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Foka FET, Mufhandu HT. Current ARTs, Virologic Failure, and Implications for AIDS Management: A Systematic Review. Viruses 2023; 15:1732. [PMID: 37632074 PMCID: PMC10458198 DOI: 10.3390/v15081732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Antiretroviral therapies (ARTs) have revolutionized the management of human immunodeficiency virus (HIV) infection, significantly improved patient outcomes, and reduced the mortality rate and incidence of acquired immunodeficiency syndrome (AIDS). However, despite the remarkable efficacy of ART, virologic failure remains a challenge in the long-term management of HIV-infected individuals. Virologic failure refers to the persistent detectable viral load in patients receiving ART, indicating an incomplete suppression of HIV replication. It can occur due to various factors, including poor medication adherence, drug resistance, suboptimal drug concentrations, drug interactions, and viral factors such as the emergence of drug-resistant strains. In recent years, extensive efforts have been made to understand and address virologic failure in order to optimize treatment outcomes. Strategies to prevent and manage virologic failure include improving treatment adherence through patient education, counselling, and supportive interventions. In addition, the regular monitoring of viral load and resistance testing enables the early detection of treatment failure and facilitates timely adjustments in ART regimens. Thus, the development of novel antiretroviral agents with improved potency, tolerability, and resistance profiles offers new options for patients experiencing virologic failure. However, new treatment options would also face virologic failure if not managed appropriately. A solution to virologic failure requires a comprehensive approach that combines individualized patient care, robust monitoring, and access to a range of antiretroviral drugs.
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Affiliation(s)
- Frank Eric Tatsing Foka
- Department of Microbiology, Virology Laboratory, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North West University, Mafikeng, Private Bag, Mmabatho X2046, South Africa
| | - Hazel Tumelo Mufhandu
- Department of Microbiology, Virology Laboratory, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North West University, Mafikeng, Private Bag, Mmabatho X2046, South Africa
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2
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Miniproteins in medicinal chemistry. Bioorg Med Chem Lett 2022; 71:128806. [PMID: 35660515 DOI: 10.1016/j.bmcl.2022.128806] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022]
Abstract
Miniproteins exhibit great potential as scaffolds for drug candidates because of their well-defined structure and good synthetic availability. Because of recently described methodologies for their de novo design, the field of miniproteins is emerging and can provide molecules that effectively bind to problematic targets, i.e., those that have been previously considered to be undruggable. This review describes methodologies for the development of miniprotein scaffolds and for the construction of biologically active miniproteins.
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3
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HIV-1 Entry and Membrane Fusion Inhibitors. Viruses 2021; 13:v13050735. [PMID: 33922579 PMCID: PMC8146413 DOI: 10.3390/v13050735] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
HIV-1 (human immunodeficiency virus type 1) infection begins with the attachment of the virion to a host cell by its envelope glycoprotein (Env), which subsequently induces fusion of viral and cell membranes to allow viral entry. Upon binding to primary receptor CD4 and coreceptor (e.g., chemokine receptor CCR5 or CXCR4), Env undergoes large conformational changes and unleashes its fusogenic potential to drive the membrane fusion. The structural biology of HIV-1 Env and its complexes with the cellular receptors not only has advanced our knowledge of the molecular mechanism of how HIV-1 enters the host cells but also provided a structural basis for the rational design of fusion inhibitors as potential antiviral therapeutics. In this review, we summarize our latest understanding of the HIV-1 membrane fusion process and discuss related therapeutic strategies to block viral entry.
