sciences Ben M'Sik; Casablanca Morocco
| | - Afaf Mikou
- Laboratoire de Catalyse et environnement; Faculté des Sciences Ain Chock; Casablanca Morocco
| | - Lahcen Wakrim
- Laboratoire de Virologie; Institut Pasteur du Maroc; Casablanca 20360 Morocco
| | - Michael Nilges
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
| | - Thérèse E. Malliavin
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
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Dewdney TG, Wang Y, Kovari IA, Reiter SJ, Kovari LC. Reduced HIV-1 integrase flexibility as a mechanism for raltegravir resistance. J Struct Biol 2013; 184:245-50. [PMID: 23891838 DOI: 10.1016/j.jsb.2013.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 11/28/2022]
Abstract
HIV-1 integrase is an essential enzyme necessary for the replication of the HIV virus as it catalyzes the insertion of the viral genome into the host chromosome. Raltegravir was the first integrase inhibitor approved by the FDA for antiretroviral treatment. HIV patients on raltegravir containing regimens often develop drug resistance mutations at residue 140 and 148 in the catalytic 140's loop resulting in a 5-10 fold decrease in susceptibility to raltegravir. Obtaining crystallographic structure information on the Q148H/R, G140S/A primary and secondary mutations has been elusive. Using 10 ns molecular dynamics simulations, we present a detailed analysis of the structural changes induced by these mutations. The formation frequency of a transient helix in the catalytic 140's loop is increased and the length of this helix is extended from 3-residues to 4 in the mutants relative to the wild type. This helix causes reduced flexibility in the protein active site and therefore serves as a gating mechanism restricting the access of raltegravir to the integrase binding pocket. These results suggest that resistance to raltegravir occurs through a common mechanism of altering the formation frequency of transient secondary structures such as α2 and β5 in addition to the conformational changes in the 140's loop therefore decreasing the flexibility of the HIV-1 integrase protein. The reduced integrase flexibility serves as a mechanism of resistance to raltegravir.
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Affiliation(s)
- Tamaria G Dewdney
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
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Arora R, de Beauchene IC, Polanski J, Laine E, Tchertanov L. Raltegravir flexibility and its impact on recognition by the HIV-1 IN targets. J Mol Recognit 2013; 26:383-401. [PMID: 23836466 DOI: 10.1002/jmr.2277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 04/04/2013] [Accepted: 04/07/2013] [Indexed: 01/10/2023]
Abstract
HIV-1 IN is a pertinent target for the development of AIDS chemotherapy. The first IN-specific inhibitor approved for the treatment of HIV/AIDS, RAL, was designed to block the ST reaction. We characterized the structural and conformational features of RAL and its recognition by putative HIV-1 targets - the unbound IN, the vDNA, and the IN•vDNA complex - mimicking the IN states over the integration process. RAL binding to the targets was studied by performing an extensive sampling of the inhibitor conformational landscape and by using four different docking algorithms: Glide, Autodock, VINA, and SurFlex. The obtained data evidenced that: (i) a large binding pocket delineated by the active site and an extended loop in the unbound IN accommodates RAL in distinct conformational states all lacking specific interactions with the target; (ii) a well-defined cavity formed by the active site, the vDNA, and the shortened loop in the IN•vDNA complex provide a more optimized inhibitor binding site in which RAL chelates Mg(2+) cations; (iii) a specific recognition between RAL and the unpaired cytosine of the processed DNA is governed by a pair of strong H-bonds similar to those observed in DNA base pair G-C. The identified RAL pose at the cleaved vDNA shed light on a putative step of RAL inhibition mechanism. This modeling study indicates that the inhibition process may include as a first step RAL recognition by the processed vDNA bound to a transient intermediate IN state, and thus provides a potentially promising route to the design of IN inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Rohit Arora
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliquée (LBPA-CNRS), Ecole Normale Supérieure de Cachan, 61 avenue du Président Wilson, 94235, Cachan, France
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26
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Niu X, Wang X, Wang H, Gao X, Wang Y, Wang S. Insights into the specific binding site of adenosine to the Stx2, the protein toxin fromEscherichia coliO157:H7 using molecular dynamics simulations and free energy calculations. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.713483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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McDonald W, Funatogawa C, Li Y, Szundi I, Chen Y, Fee JA, Stout CD, Einarsdóttir Ó. Ligand access to the active site in Thermus thermophilus ba(3) and bovine heart aa(3) cytochrome oxidases. Biochemistry 2013; 52:640-52. [PMID: 23282175 DOI: 10.1021/bi301358a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates the functions of these enzymes. Using photolabile NO and O(2) carriers, we recently found that NO and O(2) binding in Thermus thermophilus (Tt) ba(3) is ~10 times faster than in the bovine enzyme, indicating that inherent structural differences affect ligand access in these enzymes. Using X-ray crystallography, time-resolved optical absorption measurements, and theoretical calculations, we investigated ligand access in wild-type Tt ba(3) and the mutants, Y133W, T231F, and Y133W/T231F, in which tyrosine and threonine in the O(2) channel of Tt ba(3) are replaced by the corresponding bulkier tryptophan and phenylalanine, respectively, present in the aa(3) enzymes. NO binding in Y133W and Y133W/T231F was found to be 5 times slower than in wild-type ba(3) and the T231F mutant. The results show that the Tt ba(3) Y133W mutation and the bovine W126 residue physically impede NO access to the binuclear center. In the bovine enzyme, there is a hydrophobic "way station", which may further slow ligand access to the active site. Classical simulations of diffusion of Xe to the active sites in ba(3) and bovine aa(3) show conformational freedom of the bovine F238 and the F231 side chain of the Tt ba(3) Y133W/T231F mutant, with both residues rotating out of the ligand channel, resulting in no effect on ligand access in either enzyme.
