1
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Abdullahi A, Diaz AG, Fopoussi OM, Beloukas A, Defo VF, Kouanfack C, Torimiro J, Geretti AM. A detailed characterization of drug resistance during darunavir/ritonavir monotherapy highlights a high barrier to the emergence of resistance mutations in protease but identifies alternative pathways of resistance. J Antimicrob Chemother 2024; 79:339-348. [PMID: 38153241 PMCID: PMC10832591 DOI: 10.1093/jac/dkad386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/26/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Maintenance monotherapy with ritonavir-boosted darunavir has yielded variable outcomes and is not recommended. Trial samples offer valuable opportunities for detailed studies. We analysed samples from a 48 week trial in Cameroon to obtain a detailed characterization of drug resistance. METHODS Following failure of NNRTI-based therapy and virological suppression on PI-based therapy, participants were randomized to ritonavir-boosted darunavir (n = 81) or tenofovir disoproxil fumarate/lamivudine +ritonavir-boosted lopinavir (n = 39). At study entry, PBMC-derived HIV-1 DNA underwent bulk Protease and Reverse Transcriptase (RT) sequencing. At virological rebound (confirmed or last available HIV-1 RNA ≥ 60 copies/mL), plasma HIV-1 RNA underwent ultradeep Protease and RT sequencing and bulk Gag-Protease sequencing. The site-directed mutant T375A (p2/p7) was characterized phenotypically using a single-cycle assay. RESULTS NRTI and NNRTI resistance-associated mutations (RAMs) were detected in 52/90 (57.8%) and 53/90 (58.9%) HIV-1 DNA samples, respectively. Prevalence in rebound HIV-1 RNA (ritonavir-boosted darunavir, n = 21; ritonavir-boosted lopinavir, n = 2) was 9/23 (39.1%) and 10/23 (43.5%), respectively, with most RAMs detected at frequencies ≥15%. The resistance patterns of paired HIV-1 DNA and RNA sequences were partially consistent. No darunavir RAMs were found. Among eight participants experiencing virological rebound on ritonavir-boosted darunavir (n = 12 samples), all had Gag mutations associated with PI exposure, including T375N, T375A (p2/p7), K436R (p7/p1) and substitutions in p17, p24, p2 and p6. T375A conferred 10-fold darunavir resistance and increased replication capacity. CONCLUSIONS The study highlights the high resistance barrier of ritonavir-boosted darunavir while identifying alternative pathways of resistance through Gag substitutions. During virological suppression, resistance patterns in HIV-1 DNA reflect treatment history, but due to technical and biological considerations, cautious interpretation is warranted.
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Affiliation(s)
- Adam Abdullahi
- Takemi Program in International Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Ana Garcia Diaz
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK
| | - Olga Mafotsing Fopoussi
- Biomedical Sciences Department, University of West Attica, Athens, Greece
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention & Management (CIRCB), Yaoundé, Cameroon
| | - Apostolos Beloukas
- Biomedical Sciences Department, University of West Attica, Athens, Greece
- National AIDS Reference Centre of Southern Greece, School of Public Health, University of West Attica, Athens, Greece
| | - Victoire Fokom Defo
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention & Management (CIRCB), Yaoundé, Cameroon
- Department of HIV Medicine, Hôpital Central de Yaoundé, Ministry of Public Health, Yaoundé, Cameroon
| | - Charles Kouanfack
- Department of HIV Medicine, Hôpital Central de Yaoundé, Ministry of Public Health, Yaoundé, Cameroon
| | - Judith Torimiro
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention & Management (CIRCB), Yaoundé, Cameroon
| | - Anna Maria Geretti
- Department of Infectious Diseases, Fondazione PTV, University of Rome Tor Vergata, Rome, Italy
- Department of Infection, North Middlesex University Hospital, London, UK
- School of Immunity and Microbial Sciences, King’s College London, London, UK
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2
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Poongavanam V, Wieske LHE, Peintner S, Erdélyi M, Kihlberg J. Molecular chameleons in drug discovery. Nat Rev Chem 2024; 8:45-60. [PMID: 38123688 DOI: 10.1038/s41570-023-00563-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Molecular chameleons possess a flexibility that allows them to dynamically shield or expose polar functionalities in response to the properties of the environment. Although the concept of molecular chameleons was introduced already in 1970, interest in them has grown considerably since the 2010s, when drug discovery has focused to an increased extent on new chemical modalities. Such modalities include cyclic peptides, macrocycles and proteolysis-targeting chimeras, all of which reside in a chemical space far from that of traditional small-molecule drugs. Both cell permeability and aqueous solubility are required for the oral absorption of drugs. Engineering these properties, and potent target binding, into the larger new modalities is a more daunting task than for traditional small-molecule drugs. The ability of chameleons to adapt to different environments may be essential for success. In this Review, we provide both general and theoretical insights into the realm of molecular chameleons. We discuss why chameleons have come into fashion and provide a do-it-yourself toolbox for their design; we then provide a glimpse of how advanced in silico methods can support molecular chameleon design.
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Affiliation(s)
| | | | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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3
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Long Y, Donald BR. Predicting Affinity Through Homology (PATH): Interpretable Binding Affinity Prediction with Persistent Homology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567384. [PMID: 38014181 PMCID: PMC10680814 DOI: 10.1101/2023.11.16.567384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Accurate binding affinity prediction is crucial to structure-based drug design. Recent work used computational topology to obtain an effective representation of protein-ligand interactions. Although persistent homology encodes geometric features, previous works on binding affinity prediction using persistent homology employed uninterpretable machine learning models and failed to explain the underlying geometric and topological features that drive accurate binding affinity prediction. In this work, we propose a novel, interpretable algorithm for protein-ligand binding affinity prediction. Our algorithm achieves interpretability through an effective embedding of distances across bipartite matchings of the protein and ligand atoms into real-valued functions by summing Gaussians centered at features constructed by persistent homology. We name these functions internuclear persistent contours (IPCs) . Next, we introduce persistence fingerprints , a vector with 10 components that sketches the distances of different bipartite matching between protein and ligand atoms, refined from IPCs. Let the number of protein atoms in the protein-ligand complex be n , number of ligand atoms be m , and ω ≈ 2.4 be the matrix multiplication exponent. We show that for any 0 < ε < 1, after an 𝒪 ( mn log( mn )) preprocessing procedure, we can compute an ε -accurate approximation to the persistence fingerprint in 𝒪 ( m log 6 ω ( m/" )) time, independent of protein size. This is an improvement in time complexity by a factor of 𝒪 (( m + n ) 3 ) over any previous binding affinity prediction that uses persistent homology. We show that the representational power of persistence fingerprint generalizes to protein-ligand binding datasets beyond the training dataset. Then, we introduce PATH , Predicting Affinity Through Homology, an interpretable, small ensemble of shallow regression trees for binding affinity prediction from persistence fingerprints. We show that despite using 1,400-fold fewer features, PATH has comparable performance to a previous state-of-the-art binding affinity prediction algorithm that uses persistent homology features. Moreover, PATH has the advantage of being interpretable. Finally, we visualize the features captured by persistence fingerprint for variant HIV-1 protease complexes and show that persistence fingerprint captures binding-relevant structural mutations. The source code for PATH is released open-source as part of the osprey protein design software package.
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4
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Graham B, Windsor IW, Raines RT. Inhibition of HIV-1 Protease by a Boronic Acid with High Oxidative Stability. ACS Med Chem Lett 2023; 14:171-175. [PMID: 36793428 PMCID: PMC9923841 DOI: 10.1021/acsmedchemlett.2c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
HIV-1 protease is an important target for pharmaceutical intervention in HIV infection. Extensive structure-based drug design led to darunavir becoming a key chemotherapeutic agent. We replaced the aniline group of darunavir with a benzoxaborolone to form BOL-darunavir. This analogue has the same potency as darunavir as an inhibitor of catalysis by wild-type HIV-1 protease and, unlike darunavir, does not lose potency as an inhibitor of the common D30N variant. Moreover, BOL-darunavir is much more stable to oxidation than is a simple phenylboronic acid analogue of darunavir. X-ray crystallography revealed an extensive network of hydrogen bonds between the enzyme and benzoxaborolone moiety, including a novel direct hydrogen bond from a main-chain nitrogen to the carbonyl oxygen of the benzoxaborolone moiety that displaces a water molecule. These data highlight the utility of benzoxaborolone as a pharmacophore.