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4
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Suttisintong K, Kaewchangwat N, Thanayupong E, Nerungsi C, Srikun O, Pungpo P. Recent Progress in the Development of HIV-1 Entry Inhibitors: From Small Molecules to Potent Anti-HIV Agents. Curr Top Med Chem 2019; 19:1599-1620. [DOI: 10.2174/1568026619666190712204050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/07/2019] [Accepted: 06/21/2019] [Indexed: 01/21/2023]
Abstract
Viral entry, the first process in the reproduction of viruses, primarily involves attachment of the viral envelope proteins to membranes of the host cell. The crucial components that play an important role in viral entry include viral surface glycoprotein gp120, viral transmembrane glycoprotein gp41, host cell glycoprotein (CD4), and host cell chemokine receptors (CCR5 and CXCR4). Inhibition of the multiple molecular interactions of these components can restrain viruses, such as HIV-1, from fusion with the host cell, blocking them from reproducing. This review article specifically focuses on the recent progress in the development of small-molecule HIV-1 entry inhibitors and incorporates important aspects of their structural modification that lead to the discovery of new molecular scaffolds with more potency.
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Affiliation(s)
- Khomson Suttisintong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Narongpol Kaewchangwat
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Eknarin Thanayupong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chakkrapan Nerungsi
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Onsiri Srikun
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, 85 Sathonlamark Road, Warinchamrap, Ubon Ratchathani 34190, Thailand
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5
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Andrianov AM, Nikolaev GI, Kornoushenko YV, Xu W, Jiang S, Tuzikov AV. In Silico Identification of Novel Aromatic Compounds as Potential HIV-1 Entry Inhibitors Mimicking Cellular Receptor CD4. Viruses 2019; 11:v11080746. [PMID: 31412617 PMCID: PMC6723994 DOI: 10.3390/v11080746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022] Open
Abstract
Despite recent progress in the development of novel potent HIV-1 entry/fusion inhibitors, there are currently no licensed antiviral drugs based on inhibiting the critical interactions of the HIV-1 envelope gp120 protein with cellular receptor CD4. In this connection, studies on the design of new small-molecule compounds able to block the gp120-CD4 binding are still of great value. In this work, in silico design of drug-like compounds containing the moieties that make the ligand active towards gp120 was performed within the concept of click chemistry. Complexes of the designed molecules bound to gp120 were then generated by molecular docking and optimized using semiempirical quantum chemical method PM7. Finally, the binding affinity analysis of these ligand/gp120 complexes was performed by molecular dynamic simulations and binding free energy calculations. As a result, five top-ranking compounds that mimic the key interactions of CD4 with gp120 and show the high binding affinity were identified as the most promising CD4-mimemic candidates. Taken together, the data obtained suggest that these compounds may serve as promising scaffolds for the development of novel, highly potent and broad anti-HIV-1 therapeutics.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus.
| | - Grigory I Nikolaev
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - Yuri V Kornoushenko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Fuxing Building, Shanghai 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Fuxing Building, Shanghai 200032, China.
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus.
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6
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Pu J, Wang Q, Xu W, Lu L, Jiang S. Development of Protein- and Peptide-Based HIV Entry Inhibitors Targeting gp120 or gp41. Viruses 2019; 11:v11080705. [PMID: 31374953 PMCID: PMC6722851 DOI: 10.3390/v11080705] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
Application of highly active antiretroviral drugs (ARDs) effectively reduces morbidity and mortality in HIV-infected individuals. However, the emergence of multiple drug-resistant strains has led to the increased failure of ARDs, thus calling for the development of anti-HIV drugs with targets or mechanisms of action different from those of the current ARDs. The first peptide-based HIV entry inhibitor, enfuvirtide, was approved by the U.S. FDA in 2003 for treatment of HIV/AIDS patients who have failed to respond to the current ARDs, which has stimulated the development of several series of protein- and peptide-based HIV entry inhibitors in preclinical and clinical studies. In this review, we highlighted the properties and mechanisms of action for those promising protein- and peptide-based HIV entry inhibitors targeting the HIV-1 gp120 or gp41 and discussed their advantages and disadvantages, compared with the current ARDs.
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Affiliation(s)
- Jing Pu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Qian Wang
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Wei Xu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Lu Lu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China.
| | - Shibo Jiang
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China.