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Affiliation(s)
- William McDonald
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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28
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Dong J, Qiu J, Zhang Y, Lu C, Dai X, Wang J, Li H, Wang X, Tan W, Luo M, Niu X, Deng X. Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore. PLoS Comput Biol 2013; 9:e1002869. [PMID: 23349625 PMCID: PMC3547825 DOI: 10.1371/journal.pcbi.1002869] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/16/2012] [Indexed: 02/06/2023] Open
Abstract
Alpha-hemolysin (α-HL) is a self-assembling, channel-forming toxin produced by most Staphylococcus aureus strains as a 33.2-kDa soluble monomer. Upon binding to a susceptible cell membrane, the monomer self-assembles to form a 232.4-kDa heptamer that ultimately causes host cell lysis and death. Consequently, α-HL plays a significant role in the pathogenesis of S. aureus infections, such as pneumonia, mastitis, keratitis and arthritis. In this paper, experimental studies show that oroxylin A (ORO), a natural compound without anti-S. aureus activity, can inhibit the hemolytic activity of α-HL. Molecular dynamics simulations, free energy calculations, and mutagenesis assays were performed to understand the formation of the α-HL-ORO complex. This combined approach revealed that the catalytic mechanism of inhibition involves the direct binding of ORO to α-HL, which blocks the conformational transition of the critical “Loop” region of the α-HL protein thereby inhibiting its hemolytic activity. This mechanism was confirmed by experimental data obtained from a deoxycholate-induced oligomerization assay. It was also found that, in a co-culture system with S. aureus and human alveolar epithelial (A549) cells, ORO could protect against α-HL-mediated injury. These findings indicate that ORO hinders the lytic activity of α-HL through a novel mechanism, which should facilitate the design of new and more effective antibacterial agents against S. aureus. The mechanism controlling protein-ligand interactions is one of the most important processes in rational drug design. X-ray crystallography is a traditional tool used to investigate the interaction of ligands and proteins in a complex. However, protein crystallography is inefficient, and the development of crystal technology and research remains unequally distributed. Thus, it seems impractical to explore the structure of the α-hemolysin-ORO monomer complex by crystallography. Therefore, we used molecular dynamics simulations to investigate the receptor-ligand interaction in the α-HL-ORO monomer complex. In this study, we found that oroxylin A (ORO), a natural compound with little anti-S. aureus activity, can inhibit the hemolytic activity of α-HL at low concentrations. Through molecular docking and molecular dynamics simulations, we determined the potential binding mode of the protein-ligand interaction. The data revealed that ORO directly binds to α-HL, an interaction that blacks the conformational transition of the critical “Loop” region in α-HL and thus prevents the formation of the α-HL heptameric transmembrane pore, which ultimately inhibits the hemolytic activity of α-HL. This mechanism was confirmed by experimental data. Furthermore, we demonstrated that ORO could protect against α-HL-mediated injury in human alveolar epithelial (A549) cells.