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Affiliation(s)
- Brian
J. Graham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | | | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Bihani SC, Gupta GD, Hosur MV. Molecular basis for reduced cleavage activity and drug resistance in D30N HIV-1 protease. J Biomol Struct Dyn 2022; 40:13127-13135. [PMID: 34609269 DOI: 10.1080/07391102.2021.1982007] [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: 01/06/2023]
Abstract
Nelfinavir is one of the FDA-approved HIV-1 protease inhibitors and a part of highly active anti-retroviral therapy (HAART) for the treatment of HIV-AIDS. Nelfinavir was the first HIV-1 protease inhibitor to be approved as a paediatric formulation. The application of HAART had resulted in significant improvement in the lives of AIDS patients. However, the emergence of drug resistance in HIV-1 protease has limited the use of many of these drugs including nelfinavir. A unique mutation observed frequently in patients treated with nelfinavir is D30N as it is selected exclusively by nelfinavir. The D30N mutation imparts very high resistance to nelfinavir but unlike other primary mutations does not give cross-resistance to the majority of other drugs. D30N mutation also significantly reduces cleavage activity of HIV-1 protease and affects viral fitness. Here, we have determined crystal structures of D30N HIV-1 protease in unliganded form and in complex with nelfinavir. These structures provide the rationale for reduced cleavage activity and the molecular basis of drug resistance induced by D30N mutation. The loss of coulombic interaction part of a crucial hydrogen bond between the drug and the protease is likely to play a major role in reduced affinity and resistance towards nelfinavir. The decreased catalytic activity of D30N HIV-1 protease due to altered interaction with the substrates and reduced stability of folding core may be the reason for the reduced replicative capacity of the virus harboring mutant HIV-1 protease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Subhash C Bihani
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai,India.,Homi Bhabha National Institute, Mumbai, India
| | - Gagan Deep Gupta
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai,India.,Homi Bhabha National Institute, Mumbai, India
| | - Madhusoodan V Hosur
- School of Natural Sciences and Engineering, National Institute of Advanced Studies, Indian Institute of Science Campus, Bengaluru, India
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Functionalized carbon nanotubes as an alternative to traditional anti-HIV-1 protease inhibitors: An understanding towards Nano-medicine development through MD simulations. J Mol Graph Model 2022; 117:108280. [PMID: 35963109 DOI: 10.1016/j.jmgm.2022.108280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 01/14/2023]
Abstract
The Human Immunodeficiency Virus (HIV) has been the source of epidemic infection of AIDS for a longer period. One of the most difficult tasks is identifying novel medications that can help to decrease or control this global health hazard by overcoming drug resistance. In recent decades' nanoparticles are emerging as extremely relevant in drug delivery platforms. In the current study, the pristine (SWCNT) and hydroxyl functionalized (SWCNT-OH) versions of the SWCNT were investigated as inhibitors against the wild-type (WT) and three key mutants of HIV-1 protease (HIV-pr) (I50V, V82A, and I84V). Molecular docking of SWCNT in the catalytic domain and running all-atom MD simulations of all complexes are also part of this project. A thorough inspection of conformational dynamics from 50 ns trajectories reveals that both the pristine and SWCNT-OH can fit right to the pocket region of HIV-pr and govern flap dynamics. The binding affinity of the four HIV-pr-SWCNT/SWCNT-OH complexes was further investigated using MM-PBSA-dependent binding free energy studies. In most mutants and WT systems, SWCNT-OH was reported to bind proportionately many folds (kcal/mol) more than pristine SWCNTs. Hence, SWCNTs are possible HIV-pr inhibitors in terms of their stable existence in the pocket area, stronger binding to the protease, and regulation of flap dynamics in controlling the active site volume, which have vast potential for applications against drug resistance.
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7
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Shabanpour Y, Sajjadi S, Behmard E, Abdolmaleki P, Keihan AH. The structural, dynamic, and thermodynamic basis of darunavir resistance of a heavily mutated HIV-1 protease using molecular dynamics simulation. Front Mol Biosci 2022; 9:927373. [PMID: 36046605 PMCID: PMC9420863 DOI: 10.3389/fmolb.2022.927373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
The human immunodeficiency virus type 1 protease (HIV-1 PR) is an important enzyme in the life cycle of the HIV virus. It cleaves inactive pre-proteins of the virus and changes them into active proteins. Darunavir (DRV) suppresses the wild-type HIV-1 PR (WT-Pr) activity but cannot inhibit some mutant resistant forms (MUT-Pr). Increasing knowledge about the resistance mechanism can be helpful for designing more effective inhibitors. In this study, the mechanism of resistance of a highly MUT-Pr strain against DRV was investigated. For this purpose, complexes of DRV with WT-Pr (WT-Pr-D) and MUT-Pr (MUT-Pr-D) were studied by all-atom molecular dynamics simulation in order to extract the dynamic and energetic properties. Our data revealed that mutations increased the flap-tip flexibility due to the reduction of the flap-flap hydrophobic interactions. So, the protease’s conformation changed from a closed state to a semi-open state that can facilitate the disjunction of DRV from the active site. On the other hand, energy analysis limited to the final basins of the energy landscape indicated that the entropy of binding of DRV to MUT-Pr was more favorable than that of WT-Pr. However, the enthalpy penalty overcomes it and makes binding more unfavorable relative to the WT-Pr. The unfavorable interaction of DRV with R8, I50, I84, D25′, and A28′ residues in MUT-Pr-D relative to WT-Pr-D is the reason for this enthalpy penalty. Thus, mutations drive resistance to DRV. The hydrogen bond analysis showed that compared with WT-Pr, the hydrogen bonds between DRV and the active-site residues of MUT-Pr were disrupted.
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Affiliation(s)
- Yaser Shabanpour
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sharareh Sajjadi
- Department of Biology, Roudehen Branch, Islamic Azad University, Roudehen, Iran
| | - Esmaeil Behmard
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Homayoun Keihan
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- *Correspondence: Amir Homayoun Keihan, ,
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8
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Zhu M, Zhou H, Ma L, Dong B, Ding J, Zhou J, Wang J, Zhang G, Wang M, Shan Q, Cen S, Wang Y. Design, synthesis and biological evaluation of protease inhibitors containing morpholine cores with remarkable potency against both HIV-1 subtypes B and C. Eur J Med Chem 2022; 233:114251. [DOI: 10.1016/j.ejmech.2022.114251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 11/03/2022]
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9
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Taguchi M, Oyama R, Kaneso M, Hayashi S. Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease. J Chem Inf Model 2022; 62:1328-1344. [PMID: 35212226 DOI: 10.1021/acs.jcim.1c01193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A human immunodeficiency virus-1 (HIV-1) protease is a homodimeric aspartic protease essential for the replication of HIV. The HIV-1 protease is a target protein in drug discovery for antiretroviral therapy, and various inhibitor molecules of transition state analogues have been developed. However, serious drug-resistant mutants have emerged. For understanding the molecular mechanism of the drug resistance, an accurate examination of the impacts of the mutations on ligand binding and enzymatic activity is necessary. Here, we present a molecular simulation study on the ligand binding of indinavir, a potent transition state analogue inhibitor, to the wild-type protein and a V82T/I84V drug-resistant mutant of the HIV-1 protease. We employed a hybrid ab initio quantum mechanical/molecular mechanical (QM/MM) free-energy optimization technique which combines a highly accurate QM description of the ligand molecule and its interaction with statistically ample conformational sampling of the MM protein environment by long-time molecular dynamics simulations. Through the free-energy calculations of protonation states of catalytic groups at the binding pocket and of the ligand-binding affinity changes upon the mutations, we successfully reproduced the experimentally observed significant reduction of the binding affinity upon the drug-resistant mutations and elucidated the underlying molecular mechanism. The present study opens the way for understanding the molecular mechanism of drug resistance through the direct quantitative comparison of ligand binding and enzymatic reaction with the same accuracy.
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Affiliation(s)
- Masahiko Taguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| | - Ryo Oyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Kaneso
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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10
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Neela YI, Guruprasad L. Structures and energetics of darunavir and active site amino acids of native and mutant HIV–1 protease: a computational study. Struct Chem 2021. [DOI: 10.1007/s11224-021-01852-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Biswal S, Mondal S, Mondal P. A Novel Ultra Performance Liquid Chromatography-PDA Method Development and Validation for Darunavir in Bulk and Its Application to Marketed Dosage Form. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2021; 13:69-75. [PMID: 34084050 PMCID: PMC8142922 DOI: 10.4103/jpbs.jpbs_337_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 05/04/2020] [Accepted: 09/08/2020] [Indexed: 12/04/2022] Open
Abstract
Aims and Objective: The aim of this study was to develop and validate a novel ultra-performance liquid chromatographic method for estimation of darunavir in a bulk and tablet dosage form. Materials and Methods: The chromatographic separation was achieved using DIKMA Endoversil (2.1mm x 50mm, 1.7 µm) column. A mixture of 40% buffer (0.1% octa sulfonic acid) and 60% acetonitrile was used as a mobile phase with the isocratic elution mode and eluent was monitored at 281nm using UV detector. The method was continued and validated in accordance with International Conference on Harmonization Guidelines. Validation study revealed the specificity and reliability of the method. Results: In this method, darunavir was eluted with retention time of 0.516 min. Calibration curve plots were found linear over the concentration ranges 10–50 μg/mL for darunavir. Limit of detection was 0.02 μg/mL and limit of quantification was found 0.07 μg/mL. The present method was also found stable in force degradation study. Conclusion: The empirical evidences of all the study results revealed the suitability of the estimation of darunavir in bulk and tablet dosage form without any interference from the excipients.
