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Thammaporn R, Ishii K, Yagi-Utsumi M, Uchiyama S, Hannongbua S, Kato K. Mass Spectrometric Characterization of HIV-1 Reverse Transcriptase Interactions with Non-nucleoside Reverse Transcriptase Inhibitors. Biol Pharm Bull 2016; 39:450-4. [PMID: 26934936 DOI: 10.1248/bpb.b15-00880] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) have been developed for the treatment of acquired immunodeficiency syndrome. HIV-1 RT binding to NNRTIs has been characterized by various biophysical techniques. However, these techniques are often hampered by the low water solubility of the inhibitors, such as the current promising diarylpyrimidine-based inhibitors rilpivirine and etravirine. Hence, a conventional and rapid method that requires small sample amounts is desirable for studying NNRTIs with low water solubility. Here we successfully applied a recently developed mass spectrometric technique under non-denaturing conditions to characterize the interactions between the heterodimeric HIV-1 RT enzyme and NNRTIs with different inhibitory activities. Our data demonstrate that mass spectrometry serves as a semi-quantitative indicator of NNRTI binding affinity for HIV-1 RT using low and small amounts of samples, offering a new high-throughput screening tool for identifying novel RT inhibitors as anti-HIV drugs.
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Structural Maturation of HIV-1 Reverse Transcriptase-A Metamorphic Solution to Genomic Instability. Viruses 2016; 8:v8100260. [PMID: 27690082 PMCID: PMC5086598 DOI: 10.3390/v8100260] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT)—a critical enzyme of the viral life cycle—undergoes a complex maturation process, required so that a pair of p66 precursor proteins can develop conformationally along different pathways, one evolving to form active polymerase and ribonuclease H (RH) domains, while the second forms a non-functional polymerase and a proteolyzed RH domain. These parallel maturation pathways rely on the structural ambiguity of a metamorphic polymerase domain, for which the sequence–structure relationship is not unique. Recent nuclear magnetic resonance (NMR) studies utilizing selective labeling techniques, and structural characterization of the p66 monomer precursor have provided important insights into the details of this maturation pathway, revealing many aspects of the three major steps involved: (1) domain rearrangement; (2) dimerization; and (3) subunit-selective RH domain proteolysis. This review summarizes the major structural changes that occur during the maturation process. We also highlight how mutations, often viewed within the context of the mature RT heterodimer, can exert a major influence on maturation and dimerization. It is further suggested that several steps in the RT maturation pathway may provide attractive targets for drug development.
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Bolia A, Ozkan SB. Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility. J Chem Inf Model 2016; 56:734-46. [PMID: 26971620 DOI: 10.1021/acs.jcim.5b00587] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present an induced fit docking approach called Adaptive BP-Dock that integrates perturbation response scanning (PRS) with the flexible docking protocol of RosettaLigand in an adaptive manner. We first perturb the binding pocket residues of a receptor and obtain a new conformation based on the residue response fluctuation profile using PRS. Next, we dock a ligand to this new conformation by RosettaLigand, where we repeat these steps for several iterations. We test this approach on several protein test sets including difficult unbound docking cases such as HIV-1 reverse transcriptase and HIV-1 protease. Adaptive BP-Dock results show better correlation with experimental binding affinities compared to other docking protocols. Overall, the results imply that Adaptive BP-Dock can easily capture binding induced conformational changes by simultaneous sampling of protein and ligand conformations. This can provide faster and efficient docking of novel targets for rational drug design.
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Affiliation(s)
- Ashini Bolia
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - S Banu Ozkan
- Department of Physics, Center for Biological Physics, Arizona State University , Tempe, Arizona 85287, United States
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Seetaha S, Yagi-Utsumi M, Yamaguchi T, Ishii K, Hannongbua S, Choowongkomon K, Kato K. Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase. ChemMedChem 2016; 11:363-6. [PMID: 26804978 DOI: 10.1002/cmdc.201500554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Indexed: 11/07/2022]
Abstract
Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques can provide long-range structural information complemented with local information derived from chemical-shift perturbation and nuclear Overhauser effect data. Here, we address the application of paramagnetic relaxation enhancement (PRE) to detect inhibitor-induced conformational change of a drug target protein using human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) as a model protein. Using a site-specific spin-labeled HIV-1 RT mutant with selective (13) C labeling, conformation-dependent PREs were successfully observed reflecting the stabilization of an open conformation of this enzyme caused by inhibitor binding. This study demonstrates that the paramagnetism-assisted NMR approach offers an alternative strategy in protein-based drug screening to identify allosteric inhibitors of a target protein.
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Affiliation(s)
- Supaporn Seetaha
- Graduate Program in Bioscience, Faculty of Science, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Maho Yagi-Utsumi
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Takumi Yamaguchi
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, 923-1292, Japan
| | - Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. .,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
| | - Koichi Kato
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan. .,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
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Thammaporn R, Yagi-Utsumi M, Yamaguchi T, Boonsri P, Saparpakorn P, Choowongkomon K, Techasakul S, Kato K, Hannongbua S. NMR characterization of HIV-1 reverse transcriptase binding to various non-nucleoside reverse transcriptase inhibitors with different activities. Sci Rep 2015; 5:15806. [PMID: 26510386 PMCID: PMC4625163 DOI: 10.1038/srep15806] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 10/05/2015] [Indexed: 12/22/2022] Open
Abstract
Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is an important target for antiviral therapy against acquired immunodeficiency syndrome. However, the efficiency of available drugs is impaired most typically by drug-resistance mutations in this enzyme. In this study, we applied a nuclear magnetic resonance (NMR) spectroscopic technique to the characterization of the binding of HIV-1 RT to various non-nucleoside reverse transcriptase inhibitors (NNRTIs) with different activities, i.e., nevirapine, delavirdine, efavirenz, dapivirine, etravirine, and rilpivirine. 1H-13C heteronuclear single-quantum coherence (HSQC) spectral data of HIV-1 RT, in which the methionine methyl groups of the p66 subunit were selectively labeled with 13C, were collected in the presence and absence of these NNRTIs. We found that the methyl 13C chemical shifts of the M230 resonance of HIV-1 RT bound to these drugs exhibited a high correlation with their anti-HIV-1 RT activities. This methionine residue is located in proximity to the NNRTI-binding pocket but not directly involved in drug interactions and serves as a conformational probe, indicating that the open conformation of HIV-1 RT was more populated with NNRTIs with higher inhibitory activities. Thus, the NMR approach offers a useful tool to screen for novel NNRTIs in developing anti-HIV drugs.
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Affiliation(s)
- Ratsupa Thammaporn
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.,Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Japan
| | - Maho Yagi-Utsumi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
| | - Pornthip Boonsri
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | - Patchreenart Saparpakorn
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.,Center of Nanotechnology, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Supanna Techasakul
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.,Center of Nanotechnology, Kasetsart University, Chatuchak, Bangkok, Thailand
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