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
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7
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Jiang X, Yu J, Zhou Z, Kongsted J, Song Y, Pannecouque C, De Clercq E, Kang D, Poongavanam V, Liu X, Zhan P. Molecular design opportunities presented by solvent‐exposed regions of target proteins. Med Res Rev 2019; 39:2194-2238. [DOI: 10.1002/med.21581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 03/09/2019] [Accepted: 03/16/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Ji Yu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Zhongxia Zhou
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Jacob Kongsted
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Odense Denmark
| | - Yuning Song
- Department of Clinical PharmacyQilu Hospital of Shandong University Jinan China
| | - Christophe Pannecouque
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Erik De Clercq
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Dongwei Kang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | | | - Xinyong Liu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Peng Zhan
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
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8
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Adero PO, Jarois DR, Crich D. Hydrogenolytic cleavage of naphthylmethyl ethers in the presence of sulfides. Carbohydr Res 2017; 449:11-16. [PMID: 28672165 PMCID: PMC5572532 DOI: 10.1016/j.carres.2017.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 12/11/2022]
Abstract
With the aid of a series of model thioether or thioglycoside containing polyols protected with combinations of benzyl ethers and 2-naphthylmethyl ethers it is demonstrated that the latter are readily cleaved selectively under hydrogenolytic conditions in the presence of the frequently catalyst-poisoning sulfides. These results suggest the possibility of employing 2-naphthylmethyl ethers in place of benzyl ethers in synthetic schemes when hydrogenolytic deprotection is anticipated in the presence of thioether type functionality.
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Affiliation(s)
- Philip O Adero
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
| | - Dean R Jarois
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
| | - David Crich
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA.
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9
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Andrianov AM, Kashyn IA, Tuzikov AV. Computational identification of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120. J Mol Model 2017; 23:18. [DOI: 10.1007/s00894-016-3189-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/15/2016] [Indexed: 11/24/2022]
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10
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CD4-mimetic sulfopeptide conjugates display sub-nanomolar anti-HIV-1 activity and protect macaques against a SHIV162P3 vaginal challenge. Sci Rep 2016; 6:34829. [PMID: 27721488 PMCID: PMC5056392 DOI: 10.1038/srep34829] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/15/2016] [Indexed: 11/18/2022] Open
Abstract
The CD4 and the cryptic coreceptor binding sites of the HIV-1 envelope glycoprotein are key to viral attachment and entry. We developed new molecules comprising a CD4 mimetic peptide linked to anionic compounds (mCD4.1-HS12 and mCD4.1-PS1), that block the CD4-gp120 interaction and simultaneously induce the exposure of the cryptic coreceptor binding site, rendering it accessible to HS12- or PS1- mediated inhibition. Using a cynomolgus macaque model of vaginal challenge with SHIV162P3, we report that mCD4.1-PS1, formulated into a hydroxyethyl-cellulose gel provides 83% protection (5/6 animals). We next engineered the mCD4 moiety of the compound, giving rise to mCD4.2 and mCD4.3 that, when conjugated to PS1, inhibited cell-free and cell-associated HIV-1 with particularly low IC50, in the nM to pM range, including some viral strains that were resistant to the parent molecule mCD4.1. These chemically defined molecules, which target major sites of vulnerability of gp120, are stable for at least 48 hours in conditions replicating the vaginal milieu (37 °C, pH 4.5). They efficiently mimic several large gp120 ligands, including CD4, coreceptor or neutralizing antibodies, to which their efficacy compares very favorably, despite a molecular mass reduced to 5500 Da. Together, these results support the development of such molecules as potential microbicides.