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Affiliation(s)
- Sabyasachi Biswal
- Institute of Pharmacy, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, India
| | - Sumanta Mondal
- Institute of Pharmacy, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, India
| | - Prasenjit Mondal
- Vaageswari Institute of Pharmaceutical Science, Karimnagar, Telangana, India
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12
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Laville P, Petitjean M, Regad L. Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease. Molecules 2021; 26:molecules26030611. [PMID: 33503916 PMCID: PMC7865771 DOI: 10.3390/molecules26030611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
The use of antiretroviral drugs is accompanied by the emergence of HIV-2 resistances. Thus, it is important to elucidate the mechanisms of resistance to antiretroviral drugs. Here, we propose a structural analysis of 31 drug-resistant mutants of HIV-2 protease (PR2) that is an important target against HIV-2 infection. First, we modeled the structures of each mutant. We then located structural shifts putatively induced by mutations. Finally, we compared wild-type and mutant inhibitor-binding pockets and interfaces to explore the impacts of these induced structural deformations on these two regions. Our results showed that one mutation could induce large structural rearrangements in side-chain and backbone atoms of mutated residue, in its vicinity or further. Structural deformations observed in side-chain atoms are frequent and of greater magnitude, that confirms that to fight drug resistance, interactions with backbone atoms should be favored. We showed that these observed structural deformations modify the conformation, volume, and hydrophobicity of the binding pocket and the composition and size of the PR2 interface. These results suggest that resistance mutations could alter ligand binding by modifying pocket properties and PR2 stability by impacting its interface. Our results reinforce the understanding of the effects of mutations that occurred in PR2 and the different mechanisms of PR2 resistance.
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13
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Huang XS, Luo RH, Hu XL, Chen H, Xiang SY, Tang CR, Zhang CT, Shen XN, Zheng YT. The New NNRTI ACC007 Combined with Lamivudine and Tenofovir Disoproxil Fumarate Show Synergy Anti-HIV Activity In Vitro. Curr HIV Res 2020; 18:332-341. [PMID: 32562524 DOI: 10.2174/1570162x18666200620211922] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/11/2020] [Accepted: 05/06/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Acquired immunodeficiency syndrome can hardly be cured currently and people with human immunodeficiency virus (HIV) need lifelong treatment that may result in the emergence of drug resistance which leads to failed treatment. Thus, the development of new anti- HIV drugs and new treatment regimens are necessary. OBJECTIVE The aim of this study is to analyze the combined anti-HIV activity of tenofovir disoproxil fumarate, lamivudine and ACC007, a new non-nucleoside reverse transcriptase inhibitor. METHODS The antiviral activity of tenofovir disoproxil fumarate, lamivudine and ACC007 alone or in combination against different HIV-1 strains was determined by the detection of HIV-1 p24 level through enzyme-linked immunosorbent assay. RESULT ACC007 showed EC50 of nanomolar range (from 3.03 nM to 252.59 nM) against all HIV-1 strains used in this study except the HIV-1A17, with EC50 of 1.57 μM. The combined antiviral activity of ACC007, lamivudine and tenofovir disoproxil fumarate showed synergy antiviral activity against all HIV-1 strains used in this study. The three-drug combination showed moderate synergism against HIV-1A17, HIV-14755-5, HIV-1K103N and HIV-1V106M, with a combination index value ranging from 0.71 to 0.87, and showed synergism against the other HIV-1 strains with combination index value from 0.35 to 0.67. The combination with ACC007 significantly increases the dose reduction index value of lamivudine and tenofovir disoproxil fumarate, compared with two-drug combination. CONCLUSION ACC007 exhibits potent antiviral activity alone or with 3TC and TDF, and exerts synergistic effect against all HIV strains used in our investigation in vitro.
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Affiliation(s)
- Xu-Sheng Huang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Rong-Hua Luo
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Xiong-Lin Hu
- Nanjing Accelas Pharmaceutical Co. Ltd. Nanjing 210046, Jiangsu, China
| | - Huan Chen
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Si-Ying Xiang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Cheng-Run Tang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Chun-Tao Zhang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Xiao-Ning Shen
- Jiangsu Aidea Pharmaceutical Co. Ltd. Nanjing 210046, Jiangsu, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
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14
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Zhu M, Dou Y, Ma L, Dong B, Zhang F, Zhang G, Wang J, Zhou J, Cen S, Wang Y. Novel HIV-1 Protease Inhibitors with Morpholine as the P2 Ligand to Enhance Activity against DRV-Resistant Variants. ACS Med Chem Lett 2020; 11:1196-1204. [PMID: 32551001 DOI: 10.1021/acsmedchemlett.0c00043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/31/2020] [Indexed: 11/29/2022] Open
Abstract
Flexible heterocyclic moieties as the P2 ligands of HIV-1 protease inhibitors may be adapted to the minimally distorted active site of mutations easily and enhance activity against DRV-resistant HIV-1 variants. Herein, the design, synthesis, and biological evaluation of a new series of inhibitors containing morpholine derivatives as the P2 ligands were described, among which, carbamate inhibitor 23a and carbamido inhibitor 27a exhibited almost 4- and 2-fold superior activity with enzyme Ki of 0.092 nM and 0.21 nM, as well as antiviral IC50 values of 0.41 nM and 0.95 nM, respectively, compared to DRV. Besides, they exhibited excellent activity with inhibition of 94% and 91%, respectively. Furthermore, they also showed appreciable antiviral activity against DRV-resistant HIV-1 variants.
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Affiliation(s)
- Mei Zhu
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yue Dou
- Department of Pharmacy, Jinzhou Medical University, Jinzhou 121001, China
| | - Ling Ma
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Fan Zhang
- Department of Pharmacy, Jinzhou Medical University, Jinzhou 121001, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Shan Cen
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yucheng Wang
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
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15
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Bastys T, Gapsys V, Walter H, Heger E, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV. Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 2020; 17:13. [PMID: 32430025 PMCID: PMC7236880 DOI: 10.1186/s12977-020-00520-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background HIV-1 can develop resistance to antiretroviral drugs, mainly through mutations within the target regions of the drugs. In HIV-1 protease, a majority of resistance-associated mutations that develop in response to therapy with protease inhibitors are found in the protease’s active site that serves also as a binding pocket for the protease inhibitors, thus directly impacting the protease-inhibitor interactions. Some resistance-associated mutations, however, are found in more distant regions, and the exact mechanisms how these mutations affect protease-inhibitor interactions are unclear. Furthermore, some of these mutations, e.g. N88S and L76V, do not only induce resistance to the currently administered drugs, but contrarily induce sensitivity towards other drugs. In this study, mutations N88S and L76V, along with three other resistance-associated mutations, M46I, I50L, and I84V, are analysed by means of molecular dynamics simulations to investigate their role in complexes of the protease with different inhibitors and in different background sequence contexts. Results Using these simulations for alchemical calculations to estimate the effects of mutations M46I, I50L, I84V, N88S, and L76V on binding free energies shows they are in general in line with the mutations’ effect on \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. For the primary mutation L76V, however, the presence of a background mutation M46I in our analysis influences whether the unfavourable effect of L76V on inhibitor binding is sufficient to outweigh the accompanying reduction in catalytic activity of the protease. Finally, we show that L76V and N88S changes the hydrogen bond stability of these residues with residues D30/K45 and D30/T31/T74, respectively. Conclusions We demonstrate that estimating the effect of both binding pocket and distant mutations on inhibitor binding free energy using alchemical calculations can reproduce their effect on the experimentally measured \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. We show that distant site mutations L76V and N88S affect the hydrogen bond network in the protease’s active site, which offers an explanation for the indirect effect of these mutations on inhibitor binding. This work thus provides valuable insights on interplay between primary and background mutations and mechanisms how they affect inhibitor binding.
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Affiliation(s)
- Tomas Bastys
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, University of Saarland, 66123, Saarbrücken, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Hauke Walter
- Medizinisches Labor Stendal, 39576, Stendal, Germany
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Nadezhda T Doncheva
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany. .,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany. .,Faculty of Medicine, Saarland University, 66421, Homburg, Germany.
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16
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Synthesis and evaluation of potent human immunodeficiency virus 1 protease inhibitors with epimeric isopropanol as novel P1' ligands. Future Med Chem 2020; 12:775-794. [PMID: 32125179 DOI: 10.4155/fmc-2019-0331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: HIV-1 protease inhibitors regimens suffered from a number of drawbacks, among which, the most egregious issue was the growing emergence of drug-resistant strains. Materials & methods: The design strategy of maximizing the protease active site interactions with the inhibitor, especially promoting extensive hydrogen bonding with the protein backbone atoms, might be in favor of combating drug resistance. A series of HIV-1 protease inhibitors that incorporated enantiomeric isopropanols as the P1' ligands in combination with phenols as the P2 ligands were reported herein. Results: A number of inhibitors displayed potent protease enzyme inhibition activity. In particular, inhibitor 14c showed comparable potency as darunavir with IC50 value of 1.91 nM and activity against darunavir-resistant HIV-1 variants. Conclusion: The new kind of HIV-1 protease inhibitors deserves further study.
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17
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Henes M, Kosovrasti K, Lockbaum GJ, Leidner F, Nachum GS, Nalivaika EA, Bolon DN, Yilmaz NK, Schiffer CA, Whitfield TW. Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance. Biochemistry 2019; 58:3711-3726. [PMID: 31386353 PMCID: PMC6941756 DOI: 10.1021/acs.biochem.9b00446] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protease inhibitors have the highest potency among antiviral therapies against HIV-1 infections, yet the virus can evolve resistance. Darunavir (DRV), currently the most potent Food and Drug Administration-approved protease inhibitor, retains potency against single-site mutations. However, complex combinations of mutations can confer resistance to DRV. While the interdependence between mutations within HIV-1 protease is key for inhibitor potency, the molecular mechanisms that underlie this control remain largely unknown. In this study, we investigated the interdependence between the L89V and L90M mutations and their effects on DRV binding. These two mutations have been reported to be positively correlated with one another in HIV-1 patient-derived protease isolates, with the presence of one mutation making the probability of the occurrence of the second mutation more likely. The focus of our investigation is a patient-derived isolate, with 24 mutations that we call "KY"; this variant includes the L89V and L90M mutations. Three additional KY variants with back-mutations, KY(V89L), KY(M90L), and the KY(V89L/M90L) double mutation, were used to experimentally assess the individual and combined effects of these mutations on DRV inhibition and substrate processing. The enzymatic assays revealed that the KY(V89L) variant, with methionine at residue 90, is highly resistant, but its catalytic function is compromised. When a leucine to valine mutation at residue 89 is present simultaneously with the L90M mutation, a rescue of catalytic efficiency is observed. Molecular dynamics simulations of these DRV-bound protease variants reveal how the L90M mutation induces structural changes throughout the enzyme that undermine the binding interactions.