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Affiliation(s)
- Jing Dong
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
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Xue W, Jin X, Ning L, Wang M, Liu H, Yao X. Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis. J Chem Inf Model 2012; 53:210-22. [DOI: 10.1021/ci300541c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Weiwei Xue
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Xiaojie Jin
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Lulu Ning
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Meixia Wang
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
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Viral enzymes containing magnesium: Metal binding as a successful strategy in drug design. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.07.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Sgobba M, Olubiyi O, Ke S, Haider S. Molecular dynamics of HIV1-integrase in complex with 93del - a structural perspective on the mechanism of inhibition. J Biomol Struct Dyn 2012; 29:863-77. [PMID: 22292948 DOI: 10.1080/07391102.2012.10507418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class of antiviral agents. Although X-ray and NMR structures of HIV1 integrase and 93del have been reported, there is no structural information of the complex and the mechanism of inhibition still remains unexplored. A number of computational methods including automated protein-DNA docking and molecular dynamics simulation in explicit solvent were used to model the binding of 93del to HIV1 integrase. Analysis of the dynamic behaviour of the complex using principal components analysis and elastic network modelling techniques allow us to understand how the binding of 93del aptamer and its interactions with key residues affect the intrinsic motions of the catalytic loops by stabilising them in catalytically inactive conformations. Such insights into the structural mechanism of inhibition can aid in improving the design of anti-HIV aptamers.
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Affiliation(s)
- Miriam Sgobba
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, 97 Lisburn Road, BT9 7BL, Belfast, UK.
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Hu JP, He HQ, Tang DY, Sun GF, Zhang YQ, Fan J, Chang S. Study on the interactions between diketo-acid inhibitors and prototype foamy virus integrase-DNA complex via molecular docking and comparative molecular dynamics simulation methods. J Biomol Struct Dyn 2012; 31:734-47. [PMID: 22913375 DOI: 10.1080/07391102.2012.709458] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an important drug target for anti-acquired immune deficiency disease (AIDS) treatment and diketo-acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN. Due to lack of three-dimensional structures including detail interactions between HIV-1 IN and its substrate viral DNA, the drug design and screening platform remains incompleteness and deficient. In addition, the action mechanism of DKA inhibitors with HIV-1 IN is not well understood. In view of the high homology between the structure of prototype foamy virus (PFV) IN and that of HIV-1 IN, we used PFV IN as a surrogate model for HIV-1 IN to investigate the inhibitory mechanism of raltegravir (RLV) and the binding modes with a series of DKA inhibitors. Firstly, molecular dynamics simulations of PFV IN, IN-RLV, IN-DNA, and IN-DNA-RLV systems were performed for 10 ns each. The interactions and inhibitory mechanism of RLV to PFV IN were explored through overall dynamics behaviors, catalytic loop conformation distribution, and hydrogen bond network analysis. The results show that the coordinated interactions of RLV with IN and viral DNA slightly reduce the flexibility of catalytic loop region of IN, and remarkably restrict the mobility of the CA end of viral DNA, which may lead to the partial loss of the inhibitory activity of IN. Then, we docked a series of DKA inhibitors into PFV IN-DNA receptor and obtained the IN-DNA-inhibitor complexes. The docking results between PFV IN-DNA and DKA inhibitors agree well with the corresponding complex of HIV-1 IN, which proves the dependability of PFV IN-DNA used for the anti-AIDS drug screening. Our study may help to make clear some theoretical questions and to design anti-AIDS drug based on the structure of IN.
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Affiliation(s)
- Jian-Ping Hu
- Department of Chemistry and Life Science, Leshan Normal University, Leshan, China.
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Abstract
A series of HIV integrase (HIV-1 IN) inhibitors were synthesized to evaluate the role of the metal-binding group (MBG) in this class of metalloenzyme inhibitors. A total of 21 different raltegravir-chelator derivative (RCD) compounds were prepared that differed only in the nature of the MBG. These IN strand-transfer inhibitors (INSTIs) were evaluated in vitro in cell-free enzyme activity assays, and the in vitro results were further validated in cell culture experiments. All of the active compounds showed selective inhibition of the strand-transfer reaction over 3'-processing, suggesting a common mode of action with raltegravir. The results of the in vitro activity suggest that the nature of the MBG donor atoms, the overall MBG structure, and the specific arrangement of the MBG donor atom triad are essential for obtaining maximal HIV-1 IN inhibition. At least two compounds (RCD-4, RCD-5) containing a hydroxypyrone MBG were found to display superior strand-transfer inhibition when compared to an abbreviated analogue of raltegravir (RCD-1). By isolating and examining the role of the MBG in a series of INSTIs, we have identified a scaffold (hydroxypyrones) that may provide access to a unique class of HIV-1 IN inhibitors, and may help overcome rising raltegravir resistance.