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11
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Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex. PLoS One 2015; 10:e0143245. [PMID: 26579711 PMCID: PMC4651434 DOI: 10.1371/journal.pone.0143245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/02/2015] [Indexed: 11/19/2022] Open
Abstract
The HIV-1 Env spike is the main protein complex that facilitates HIV-1 entry into CD4+ host cells. HIV-1 entry is a multistep process that is not yet completely understood. This process involves several protein-protein interactions between HIV-1 Env and a variety of host cell receptors along with many conformational changes within the spike. HIV-1 Env developed due to high mutation rates and plasticity escape strategies from immense immune pressure and entry inhibitors. We applied a coevolution and residue-residue contact detecting method to identify coevolution patterns within HIV-1 Env protein sequences representing all group M subtypes. We identified 424 coevolving residue pairs within HIV-1 Env. The majority of predicted pairs are residue-residue contacts and are proximal in 3D structure. Furthermore, many of the detected pairs have functional implications due to contributions in either CD4 or coreceptor binding, or variable loop, gp120-gp41, and interdomain interactions. This study provides a new dimension of information in HIV research. The identified residue couplings may not only be important in assisting gp120 and gp41 coordinate structure prediction, but also in designing new and effective entry inhibitors that incorporate mutation patterns of HIV-1 Env.
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12
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Curreli F, Haque K, Xie L, Qiu Q, Xu J, Yong W, Tong X, Debnath AK. Synthesis, antiviral activity and resistance of a novel small molecule HIV-1 entry inhibitor. Bioorg Med Chem 2015; 23:7618-28. [PMID: 26602829 DOI: 10.1016/j.bmc.2015.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/28/2015] [Accepted: 11/05/2015] [Indexed: 11/30/2022]
Abstract
One of the most critical requirements of the infection of the human immunodeficiency virus type 1 (HIV-1) is the interaction of its surface envelope glycoprotein gp120 with the cellular receptor CD4, which initiates virus entry to cells. Therefore, envelope glycoprotein gp120 has been validated as a potential target to develop HIV-1 entry inhibitors. Here we report the evaluation of a novel non-natural amino acid, termed 882376, reported earlier as a precursor of a CD4-mimetic miniprotein, as HIV-1 entry inhibitor. 882376 showed HIV-1 inhibitory activity against a large panel of primary isolates of different subtype. Moreover, genotyping of 882376 resistant HIV-1 virus revealed three amino acid substitutions in the gp120 including one in the CD4 binding site suggesting that this molecule may bind to gp120 and prevent its binding to CD4. Additional neutralization experiments indicate that 882376 is not active against mutant pseudoviruses carrying the amino acid substitutions S375H and S375Y located in the 'Phe43 cavity' which is the major site of CD4 binding, suggesting that this compound may interfere with the interaction between gp120 and CD4. The unnatural amino acid, 882376, is expected to serve as a lead for further optimization to more potent HIV-1 entry inhibitors.
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Affiliation(s)
- Francesca Curreli
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
| | - Kashfia Haque
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Lihua Xie
- CPC Scientific, Inc., 1245 Reamwood Ave., Sunnyvale, CA 94089, USA
| | - Qian Qiu
- CPC Scientific, Inc., 1245 Reamwood Ave., Sunnyvale, CA 94089, USA
| | - Jinfeng Xu
- CPC Scientific, Inc., 1245 Reamwood Ave., Sunnyvale, CA 94089, USA
| | - Weizhong Yong
- CPC Scientific, Inc., 1245 Reamwood Ave., Sunnyvale, CA 94089, USA
| | - Xiaohe Tong
- CPC Scientific, Inc., 1245 Reamwood Ave., Sunnyvale, CA 94089, USA
| | - Asim K Debnath
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
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Rashad AA, Kalyana Sundaram RV, Aneja R, Duffy C, Chaiken I. Macrocyclic Envelope Glycoprotein Antagonists that Irreversibly Inactivate HIV-1 before Host Cell Encounter. J Med Chem 2015; 58:7603-8. [PMID: 26331669 DOI: 10.1021/acs.jmedchem.5b00935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We derived macrocyclic HIV-1 antagonists as a new class of peptidomimetic drug leads. Cyclic peptide triazoles (cPTs) retained the gp120 inhibitory and virus-inactivating signature of parent PTs, arguing that cyclization locked an active conformation. The six-residue cPT 9 (AAR029b) exhibited submicromolar antiviral potencies in inhibiting cell infection and triggering gp120 shedding that causes irreversible virion inactivation. Importantly, cPTs were stable to trypsin and chymotrypsin compared to substantial susceptibility of corresponding linear PTs.