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Affiliation(s)
- Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Gily S. Nachum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Daniel N.A. Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA,Corresponding Author Celia A. Schiffer: Phone: +1 508 856 8008; , Troy W. Whitfield: Phone: +1 508 856 4401;
| | - Troy W. Whitfield
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA,Corresponding Author Celia A. Schiffer: Phone: +1 508 856 8008; , Troy W. Whitfield: Phone: +1 508 856 4401;
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18
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Huang M, Song J, Huang P, Chen X, Wang W, Zhu Z, Song Y, Yang C. Molecular Crowding Evolution for Enabling Discovery of Enthalpy-Driven Aptamers for Robust Biomedical Applications. Anal Chem 2019; 91:10879-10886. [PMID: 31347355 DOI: 10.1021/acs.analchem.9b02697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An enthalpy-driven ligand is an ideal probe for practical applications because of the formation of abundant specific bonds between the ligand and target, compared to an entropy-driven ligand with a similar Gibbs free energy change. However, there has been a lack of direct discovery strategy for identifying enthalpy-driven ligands. In this work, a molecular crowding SELEX (systematic evolution of ligands by exponential enrichment) strategy for discovering enthalpy-driven aptamers was developed to improve the affinity and selectivity of aptamers in complex samples. Three aptamer sequences were successfully evolved against a tumor biomarker protein, and all proved to be enthalpy-driven by thermodynamics analysis, establishing the feasibility of molecular crowding SELEX for effective discovery of enthalpy-driven aptamers. Further comparison of aptamers evolved from conventional SELEX in buffer and molecular crowding SELEX (SYL-H2C) revealed much higher affinity of SYL-H2C. With its improved thermodynamic properties, the enthalpy-driven SYL-H2C aptamer was able to detect circulating tumor cells in real cancer patient blood samples with excellent detection accuracy (10/10). The proposed molecular crowding screening strategy offers a promising direction for discovering robust binding probes for a great variety of biomedical applications.
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Affiliation(s)
- Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Peifeng Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Xiaofeng Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
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19
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Karnati KR, Wang Y. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis. J Mol Graph Model 2019; 92:112-122. [PMID: 31351319 DOI: 10.1016/j.jmgm.2019.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/15/2022]
Abstract
HIV-1 protease (HIV-1-pr) plays an important role in viral replication and maturation, making it one of the most attractive targets for anti-retroviral therapy. To design new effective inhibitors able to combat drug resistance in mutant HIV-1-pr variants, it is essential to gain further understanding about the mechanisms by which the recently proposed inhibitors deactivate the mutant HIV-1-pr variants. In the present work, we explored the interactions between two P2-ligands (DRV, and one new derivative, 4UY) with wild type (WT) and two multiple mutant HIV-1-pr variants (p20 and p51) with all atom molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA). The trajectories of MD simulations show that both 4UY and DRV primarily bind with the active sites, flap and 80s loop regions of HIV-1-pr variants through either hydrogen bonds or hydrophobic interactions. More hydrogen bonds and hydrophobic interactions were located for 4UY/HIV-1-pr complexes than for DRV/HIV-1-pr counterparts. More importantly, 4UY was found to have an extra hydrogen bond with the backbone of Gly48' in the flap region of the HIV-1-prs. The flap tip-tip distance (I50-I50') and flap tip-active site distance (I50-D25 and I50'-D25') indicate that the flaps turn more closed in 4UY bound HIV-1-prs than DRV bound ones, and the former also have more compact hydrophobic cavities than the latter. Further, the vector projections from PCA indicate that 4UY/DRV inhibitor binding projects the closing of flap in HIV-1-pr variants. In line with the above trajectory analysis, the thermodynamics calculation with MM-PBSA method suggests much stronger binding affinity for 4UY/HIV-1-pr than DRV/HIV-1-pr by 4.3-6.4 kcal/mol. Although p20 and p51 also induce weaker binding due to multiple mutants for 4UY inhibitor by 1.9-1.8 kcal/mol, their bindings to the new P2 ligand (4UY) are indeed significantly enhanced as compared to DRV. The thermodynamic components responsible for the binding differences and the contribution from key residues to the binding were also discussed in detail.
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Affiliation(s)
- Konda Reddy Karnati
- Department of Chemistry and Forensic Science, Albany State University, Albany, GA, 31705, USA
| | - Yixuan Wang
- Department of Chemistry and Forensic Science, Albany State University, Albany, GA, 31705, USA.
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20
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C.S. V, Tamizhselvi R, Munusami P. Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations. J Biomol Struct Dyn 2019; 37:2608-2626. [DOI: 10.1080/07391102.2018.1492459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Vasavi C.S.
- School of Biosciences and Technology, VIT University, Vellore, India
| | | | - Punnagai Munusami
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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21
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Windsor IW, Palte MJ, Lukesh JC, Gold B, Forest KT, Raines RT. Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid. J Am Chem Soc 2018; 140:14015-14018. [PMID: 30346745 PMCID: PMC6249028 DOI: 10.1021/jacs.8b07366] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Boronic acids have been typecast as moieties for covalent complexation and are employed only rarely as agents for non-covalent recognition. By exploiting the profuse ability of a boronic acid group to form hydrogen bonds, we have developed an inhibitor of HIV-1 protease with extraordinary affinity. Specifically, we find that replacing an aniline moiety in darunavir with a phenylboronic acid leads to 20-fold greater affinity for the protease. X-ray crystallography demonstrates that the boronic acid group participates in three hydrogen bonds, more than the amino group of darunavir or any other analog. Importantly, the boronic acid maintains its hydrogen bonds and its affinity for the drug-resistant D30N variant of HIV-1 protease. The BOH···OC hydrogen bonds between the boronic acid hydroxy group and Asp30 (or Asn30) of the protease are short ( rO···O = 2.2 Å), and density functional theory analysis reveals a high degree of covalency. These data highlight the utility of boronic acids as versatile functional groups in the design of small-molecule ligands.
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Affiliation(s)
- Ian W. Windsor
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael J. Palte
- Medical Scientist Training Program, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Molecular & Cellular Pharmacology Graduate Training Program, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - John C. Lukesh
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Katrina T. Forest
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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22
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Gao Y, Zhu T, Chen J. Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.06.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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23
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Bastys T, Gapsys V, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV. Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations. J Chem Theory Comput 2018; 14:3397-3408. [PMID: 29847122 DOI: 10.1021/acs.jctc.7b01109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy Δ G, as well as in mechanistic terms. In this study, we analyze ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial drug binding regions of the protease.