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Xue W, Qi J, Yang Y, Jin X, Liu H, Yao X. Understanding the effect of drug-resistant mutations of HIV-1 intasome on raltegravir action through molecular modeling study. MOLECULAR BIOSYSTEMS 2012; 8:2135-44. [DOI: 10.1039/c2mb25114k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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35
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Zhao XZ, Maddali K, Metifiot M, Smith SJ, Vu BC, Marchand C, Hughes SH, Pommier Y, Burke TR. Bicyclic hydroxy-1H-pyrrolopyridine-trione containing HIV-1 integrase inhibitors. Chem Biol Drug Des 2011; 79:157-65. [PMID: 22107736 DOI: 10.1111/j.1747-0285.2011.01270.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
HIV-1 integrase (IN) is a validated therapeutic target for the treatment of AIDS. However, the emergence of resistance to raltegravir, the sole marketed FDA-approved IN inhibitor, emphasizes the need to develop second-generation inhibitors that retain efficacy against clinically relevant IN mutants. We report herein bicyclic hydroxy-1H-pyrrolopyridine-triones as a new family of HIV-1 integrase inhibitors that were efficiently prepared using a key 'Pummerer cyclization deprotonation cycloaddition' cascade of imidosulfoxides. In in vitro HIV-1 integrase assays, the analogs showed low micromolar inhibitory potencies with selectivity for strand transfer reactions as compared with 3'-processing inhibition. A representative inhibitor (5e) retained most of its inhibitory potency against the three major raltegravir-resistant IN mutant enzymes, G140S/Q148H, Y143R, and N155H. In antiviral assays employing viral vectors coding these IN mutants, compound 5e was approximately 200- and 20-fold less affected than raltegravir against the G140S/Q148H and Y143R mutations, respectively. Against the N155H mutation, 5e was approximately 10-fold less affected than raltegravir. Thus, our new compounds represent a novel structural class that may be further developed to overcome resistance to raltegravir, particularly in the case of the G140S/Q148H mutations.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702, USA
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Xue W, Liu H, Yao X. Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective. J Comput Chem 2011; 33:527-36. [DOI: 10.1002/jcc.22887] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 09/25/2011] [Accepted: 10/20/2011] [Indexed: 01/03/2023]
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Ivetac A, McCammon JA. Molecular recognition in the case of flexible targets. Curr Pharm Des 2011; 17:1663-71. [PMID: 21619526 DOI: 10.2174/138161211796355056] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 05/05/2011] [Indexed: 11/22/2022]
Abstract
A protein's flexibility is well recognized to underlie its capacity to engage in critical functions, such as signal transduction, biomolecular transport and biochemical reactivity. Molecular recognition is also tightly linked to the dynamics of the binding partners, yet protein flexibility has largely been ignored by the growing field of structure-based drug design (SBDD). In combination with experimentally determined structures, a number of computational methods have been proposed to model protein movements, which may be important for small molecule binding. Such techniques have the ability to expose new binding site conformations, which may in turn recognize and lead to the discovery of more potent and selective drugs through molecular docking. In this article, we discuss various methods and focus on the Relaxed Complex Scheme (RCS), which uses Molecular Dynamics (MD) simulations to model full protein flexibility and enhance virtual screening programmes. We review practical applications of the RCS and use a recent study of the HIV-1 reverse transcriptase to illustrate the various phases of the scheme. We also discuss some encouraging developments, aimed at addressing current weaknesses of the RCS.
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Affiliation(s)
- Anthony Ivetac
- Department of Chemistry and Biochemistry University of California San Diego, La Jolla, CA 92093-0365, USA.
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Structure-analysis of the HIV-1 integrase Y143C/R raltegravir resistance mutation in association with the secondary mutation T97A. Antimicrob Agents Chemother 2011; 55:3187-94. [PMID: 21576445 DOI: 10.1128/aac.00071-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The HIV-1 integrase (IN) mutations Y143C/R are known as raltegravir (RAL) primary resistance mutations. In a previous study (S. Reigadas et al., PLoS One 5:e10311, 2010), we investigated the genetic pathway and the dynamics of emergence of the Y143C/R mutations in three patients failing RAL-containing regimens. In these patients, the Y143C/R mutation was associated with the T97A mutation. The aim of the present biochemical and molecular studies in vitro was to evaluate whether the secondary mutation, T97A, associated with the Y143C/R mutation could increase the level of resistance to RAL and impact IN activities. Site-directed mutagenesis experiments were performed with expression vectors harboring the region of the pol gene coding for IN. With a 3'-end processing assay, the 50% inhibitory concentrations (IC(50)) were 1.2 μM, 1.2 μM, 2.4 μM (fold change [FC], 2), and 20 μM (FC, 16.7) for IN wild type (WT), the IN T97A mutation, the IN Y143C/T97A mutation, and the IN Y143R/T97A mutation, respectively. FCs of 18 and 100 were observed with the strand transfer assay for IN Y143C/T97A and Y143R/T97A mutations, with IC(50) of 0.625 μM and 2.5 μM, respectively. In the strand transfer assay, the IN Y143C or R mutation combined with the secondary mutation T97A severely impaired susceptibility to RAL compared to results with the IN Y143C or R mutation alone. Assays without RAL suggested that the T97A mutation could rescue the catalytic activity which was impaired by the presence of the Y143C/R mutation. The combination of the T97A mutation with the primary RAL resistance mutations Y143C/R strongly reduces the susceptibility to RAL and rescues the catalytic defect due to the Y143C/R mutation. This result indicates that the emergence of the Y143C/R/T97A double-mutation pattern in patients is a signature of a high resistance level.