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Affiliation(s)
- Adel A Rashad
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States
| | - Ramalingam Venkat Kalyana Sundaram
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States.,School of Biomedical Engineering, Science and Health Systems, Drexel University , Philadelphia, Pennsylvania 19104 United States
| | - Rachna Aneja
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States
| | - Caitlin Duffy
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States
| | - Irwin Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States
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Černý J, Biedermannová L, Mikulecký P, Zahradník J, Charnavets T, Šebo P, Schneider B. Redesigning protein cavities as a strategy for increasing affinity in protein-protein interaction: interferon- γ receptor 1 as a model. BIOMED RESEARCH INTERNATIONAL 2015; 2015:716945. [PMID: 26060819 PMCID: PMC4427845 DOI: 10.1155/2015/716945] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/22/2014] [Accepted: 12/28/2014] [Indexed: 12/04/2022]
Abstract
Combining computational and experimental tools, we present a new strategy for designing high affinity variants of a binding protein. The affinity is increased by mutating residues not at the interface, but at positions lining internal cavities of one of the interacting molecules. Filling the cavities lowers flexibility of the binding protein, possibly reducing entropic penalty of binding. The approach was tested using the interferon-γ receptor 1 (IFNγR1) complex with IFNγ as a model. Mutations were selected from 52 amino acid positions lining the IFNγR1 internal cavities by using a protocol based on FoldX prediction of free energy changes. The final four mutations filling the IFNγR1 cavities and potentially improving the affinity to IFNγ were expressed, purified, and refolded, and their affinity towards IFNγ was measured by SPR. While individual cavity mutations yielded receptor constructs exhibiting only slight increase of affinity compared to WT, combinations of these mutations with previously characterized variant N96W led to a significant sevenfold increase. The affinity increase in the high affinity receptor variant N96W+V35L is linked to the restriction of its molecular fluctuations in the unbound state. The results demonstrate that mutating cavity residues is a viable strategy for designing protein variants with increased affinity.
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Affiliation(s)
- Jiří Černý
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Lada Biedermannová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Pavel Mikulecký
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jiří Zahradník
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Tatsiana Charnavets
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Peter Šebo
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
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Acharya P, Lusvarghi S, Bewley CA, Kwong PD. HIV-1 gp120 as a therapeutic target: navigating a moving labyrinth. Expert Opin Ther Targets 2015; 19:765-83. [PMID: 25724219 DOI: 10.1517/14728222.2015.1010513] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION The HIV-1 gp120 envelope (Env) glycoprotein mediates attachment of virus to human target cells that display requisite receptors, CD4 and co-receptor, generally CCR5. Despite high-affinity interactions with host receptors and proof-of-principle by the drug maraviroc that interference with CCR5 provides therapeutic benefit, no licensed drug currently targets gp120. AREAS COVERED An overview of the role of gp120 in HIV-1 entry and of sites of potential gp120 vulnerability to therapeutic inhibition is presented. Viral defenses that protect these sites and turn gp120 into a moving labyrinth are discussed together with strategies for circumventing these defenses to allow therapeutic targeting of gp120 sites of vulnerability. EXPERT OPINION The gp120 envelope glycoprotein interacts with host proteins through multiple interfaces and has conserved structural features at these interaction sites. In spite of this, targeting gp120 for therapeutic purposes is challenging. Env mechanisms that have evolved to evade the humoral immune response also shield it from potential therapeutics. Nevertheless, substantial progress has been made in understanding HIV-1 gp120 structure and its interactions with host receptors, and in developing therapeutic leads that potently neutralize diverse HIV-1 strains. Synergies between advances in understanding, needs for therapeutics against novel viral targets and characteristics of breadth and potency for a number of gp120-targetting lead molecules bodes well for gp120 as a HIV-1 therapeutic target.