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Affiliation(s)
- Tomas Bastys
- Department for Computational Biology and Applied Algorithmics , Max Planck Institute for Informatics , D-66123 Saarbrücken , Germany.,Saarbrücken Graduate School of Computer Science , University of Saarland , D-66123 Saarbrücken , Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics , Max Planck Institute for Biophysical Chemistry , D-37077 Göttingen , Germany
| | - Nadezhda T Doncheva
- Department for Computational Biology and Applied Algorithmics , Max Planck Institute for Informatics , D-66123 Saarbrücken , Germany.,Faculty of Health and Medical Sciences , University of Copenhagen , 2200 Copenhagen , Denmark
| | - Rolf Kaiser
- Institute for Virology , University Clinic of Cologne , D-50935 Köln , Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics , Max Planck Institute for Biophysical Chemistry , D-37077 Göttingen , Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics , Max Planck Institute for Informatics , D-66123 Saarbrücken , Germany
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24
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Ghosh AK, Fyvie WS, Brindisi M, Steffey M, Agniswamy J, Wang YF, Aoki M, Amano M, Weber IT, Mitsuya H. Design, Synthesis, Biological Evaluation, and X-ray Studies of HIV-1 Protease Inhibitors with Modified P2' Ligands of Darunavir. ChemMedChem 2017; 12:1942-1952. [PMID: 29110408 PMCID: PMC5896574 DOI: 10.1002/cmdc.201700614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/30/2017] [Indexed: 01/07/2023]
Abstract
The structure-based design, synthesis, and biological evaluation of a series of nonpeptidic HIV-1 protease inhibitors with rationally designed P2' ligands are described. The inhibitors are designed to enhance backbone binding interactions, particularly at the S2' subsite. Synthesis of inhibitors was carried out efficiently. The stereochemistry of alcohol functionalities of the P2' ligands was set by asymmetric reduction of the corresponding ketone using (R,R)- or (S,S)-Noyori catalysts. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 3g and 3h showed enzyme Ki values of 27.9 and 49.7 pm and antiviral activity of 6.2 and 3.9 nm, respectively. These inhibitors also remained quite potent against darunavir-resistant HIV-1 variants. An X-ray structure of inhibitor 3g in complex with HIV-1 protease revealed key interactions in the S2' subsite.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - W. Sean Fyvie
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Melinda Steffey
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Johnson Agniswamy
- Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303 (USA)
| | - Yuan-Fang Wang
- Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303 (USA)
| | - Manabu Aoki
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556 (Japan)
| | - Masayuki Amano
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556 (Japan)
| | - Irene T. Weber
- Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303 (USA)
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556 (Japan),Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892 (USA),Center for Clinical Sciences, National Center for Global Heath and Medicine, Shinjuku, Tokyo 162-8655 (Japan)
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25
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Ghosh AK, Sean Fyvie W, Brindisi M, Steffey M, Agniswamy J, Wang YF, Aoki M, Amano M, Weber IT, Mitsuya H. Design, synthesis, X-ray studies, and biological evaluation of novel macrocyclic HIV-1 protease inhibitors involving the P1'-P2' ligands. Bioorg Med Chem Lett 2017; 27:4925-4931. [PMID: 28958624 DOI: 10.1016/j.bmcl.2017.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/03/2017] [Indexed: 11/30/2022]
Abstract
Design, synthesis, and evaluation of a new class of HIV-1 protease inhibitors containing diverse flexible macrocyclic P1'-P2' tethers are reported. Inhibitor 5a with a pyrrolidinone-derived macrocycle exhibited favorable enzyme inhibitory and antiviral activity (Ki=13.2nM, IC50=22nM). Further incorporation of heteroatoms in the macrocyclic skeleton provided macrocyclic inhibitors 5m and 5o. These compounds showed excellent HIV-1 protease inhibitory (Ki=62pM and 14pM, respectively) and antiviral activity (IC50=5.3nM and 2.0nM, respectively). Inhibitor 5o also remained highly potent against a DRV-resistant HIV-1 variant.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - W Sean Fyvie
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Melinda Steffey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Johnson Agniswamy
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yuan-Fang Wang
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Manabu Aoki
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
| | - Masayuki Amano
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
| | - Irene T Weber
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892, USA; Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
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26
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Flynn WF, Haldane A, Torbett BE, Levy RM. Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease. Mol Biol Evol 2017; 34:1291-1306. [PMID: 28369521 PMCID: PMC5435099 DOI: 10.1093/molbev/msx095] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Understanding the complex mutation patterns that give rise to drug resistant viral strains provides a foundation for developing more effective treatment strategies for HIV/AIDS. Multiple sequence alignments of drug-experienced HIV-1 protease sequences contain networks of many pair correlations which can be used to build a (Potts) Hamiltonian model of these mutation patterns. Using this Hamiltonian model, we translate HIV-1 protease sequence covariation data into quantitative predictions for the probability of observing specific mutation patterns which are in agreement with the observed sequence statistics. We find that the statistical energies of the Potts model are correlated with the fitness of individual proteins containing therapy-associated mutations as estimated by in vitro measurements of protein stability and viral infectivity. We show that the penalty for acquiring primary resistance mutations depends on the epistatic interactions with the sequence background. Primary mutations which lead to drug resistance can become highly advantageous (or entrenched) by the complex mutation patterns which arise in response to drug therapy despite being destabilizing in the wildtype background. Anticipating epistatic effects is important for the design of future protease inhibitor therapies.
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Affiliation(s)
- William F. Flynn
- Department of Physics and Astronomy, Rutgers University, New Brunswick, NJ
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA
- Department of Chemistry, Temple University, Philadelphia, PA
| | - Bruce E. Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA
- Department of Chemistry, Temple University, Philadelphia, PA
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27
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Agniswamy J, Louis JM, Roche J, Harrison RW, Weber IT. Structural Studies of a Rationally Selected Multi-Drug Resistant HIV-1 Protease Reveal Synergistic Effect of Distal Mutations on Flap Dynamics. PLoS One 2016; 11:e0168616. [PMID: 27992544 PMCID: PMC5161481 DOI: 10.1371/journal.pone.0168616] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/02/2016] [Indexed: 12/20/2022] Open
Abstract
We report structural analysis of HIV protease variant PRS17 which was rationally selected by machine learning to represent wide classes of highly drug-resistant variants. Crystal structures were solved of PRS17 in the inhibitor-free form and in complex with antiviral inhibitor, darunavir. Despite its 17 mutations, PRS17 has only one mutation (V82S) in the inhibitor/substrate binding cavity, yet exhibits high resistance to all clinical inhibitors. PRS17 has none of the major mutations (I47V, I50V, I54ML, L76V and I84V) associated with darunavir resistance, but has 10,000-fold weaker binding affinity relative to the wild type PR. Comparable binding affinity of 8000-fold weaker than PR is seen for drug resistant mutant PR20, which bears 3 mutations associated with major resistance to darunavir (I47V, I54L and I84V). Inhibitor-free PRS17 shows an open flap conformation with a curled tip correlating with G48V flap mutation. NMR studies on inactive PRS17D25N unambiguously confirm that the flaps adopt mainly an open conformation in solution very similar to that in the inhibitor-free crystal structure. In PRS17, the hinge loop cluster of mutations, E35D, M36I and S37D, contributes to the altered flap dynamics by a mechanism similar to that of PR20. An additional K20R mutation anchors an altered conformation of the hinge loop. Flap mutations M46L and G48V in PRS17/DRV complex alter the Phe53 conformation by steric hindrance between the side chains. Unlike the L10F mutation in PR20, L10I in PRS17 does not break the inter-subunit ion pair or diminish the dimer stability, consistent with a very low dimer dissociation constant comparable to that of wild type PR. Distal mutations A71V, L90M and I93L propagate alterations to the catalytic site of PRS17. PRS17 exhibits a molecular mechanism whereby mutations act synergistically to alter the flap dynamics resulting in significantly weaker binding yet maintaining active site contacts with darunavir.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, United States of America
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, United States of America
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Robert W. Harrison
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
- Department of Computer Science, Georgia State University, Atlanta, Georgia, United States of America
| | - Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
- Department of Chemistry, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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28
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De Luca A, Flandre P, Dunn D, Zazzi M, Wensing A, Santoro MM, Günthard HF, Wittkop L, Kordossis T, Garcia F, Castagna A, Cozzi-Lepri A, Churchill D, De Wit S, Brockmeyer NH, Imaz A, Mussini C, Obel N, Perno CF, Roca B, Reiss P, Schülter E, Torti C, van Sighem A, Zangerle R, Descamps D. Improved darunavir genotypic mutation score predicting treatment response for patients infected with HIV-1 subtype B and non-subtype B receiving a salvage regimen. J Antimicrob Chemother 2016; 71:1352-60. [PMID: 26825119 PMCID: PMC5808835 DOI: 10.1093/jac/dkv465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/03/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The objective of this study was to improve the prediction of the impact of HIV-1 protease mutations in different viral subtypes on virological response to darunavir. METHODS Darunavir-containing treatment change episodes (TCEs) in patients previously failing PIs were selected from large European databases. HIV-1 subtype B-infected patients were used as the derivation dataset and HIV-1 non-B-infected patients were used as the validation dataset. The adjusted association of each mutation with week 8 HIV RNA change from baseline was analysed by linear regression. A prediction model was derived based on best subset least squares estimation with mutational weights corresponding to regression coefficients. Virological outcome prediction accuracy was compared with that from existing genotypic resistance interpretation systems (GISs) (ANRS 2013, Rega 9.1.0 and HIVdb 7.0). RESULTS TCEs were selected from 681 subtype B-infected and 199 non-B-infected adults. Accompanying drugs were NRTIs in 87%, NNRTIs in 27% and raltegravir or maraviroc or enfuvirtide in 53%. The prediction model included weighted protease mutations, HIV RNA, CD4 and activity of accompanying drugs. The model's association with week 8 HIV RNA change in the subtype B (derivation) set was R(2) = 0.47 [average squared error (ASE) = 0.67, P < 10(-6)]; in the non-B (validation) set, ASE was 0.91. Accuracy investigated by means of area under the receiver operating characteristic curves with a binary response (above the threshold value of HIV RNA reduction) showed that our final model outperformed models with existing interpretation systems in both training and validation sets. CONCLUSIONS A model with a new darunavir-weighted mutation score outperformed existing GISs in both B and non-B subtypes in predicting virological response to darunavir.