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Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X. Biomolecularmodeling and simulation: a field coming of age. Q Rev Biophys 2011; 44:191-228. [PMID: 21226976 PMCID: PMC3700731 DOI: 10.1017/s0033583510000284] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field’s history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA.
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Rhodes DI, Peat TS, Vandegraaff N, Jeevarajah D, Le G, Jones ED, Smith JA, Coates JAV, Winfield LJ, Thienthong N, Newman J, Lucent D, Ryan JH, Savage GP, Francis CL, Deadman JJ. Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design. Antivir Chem Chemother 2011; 21:155-68. [PMID: 21602613 DOI: 10.3851/imp1716] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND HIV-1 integrase is a clinically validated therapeutic target for the treatment of HIV-1 infection, with one approved therapeutic currently on the market. This enzyme represents an attractive target for the development of new inhibitors to HIV-1 that are effective against the current resistance mutations. METHODS A fragment-based screening method employing surface plasmon resonance and NMR was initially used to detect interactions between integrase and fragments. The binding sites of the fragments were elucidated by crystallography and the structural information used to design and synthesize improved ligands. RESULTS The location of binding of fragments to the catalytic core of integrase was found to be in a previously undescribed binding site, adjacent to the mobile loop. Enzyme assays confirmed that formation of enzyme-fragment complexes inhibits the catalytic activity of integrase and the structural data was utilized to further develop these fragments into more potent novel enzyme inhibitors. CONCLUSIONS We have defined a new site in integrase as a valid region for the structure-based design of allosteric integrase inhibitors. Using a structure-based design process we have improved the activity of the initial fragments 45-fold.
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Computer-aided drug-discovery techniques that account for receptor flexibility. Curr Opin Pharmacol 2010; 10:770-4. [PMID: 20888294 DOI: 10.1016/j.coph.2010.09.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 09/01/2010] [Indexed: 11/23/2022]
Abstract
Protein flexibility plays a critical role in ligand binding to both orthosteric and allosteric sites. We here review some of the computer-aided drug-design techniques currently used to account for protein flexibility, ranging from methods that probe local receptor flexibility in the region of the protein immediately adjacent to the binding site, to those that account for general flexibility in all protein regions.
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Structure-based modeling of the functional HIV-1 intasome and its inhibition. Proc Natl Acad Sci U S A 2010; 107:15910-5. [PMID: 20733078 DOI: 10.1073/pnas.1002346107] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The intasome is the basic recombination unit of retroviral integration, comprising the integrase protein and the ends of the viral DNA made by reverse transcription. Clinical inhibitors preferentially target the DNA-bound form of integrase as compared with the free protein, highlighting the critical requirement for detailed understanding of HIV-1 intasome structure and function. Although previous biochemical studies identified integrase residues that contact the DNA, structural details of protein-protein and protein-DNA interactions within the functional intasome were lacking. The recent crystal structure of the prototype foamy virus (PFV) integrase-viral DNA complex revealed numerous details of this related integration machine. Structures of drug-bound PFV intasomes moreover elucidated the mechanism of inhibitor action. Herein we present a model for the HIV-1 intasome assembled using the PFV structure as template. Our results pinpoint previously identified protein-DNA contacts within the quaternary structure and reveal hitherto unknown roles for Arg20 and Lys266 in DNA binding and integrase function. Models for clinical inhibitors bound at the HIV-1 integrase active site were also constructed and compared with previous studies. Our findings highlight the structural basis for HIV-1 integration and define the mechanism of its inhibition, which should help in formulating new drugs to inhibit viruses resistant to first-in-class compounds.
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