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Affiliation(s)
- Priyamvada Acharya
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Vaccine Research Center, Structural Biology Section , Room 4609B, 40 Convent Drive, Bethesda, MD 20892 , USA
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Park J, Pham HV, Mogensen K, Solling TI, Bennetzen MV, Houk KN. Hydrocarbon binding by proteins: structures of protein binding sites for ≥C10 linear alkanes or long-chain alkyl and alkenyl groups. J Org Chem 2015; 80:997-1005. [PMID: 25526284 DOI: 10.1021/jo502488e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to identify potential de novo enzyme templates for the cleavage of C–C single bonds in long-chain hydrocarbons, we analyzed protein structures that bind substrates containing alkyl and alkenyl functional groups. A survey of ligand-containing protein structures deposited in the Protein Data Bank resulted in 874 entries, consisting of 194 unique ligands that have ≥10 carbons in a linear chain. Fatty acids and phospholipids are the most abundant types of ligands. Hydrophobic amino acids forming α-helical structures frequently line the binding pockets. Occupation of these binding sites was evaluated by calculating both the buried surface area and volume employed by the ligands; these quantities are similar to those computed for drug–protein complexes. Surface complementarity is relatively low due to the nonspecific nature of the interaction between the long-chain hydrocarbons and the hydrophobic amino acids. The selected PDB structures were annotated on the basis of their SCOP and EC identification numbers, which will facilitate design template searches based on structural and functional homologies. Relatively low surface complementarity and ∼55% volume occupancy, also observed in synthetic-host, alkane-guest systems, suggest general principles for the recognition of long-chain linear hydrocarbons.
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Abstract
PURPOSE OF REVIEW The HIV-1 site of binding for the CD4 receptor has long attracted attention as a potential supersite of vulnerability to antibody-mediated neutralization. We review recent findings related to effective CD4-binding site antibodies isolated from HIV-1-infected individuals and discuss implications for immunogen design. RECENT FINDINGS Highly effective CD4-binding site antibodies such as antibody VRC01 have the ability to neutralize over 90% of circulating HIV-1 strains. Sequence and structural analysis of these antibodies from over half a dozen HIV-1-infected donors reveals remarkable similarity in their ontogenies and their modes of recognition, all of which involve mimicry of CD4 receptor by antibody-heavy chain. Meanwhile, other effective CD4-binding site neutralizers such as antibody CH103 have been shown to utilize a different mode of recognition, with next-generation sequencing of both virus and antibody suggesting co-evolution to drive the development of antibody-neutralization breadth. SUMMARY The nexus of information concerning the CD4-binding site and its recognition by human antibodies capable of effective neutralization has expanded remarkably in the last few years. Although barriers are substantial, new insights from donor-serum responses, atomic-level structures of antibody-Env complexes, and next-generation sequencing of B-cell transcripts are invigorating vaccine-design efforts to elicit effective CD4-binding site antibodies.
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Kwon YD, LaLonde JM, Yang Y, Elban MA, Sugawara A, Courter JR, Jones DM, Smith AB, Debnath AK, Kwong PD. Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site. PLoS One 2014; 9:e85940. [PMID: 24489681 PMCID: PMC3904841 DOI: 10.1371/journal.pone.0085940] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/05/2013] [Indexed: 11/19/2022] Open
Abstract
Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.
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Affiliation(s)
- Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania, United States of America
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark A. Elban
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Akihiro Sugawara
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David M. Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Asim K. Debnath
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute of the New York Blood Center, New York, New York, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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