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Affiliation(s)
- Andrea De Luca
- Division of Infectious Diseases, Siena University Hospital, Siena, Italy Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - David Dunn
- MRC Clinical Trials Unit at University College London, London, UK
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland and Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Linda Wittkop
- Inserm U897, ISPED, Université de Bordeaux, CHU Bordeaux, France/Cohere in Eurocoord RCC, Bordeaux, France
| | | | | | | | | | - Duncan Churchill
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | | | - Norbert H Brockmeyer
- Department of Dermatology and Venereology, Center for Sexual Health and Medicine, Ruhr University Bochum, Bochum, Germany and Competence Network for HIV/AIDS, Ruhr University Bochum, Bochum, Germany
| | - Arkaitz Imaz
- Bellvitge University Hospital, Barcelona, Catalonia, Spain
| | | | - Niels Obel
- Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, The Netherlands, and Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands/Cohere in Eurocoord RCC, Copenhagen, Denmark
| | | | | | | | - Robert Zangerle
- Universitätsklinik für Dermatologie und Venerologie, Innsbruck, Austria
| | - Diane Descamps
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, IAME, UMR_1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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29
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Nakashima M, Ode H, Suzuki K, Fujino M, Maejima M, Kimura Y, Masaoka T, Hattori J, Matsuda M, Hachiya A, Yokomaku Y, Suzuki A, Watanabe N, Sugiura W, Iwatani Y. Unique Flap Conformation in an HIV-1 Protease with High-Level Darunavir Resistance. Front Microbiol 2016; 7:61. [PMID: 26870021 PMCID: PMC4737996 DOI: 10.3389/fmicb.2016.00061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/14/2016] [Indexed: 11/13/2022] Open
Abstract
Darunavir (DRV) is one of the most powerful protease inhibitors (PIs) for treating human immunodeficiency virus type-1 (HIV-1) infection and presents a high genetic barrier to the generation of resistant viruses. However, DRV-resistant HIV-1 infrequently emerges from viruses exhibiting resistance to other protease inhibitors. To address this resistance, researchers have gathered genetic information on DRV resistance. In contrast, few structural insights into the mechanism underlying DRV resistance are available. To elucidate this mechanism, we determined the crystal structure of the ligand-free state of a protease with high-level DRV resistance and six DRV resistance-associated mutations (including I47V and I50V), which we generated by in vitro selection. This crystal structure showed a unique curling conformation at the flap regions that was not found in the previously reported ligand-free protease structures. Molecular dynamics simulations indicated that the curled flap conformation altered the flap dynamics. These results suggest that the preference for a unique flap conformation influences DRV binding. These results provide new structural insights into elucidating the molecular mechanism of DRV resistance and aid to develop PIs effective against DRV-resistant viruses.
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Affiliation(s)
- Masaaki Nakashima
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Hirotaka Ode
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Koji Suzuki
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Masami Maejima
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yuki Kimura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Takashi Masaoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Junko Hattori
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Masakazu Matsuda
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuko Hachiya
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yoshiyuki Yokomaku
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuo Suzuki
- Department of Biotechnology, Nagoya University Graduate School of Engineering Nagoya, Japan
| | - Nobuhisa Watanabe
- Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan; Synchrotron Radiation Research Center, Nagoya UniversityNagoya, Japan
| | - Wataru Sugiura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of AIDS Research, Nagoya University Graduate School of MedicineNagoya, Japan
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30
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Chen J. Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free energy predictions. RSC Adv 2016. [DOI: 10.1039/c6ra09201b] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Molecular dynamics simulation and binding free energy calculations were used to probe drug resistance of HIV-1 protease mutations toward inhibitors.
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Affiliation(s)
- Jianzhong Chen
- School of Science
- Shandong Jiaotong University
- Jinan 250357
- China
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31
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Shen Y, Radhakrishnan ML, Tidor B. Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition. Proteins 2015; 83:351-72. [PMID: 25410041 PMCID: PMC4829108 DOI: 10.1002/prot.24730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/14/2014] [Accepted: 11/06/2014] [Indexed: 11/16/2022]
Abstract
Molecular recognition is central to biology and ranges from highly selective to broadly promiscuous. The ability to modulate specificity at will is particularly important for drug development, and discovery of mechanisms contributing to binding specificity is crucial for our basic understanding of biology and for applications in health care. In this study, we used computational molecular design to create a large dataset of diverse small molecules with a range of binding specificities. We then performed structural, energetic, and statistical analysis on the dataset to study molecular mechanisms of achieving specificity goals. The work was done in the context of HIV‐1 protease inhibition and the molecular designs targeted a panel of wild‐type and drug‐resistant mutant HIV‐1 protease structures. The analysis focused on mechanisms for promiscuous binding to bind robustly even to resistance mutants. Broadly binding inhibitors tended to be smaller in size, more flexible in chemical structure, and more hydrophobic in nature compared to highly selective ones. Furthermore, structural and energetic analyses illustrated mechanisms by which flexible inhibitors achieved binding; we found ligand conformational adaptation near mutation sites and structural plasticity in targets through torsional flips of asymmetric functional groups to form alternative, compensatory packing interactions or hydrogen bonds. As no inhibitor bound to all variants, we designed small cocktails of inhibitors to do so and discovered that they often jointly covered the target set through mechanistic complementarity. Furthermore, using structural plasticity observed in experiments, and potentially in simulations, is suggested to be a viable means of designing adaptive inhibitors that are promiscuous binders. Proteins 2015; 83:351–372. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Yang Shen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Computer Science and Artificial Intelligence LaboratoryMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Present address:
Center for Bioinformatics and Genomic Systems EngineeringDepartment of Electrical and Computer EngineeringTexas A&M UniversityCollege StationTexas77843
| | | | - Bruce Tidor
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Computer Science and Artificial Intelligence LaboratoryMassachusetts Institute of TechnologyCambridgeMassachusetts02139
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32
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Yang ZH, Bai XG, Zhou L, Wang JX, Liu HT, Wang YC. Synthesis and biological evaluation of novel HIV-1 protease inhibitors using tertiary amine as P2-ligands. Bioorg Med Chem Lett 2015; 25:1880-3. [PMID: 25838144 DOI: 10.1016/j.bmcl.2015.03.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/13/2015] [Accepted: 03/17/2015] [Indexed: 11/29/2022]
Abstract
A series of tertiary amine derivatives exhibiting potent HIV-1 protease inhibiting properties were identified. These novel inhibitors were designed based on the structure of Darunavir with modification on the P2 and P2' position. This effort led to discovery of 35e and 38e, which exhibited excellent HIV-1 protease inhibition with IC50 values of 15 nM and 64 nM, respectively.
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Affiliation(s)
- Zhi-Heng Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Xiao-Guang Bai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Lei Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Ju-Xian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Tao Liu
- Department of Pharmacy, Hebei General Hospital, Hebei, Shijiazhuang 050051, PR China
| | - Yu-Cheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China.
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33
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Prashar V, Bihani SC, Ferrer JL, Hosur MV. Structural Basis of Why Nelfinavir-Resistant D30N Mutant of HIV-1 Protease Remains Susceptible to Saquinavir. Chem Biol Drug Des 2015; 86:302-8. [DOI: 10.1111/cbdd.12494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 11/13/2014] [Accepted: 11/21/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Vishal Prashar
- Solid State Physics Division; Bhabha Atomic Research Centre; Trombay, Mumbai 400085 India
| | - Subhash C. Bihani
- Solid State Physics Division; Bhabha Atomic Research Centre; Trombay, Mumbai 400085 India
| | - Jean-Luc Ferrer
- Institut de Biologie Structurale Jean-Pierre Ebel; Groupe Synchrotron; Commissariat a l'Energie Atomique et aux Energies Alternatives; Centre National de la Recherche Scientifique; Universite de Grenoble Alpes; Grenoble 38027 France
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34
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Meher BR, Wang Y. Exploring the drug resistance of V32I and M46L mutant HIV-1 protease to inhibitor TMC114: flap dynamics and binding mechanism. J Mol Graph Model 2014; 56:60-73. [PMID: 25562662 DOI: 10.1016/j.jmgm.2014.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 10/14/2014] [Accepted: 11/07/2014] [Indexed: 12/22/2022]
Abstract
Inhibitors of HIV-1 protease (HIV-1-pr) generally only bind to the active site of the protease. However, for some mutants such as V32I and M46L the TMC114 can bind not only to the active cavity but also to the groove of the flexible flaps. Although the second binding site suggests the higher efficiency of the drug against HIV-1-pr, the drug resistance in HIV-1-pr due to mutations cannot be ignored, which prompts us to investigate the molecular mechanisms of drug resistance and behavior of double bound TMC114 (2T) to HIV-1-pr. The conformational dynamics of HIV-1-pr and the binding of TMC114 to the WT, V32I and M46L mutants were investigated with all-atom molecular dynamic (MD) simulation. The 20 ns MD simulation shows many fascinating effects of the inhibitor binding to the WT and mutant proteases. MM-PBSA calculations explain the binding free energies unfavorable for the M46L and V32I mutants as compared to the WT. For the single binding (1T) the less binding affinity can be attributed to the entropic loss for both V32I-1T and M46L-1T. Although the second binding of TMC114 with flap does increase binding energy for the mutants (V32I-2T and M46L-2T), the considerable entropy loss results in the lower binding Gibbs free energies. Thus, binding of TMC114 in the flap region does not help much in the total gain in binding affinity of the system, which was verified from this study and thereby validating experiments.
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Affiliation(s)
- Biswa Ranjan Meher
- Computational Chemistry Laboratory, Department of Natural Sciences, Albany State University, Albany, GA 31705, USA
| | - Yixuan Wang
- Computational Chemistry Laboratory, Department of Natural Sciences, Albany State University, Albany, GA 31705, USA.
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35
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Ragland DA, Nalivaika EA, Nalam MNL, Prachanronarong KL, Cao H, Bandaranayake RM, Cai Y, Kurt-Yilmaz N, Schiffer CA. Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease. J Am Chem Soc 2014; 136:11956-63. [PMID: 25091085 PMCID: PMC4151706 DOI: 10.1021/ja504096m] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
HIV-1 protease inhibitors are part
of the highly active antiretroviral
therapy effectively used in the treatment of HIV infection and AIDS.
Darunavir (DRV) is the most potent of these inhibitors, soliciting
drug resistance only when a complex combination of mutations occur
both inside and outside the protease active site. With few exceptions,
the role of mutations outside the active site in conferring resistance
remains largely elusive. Through a series of DRV–protease complex
crystal structures, inhibition assays, and molecular dynamics simulations,
we find that single and double site mutations outside the active site
often associated with DRV resistance alter the structure and dynamic
ensemble of HIV-1 protease active site. These alterations correlate
with the observed inhibitor binding affinities for the mutants, and
suggest a network hypothesis on how the effect of
distal mutations are propagated to pivotal residues at the active
site and may contribute to conferring drug resistance.
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Affiliation(s)
- Debra A Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
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36
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Tzoupis H, Leonis G, Avramopoulos A, Mavromoustakos T, Papadopoulos MG. Systematic molecular dynamics, MM-PBSA, and ab initio approaches to the saquinavir resistance mechanism in HIV-1 PR due to 11 double and multiple mutations. J Phys Chem B 2014; 118:9538-52. [PMID: 25036111 DOI: 10.1021/jp502687q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutations in the human immunodeficiency virus (HIV) enable virus replication even when appropriate antiretroviral therapy is followed, thus leading to the emergence of drug resistance. In a previous work, we systematically examined seven single mutations that are associated with saquinavir (SQV) resistance in HIV-1 protease (Tzoupis, H.; Leonis, G.; Mavromoustakos, T.; Papadopoulos, M. G. J. Chem. Theory Comput. 2013, 9, 1754-1764). Herein, we extend our analysis, which includes seven double (G48V-V82A, L10I-G48V, G48V-L90M, I84V-L90M, L10I-V82A, L10I-L63P, A71V-G73S) and four multiple (L10I-L63P-A71V, L10I-G48V-V82A, G73S-I84V-L90M, L10I-L63P-A71V-G73S-I84V-L90M) SQV-HIV-1 PR mutant complexes, in an attempt to generalize our findings and formulate the main elements of the SQV resistance mechanism in the protease. On the basis of molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and ab initio computational approaches, we identified specific features that constitute the HIV-1 PR mechanism of resistance at the molecular level: the low flexibility of SQV in the binding cavity and the preservation of hydrogen bonding (HB) and van der Waals interactions between SQV and several active-site (Gly27/27', Asp29/29'/30/30', especially Asp25/25') and flap (Ile50/50', Gly48/48') residues of the protease contribute significantly to efficient binding. The total enthalpy loss in all mutants is mostly due to the loss in enthalpy of the active-site region. Furthermore, it was observed that mutation accumulation may induce stabilization to SQV and to the flaps through enhanced HB interactions that lead to improved inhibition (e.g., accumulation of mutations in complexes containing L10I, G48V, L63P, I84V, or L90M single mutations). It was also concluded that permanent flap closure is obtained independently of mutations and SQV binding is mostly driven by van der Waals, nonpolar, and exchange-energy contributions. Importantly, it was indicated that the optimal positioning of SQV and the structure of the binding cavity are tightly coupled, since small changes in geometry may affect the binding energy greatly. The results of our theoretical approaches are in agreement with experimental evidence and provide a reliable description of SQV resistance in HIV-1 PR.
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Affiliation(s)
- Haralambos Tzoupis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
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37
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Nunthanavanit P, Ungwitayatorn J. Molecular docking studies of chromone derivatives against wild type and mutant strains of HIV-1 protease. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0992-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Li D, Zhang Y, Zhao RN, Fan S, Han JG. Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation. J Mol Model 2014; 20:2122. [PMID: 24526384 DOI: 10.1007/s00894-014-2122-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/19/2013] [Indexed: 12/01/2022]
Abstract
Residue Gly86 is considered as the highly conversed residue in the HIV-1 protease. In our work, the detailed binding free energies for the wild-type (WT) and mutated proteases binding to the TMC-114 are estimated to investigate the protein-inhibitor binding and drug resistance mechanism by molecule dynamic simulations and molecular mechanics Poisson Boltzmann surface area (MM-PBSA) method. The binding affinities between the mutants and inhibitor are different than that in the wild-type complex and the major resistance to Darunavir (DRV) of G86A and G86S originate from the electrostatic energy and entropy, respectively. Furthermore, free energy decomposition analysis for the WT and mutated complexes on the basis of per-residue indicates that the mutagenesis influences the energy contribution of the residue located at three regions: active site region (residue 24-32), the flap region, and the region around the mutated residue G86 (residue 79-88), especially the flap region. Finally, further hydrogen bonds and structure analysis are carried out to detect the relationship between the energy and conformation. In all, the G86 mutations change the flap region's conformation. The experimental results are in good agreement with available results.
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Affiliation(s)
- Dan Li
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China
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Ni Z, Chen H, Qi X, Jin R. Why is Substrate Peptide Binding Unsusceptible to Multidrug-Resistant Mutations in HIV-1 Protease? A Structural and Energetic Analysis. Int J Pept Res Ther 2013. [DOI: 10.1007/s10989-013-9365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Agniswamy J, Shen CH, Wang YF, Ghosh AK, Rao KV, Xu CX, Sayer JM, Louis JM, Weber IT. Extreme multidrug resistant HIV-1 protease with 20 mutations is resistant to novel protease inhibitors with P1'-pyrrolidinone or P2-tris-tetrahydrofuran. J Med Chem 2013; 56:4017-27. [PMID: 23590295 DOI: 10.1021/jm400231v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Extreme drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with the clinical inhibitor amprenavir (1) and two potent antiviral investigational inhibitors GRL-02031 (2) and GRL-0519 (3). Clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme, which is consistent with dissociation constants (KL) from isothermal titration calorimetry of 40 nM for 3, 178 nM for amprenavir, and 960 nM for 2. High resolution crystal structures of PR20-inhibitor complexes revealed altered interactions compared with the corresponding wild-type PR complexes in agreement with relative inhibition. Amprenavir lacks interactions due to PR20 mutations in the S2/S2' subsites relative to PR. Inhibitors 2 and 3 lose interactions with Arg8' in PR20 relative to the wild-type enzyme because Arg8' shifts to interact with mutated L10F side chain. Overall, inhibitor 3 compares favorably with darunavir in affinity for PR20 and shows promise for further development.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, USA
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41
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Tzoupis H, Leonis G, Mavromoustakos T, Papadopoulos MG. A Comparative Molecular Dynamics, MM–PBSA and Thermodynamic Integration Study of Saquinavir Complexes with Wild-Type HIV-1 PR and L10I, G48V, L63P, A71V, G73S, V82A and I84V Single Mutants. J Chem Theory Comput 2013; 9:1754-64. [DOI: 10.1021/ct301063k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haralambos Tzoupis
- Institute of Biology, Medicinal
Chemistry and Biotechnology, National Hellenic Research Foundation,
48 Vas. Constantinou Ave., Athens 11635, Greece
- Department of Chemistry, National
and Kapodistrian University of Athens, Panepistimioupolis Zographou
15771, Greece
| | - Georgios Leonis
- Institute of Biology, Medicinal
Chemistry and Biotechnology, National Hellenic Research Foundation,
48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, National
and Kapodistrian University of Athens, Panepistimioupolis Zographou
15771, Greece
| | - Manthos G. Papadopoulos
- Institute of Biology, Medicinal
Chemistry and Biotechnology, National Hellenic Research Foundation,
48 Vas. Constantinou Ave., Athens 11635, Greece
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42
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How conformational changes can affect catalysis, inhibition and drug resistance of enzymes with induced-fit binding mechanism such as the HIV-1 protease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:867-73. [PMID: 23376188 DOI: 10.1016/j.bbapap.2013.01.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/21/2013] [Accepted: 01/24/2013] [Indexed: 11/21/2022]
Abstract
A central question is how the conformational changes of proteins affect their function and the inhibition of this function by drug molecules. Many enzymes change from an open to a closed conformation upon binding of substrate or inhibitor molecules. These conformational changes have been suggested to follow an induced-fit mechanism in which the molecules first bind in the open conformation in those cases where binding in the closed conformation appears to be sterically obstructed such as for the HIV-1 protease. In this article, we present a general model for the catalysis and inhibition of enzymes with induced-fit binding mechanism. We derive general expressions that specify how the overall catalytic rate of the enzymes depends on the rates for binding, for the conformational changes, and for the chemical reaction. Based on these expressions, we analyze the effect of mutations that mainly shift the conformational equilibrium on catalysis and inhibition. If the overall catalytic rate is limited by product unbinding, we find that mutations that destabilize the closed conformation relative to the open conformation increase the catalytic rate in the presence of inhibitors by a factor exp(ΔΔGC/RT) where ΔΔGC is the mutation-induced shift of the free-energy difference between the conformations. This increase in the catalytic rate due to changes in the conformational equilibrium is independent of the inhibitor molecule and, thus, may help to understand how non-active-site mutations can contribute to the multi-drug-resistance that has been observed for the HIV-1 protease. A comparison to experimental data for the non-active-site mutation L90M of the HIV-1 protease indicates that the mutation slightly destabilizes the closed conformation of the enzyme. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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Zhang H, Wang YF, Shen CH, Agniswamy J, Rao KV, Xu CX, Ghosh AK, Harrison RW, Weber IT. Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease. J Med Chem 2013; 56:1074-83. [PMID: 23298236 DOI: 10.1021/jm301519z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
GRL-0519 (1) is a potent antiviral inhibitor of HIV-1 protease (PR) possessing tris-tetrahydrofuran (tris-THF) at P2. The high resolution X-ray crystal structures of inhibitor 1 in complexes with single substitution mutants PR(R8Q), PR(D30N), PR(I50V), PR(I54M), and PR(V82A) were analyzed in relation to kinetic data. The smaller valine side chain in PR(I50V) eliminated hydrophobic interactions with inhibitor and the other subunit consistent with 60-fold worse inhibition. Asn30 in PR(D30N) showed altered interactions with neighboring residues and 18-fold worse inhibition. Mutations V82A and I54M showed compensating structural changes consistent with 6-7-fold lower inhibition. Gln8 in PR(R8Q) replaced the ionic interactions of wild type Arg8 with hydrogen bond interactions without changing the inhibition significantly. The carbonyl oxygen of Gly48 showed two alternative conformations in all structures likely due to the snug fit of the large tris-THF group in the S2 subsite in agreement with high antiviral efficacy of 1 on resistant virus.
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Affiliation(s)
- Hongmei Zhang
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
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Ramesh B, Ramakrishna S, Reddy RKK, babu KH, Sarma VUM, Devi PS. HPTLC METHOD FOR DETERMINATION OF DARUNAVIR IN RAT PLASMA AND ITS APPLICATION IN PHARMACOKINETIC STUDIES. J LIQ CHROMATOGR R T 2013. [DOI: 10.1080/10826076.2011.647194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Bokka Ramesh
- a Analytical Chemistry Division, Indian Institute of Chemical Technology , Hyderabad , India
| | - Sisla Ramakrishna
- b Pharmacology Division, Indian Institute of Chemical Technology , Hyderabad , India
| | | | - Kothapalli Hari babu
- c Natural Products Lab Division, Indian Institute of Chemical Technology , Hyderabad , India
| | | | - Potturi Sita Devi
- a Analytical Chemistry Division, Indian Institute of Chemical Technology , Hyderabad , India
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Meher BR, Wang Y. Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: analysis of flap dynamics and binding mechanism. J Mol Graph Model 2012; 38:430-45. [PMID: 23142620 DOI: 10.1016/j.jmgm.2012.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/31/2012] [Accepted: 10/05/2012] [Indexed: 10/27/2022]
Abstract
Most of the currently treated HIV-1 protease (HIV-PR) inhibitors have been prone to suffer from the mutations associated drug resistance. Therefore, it is necessary to search for potent alternatives against the drug resistance. In the current study we have tested the single-walled carbon nanotube (SWCNT) as an inhibitor in wild type (WT) as well as in three primary mutants (I50V(PR), V82A(PR) and I84V(PR)) of the HIV-1-PR through docking the SWCNT in the active site region, and then performed all-atom MD simulations for the complexes. The conformational dynamics of HIV-PR with a 20 ns trajectory reveals that the SWCNT can effectively bind to the HIV-1-PR active site and regulate the flap dynamics such as maintaining the flap-flap closed. To gain an insight into the binding affinity, we also performed the MM-PBSA based binding free energy calculations for the four HIV-PR/SWCNT complexes. It was observed that, although the binding between the SWCNT and the HIV-PR decreases due to the mutations, the SWCNTs bind to the HIV-PRs 3-5 folds stronger than the most potent HIV-1-PR inhibitor, TMC114. Remarkably, the significant interactions with binding energy higher than 1kcal/mol focus on the flap and active regions, which favors closing flap-flap and deactivating the active residues of the HIV-PR. The flap dynamics and binding strength information for HIV-PR and SWCNTs can help design SWCNT-based HIV-1-PR inhibitors.
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Affiliation(s)
- Biswa Ranjan Meher
- Computational Chemistry Laboratory, Department of Natural Sciences, Albany State University, Albany, GA 31705, USA
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Shen CH, Tie Y, Yu X, Wang YF, Kovalevsky AY, Harrison RW, Weber IT. Capturing the reaction pathway in near-atomic-resolution crystal structures of HIV-1 protease. Biochemistry 2012; 51:7726-32. [PMID: 22963370 DOI: 10.1021/bi3008092] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Snapshots of three consecutive steps in the proteolytic reaction of HIV-1 protease (PR) were obtained in crystal structures at resolutions of 1.2-1.4 Å. Structures of wild-type protease and two mutants (PR(V32I) and PR(I47V)) with V32I and I47V substitutions, which are common in drug resistance, reveal the gem-diol tetrahedral intermediate, the separating N- and C-terminal products, and the C-terminal product of an autoproteolytic peptide. These structures represent three stages in the reaction pathway and shed light on the reaction mechanism. The near-atomic-resolution geometric details include a short hydrogen bond between the intermediate and the outer carboxylate oxygen of one catalytic Asp25 that is conserved in all three structures. The two products in the complex with mutant PR(I47V) have a 2.2 Å separation of the amide and carboxyl carbon of the adjacent ends, suggesting partial cleavage prior to product release. The complex of mutant PR(V32I) with a single C-terminal product shows density for water molecules in the other half of the binding site, including a partial occupancy water molecule interacting with the product carboxylate end and the carbonyl oxygen of one conformation of Gly27, which suggests a potential role of Gly27 in recycling from the product complex to the ligand-free enzyme. These structural details at near-atomic resolution enhance our understanding of the reaction pathway and will assist in the design of mechanism-based inhibitors as antiviral agents.
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Affiliation(s)
- Chen-Hsiang Shen
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
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Parai MK, Huggins DJ, Cao H, Nalam MNL, Ali A, Schiffer CA, Tidor B, Rana TM. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. J Med Chem 2012; 55:6328-41. [PMID: 22708897 PMCID: PMC3409094 DOI: 10.1021/jm300238h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of new HIV-1 protease inhibitors (PIs) were designed using a general strategy that combines computational structure-based design with substrate-envelope constraints. The PIs incorporate various alcohol-derived P2 carbamates with acyclic and cyclic heteroatomic functionalities into the (R)-hydroxyethylamine isostere. Most of the new PIs show potent binding affinities against wild-type HIV-1 protease and three multidrug resistant (MDR) variants. In particular, inhibitors containing the 2,2-dichloroacetamide, pyrrolidinone, imidazolidinone, and oxazolidinone moieties at P2 are the most potent with K(i) values in the picomolar range. Several new PIs exhibit nanomolar antiviral potencies against patient-derived wild-type viruses from HIV-1 clades A, B, and C and two MDR variants. Crystal structure analyses of four potent inhibitors revealed that carbonyl groups of the new P2 moieties promote extensive hydrogen bond interactions with the invariant Asp29 residue of the protease. These structure-activity relationship findings can be utilized to design new PIs with enhanced enzyme inhibitory and antiviral potencies.
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Affiliation(s)
- Maloy Kumar Parai
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - David J. Huggins
- Department of Biological Engineering and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hong Cao
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Bruce Tidor
- Department of Biological Engineering and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tariq M. Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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Leonis G, Czyżnikowska Ż, Megariotis G, Reis H, Papadopoulos MG. Computational studies of darunavir into HIV-1 protease and DMPC bilayer: necessary conditions for effective binding and the role of the flaps. J Chem Inf Model 2012; 52:1542-58. [PMID: 22587384 DOI: 10.1021/ci300014z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the main targets toward AIDS therapy. We have selected the potent drug darunavir and a weak inhibitor (fullerene analog) as HIV-1 PR substrates to compare protease's conformational features upon binding. Molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and quantum-mechanical (QM) calculations indicated the importance of the stability of HIV-1 PR flaps toward effective binding: a weak inhibitor may induce flexibility to the flaps, which convert between closed and semiopen states. A water molecule in the darunavir-HIV-1 PR complex bridged the two flap tips of the protease through hydrogen bonding (HB) interactions in a stable structure, a feature that was not observed for the fullerene-HIV-1 PR complex. Additionally, despite that van der Waals interactions and nonpolar contribution to solvation favored permanent fullerene entrapment into the cavity, these interactions alone were not sufficient for effective binding; enhanced electrostatic interactions as observed in the darunavir-complex were the crucial component of the binding energy. An alternative pathway to the usual way of a ligand to access the cavity was also observed for both compounds. Each ligand entered the binding cavity through an opening between the one flap of the protease and a neighboring loop. This suggested that access to the cavity is not necessarily regulated by flap opening. Darunavir exerts its biological action inside the cell, after crossing the membrane barrier. Thus, we also initiated a study on the interactions between darunavir and the DMPC bilayer to reveal that the drug was accommodated inside the bilayer in conformations that resembled its structure into HIV-1 PR, being stabilized via HBs with the lipids and water molecules.
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Affiliation(s)
- Georgios Leonis
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece.
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Eissenstat M, Guerassina T, Gulnik S, Afonina E, Silva AM, Ludtke D, Yokoe H, Yu B, Erickson J. Enamino-oxindole HIV protease inhibitors. Bioorg Med Chem Lett 2012; 22:5078-83. [PMID: 22749283 DOI: 10.1016/j.bmcl.2012.05.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
Abstract
We have designed and synthesized a series of HIV protease inhibitors (PIs) with enamino-oxindole substituents optimized to interact with the S2' subsite of the HIV protease binding pocket. Several of these inhibitors have sub-nanomolar K(i) and antiviral IC(50) in the low nM range against WT HIV and against a panel of multi-drug resistant (MDR) strains.
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