1
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Zhao X, Liu H, Zhang JC, Cai J. Helical sulfonyl-γ-AApeptides for the inhibition of HIV-1 fusion and HIF-1α signaling. RSC Med Chem 2024; 15:1418-1423. [PMID: 38784464 PMCID: PMC11110726 DOI: 10.1039/d4md00110a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/19/2024] [Indexed: 05/25/2024] Open
Abstract
Synthetic helical peptidic foldamers show promising applications in chemical biology and biomedical sciences by mimicking protein helical segments. Sulfonyl-γ-AApeptide helices developed by our group exhibit good chemodiversity, predictable folding structures, proteolytic resistance, favorable cell permeability, and enhanced bioavailability. Herein, in this minireview, we highlight two recent examples of homogeneous left-handed sulfonyl-γ-AApeptide helices to modulate protein-protein interactions (PPIs). One is sulfonyl-γ-AApeptides as anti-HIV-1 fusion inhibitors mimicking the helical C-terminal heptad repeat (CHR), which show excellent anti-HIV-1 activities through tight binding with the N-terminal heptad repeat (NHR) and inhibiting the formation of the 6-helical bundle (HB) structure. Another example is helical sulfonyl-γ-AApeptides disrupting hypoxia-inducible factor 1α (HIF-1α) and p300 PPI, thus selectively inhibiting the relevant signaling cascade. We hope these findings could help to elucidate the principles of the structural design of sulfonyl-γ-AApeptides and inspire their future applications in PPI modulations.
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Affiliation(s)
- Xue Zhao
- Department of Chemistry, University of South Florida Tampa FL 33620 USA
| | - Heng Liu
- Department of Chemistry, University of South Florida Tampa FL 33620 USA
| | - Justin C Zhang
- Department of Chemistry, University of South Florida Tampa FL 33620 USA
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida Tampa FL 33620 USA
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2
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Cheng S, Li M, Feng Y, Liu T, He L, Xu M, Ma L, Li X. Glycan-Modified Peptides for Dual Inhibition of Human Immunodeficiency Virus Entry into Dendritic Cells and T Cells. J Med Chem 2024; 67:4225-4233. [PMID: 38364308 DOI: 10.1021/acs.jmedchem.4c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
Dendritic cells (DCs) play a crucial role in HIV-1 infection of CD4+ T cells. DC-SIGN, a lectin expressed on the surface of DCs, binds to the highly mannosylated viral membrane protein gp120 to capture HIV-1 virions and then transport them to target T cells. In this study, we modified peptide C34, an HIV-1 fusion inhibitor, at different sites using different sizes of the DC-SIGN-specific carbohydrates to provide dual-targeted HIV inhibition. The dual-target binding was confirmed by mechanistic studies. Pentamannose-modified C34 inhibited virus entry into both DC-SIGN+ 293T cells (52%-71% inhibition at 500 μM) and CD4+ TZM-b1 cells (EC50 = 0.7-1.7 nM). One conjugate, NC-M5, showed an extended half-life relative to C34 in rats (T1/2: 7.8 vs 1.02 h). These improvements in antiviral activity and pharmacokinetics have potential for HIV treatment and the development of dual-target inhibitors for pathogens that require the involvement of DC-SIGN for infection.
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Affiliation(s)
- Shuihong Cheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing 101408, China
| | - Mingli Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing 101408, China
| | - Yong Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing 101408, China
| | - Tong Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing 101408, China
| | - Lin He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Mingyue Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing 101408, China
| | - Liying Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing 101408, China
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3
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Bird GH, Patten JJ, Zavadoski W, Barucci N, Godes M, Moyer BM, Owen CD, DaSilva-Jardine P, Neuberg DS, Bowen RA, Davey RA, Walensky LD. A stapled lipopeptide platform for preventing and treating highly pathogenic viruses of pandemic potential. Nat Commun 2024; 15:274. [PMID: 38177138 PMCID: PMC10766962 DOI: 10.1038/s41467-023-44361-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024] Open
Abstract
The continued emergence of highly pathogenic viruses, which either thwart immune- and small molecule-based therapies or lack interventions entirely, mandates alternative approaches, particularly for prompt and facile pre- and post-exposure prophylaxis. Many highly pathogenic viruses, including coronaviruses, employ the six-helix bundle heptad repeat membrane fusion mechanism to achieve infection. Although heptad-repeat-2 decoys can inhibit viral entry by blocking six-helix bundle assembly, the biophysical and pharmacologic liabilities of peptides have hindered their clinical development. Here, we develop a chemically stapled lipopeptide inhibitor of SARS-CoV-2 as proof-of-concept for the platform. We show that our lead compound blocks infection by a spectrum of SARS-CoV-2 variants, exhibits mucosal persistence upon nasal administration, demonstrates enhanced stability compared to prior analogs, and mitigates infection in hamsters. We further demonstrate that our stapled lipopeptide platform yields nanomolar inhibitors of respiratory syncytial, Ebola, and Nipah viruses by targeting heptad-repeat-1 domains, which exhibit strikingly low mutation rates, enabling on-demand therapeutic intervention to combat viral outbreaks.
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Affiliation(s)
- Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - J J Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | | | | | - Marina Godes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin M Moyer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Callum D Owen
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | | | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Richard A Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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4
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Wang R, Tsuji K, Kobayakawa T, Liu Y, Yoshimura K, Matsushita S, Harada S, Tamamura H. Hybrids of small CD4 mimics and gp41-related peptides as dual-target HIV entry inhibitors. Bioorg Med Chem 2022; 76:117083. [PMID: 36403413 DOI: 10.1016/j.bmc.2022.117083] [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: 10/03/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Hybrid molecules containing small CD4 mimics and gp41-C-terminal heptad repeat (CHR)-related peptides have been developed. A YIR-821 derivative was adopted as a CD4 mimic, which inhibits the interaction of gp120 with CD4. SC-peptides, SC34 and SC22EK, were also used as CHR-related peptides, which inhibit the interaction between the N-terminal heptad repeat (NHR) and CHR and thereby membrane fusion. Therefore, these hybrid molecules have dual-targets of gp120 and gp41. In the synthesis of the hybrid molecules of CD4 mimic-SC-peptides with different lengths of linkers, two conjugating methods, Cu-catalyzed azide-alkyne cycloaddition and direct cysteine alkylation, were performed. The latter reaction caused simpler operation procedures and higher synthetic yields than the former. The synthesized hybrid molecules of CD4 mimic-SC22EK have significantly higher anti-HIV activity than each sole agent. The present data should be useful in the future design of anti-HIV agents as dual-target entry inhibitors.
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Affiliation(s)
- Rongyi Wang
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kohei Tsuji
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Yishan Liu
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kazuhisa Yoshimura
- Institute of Public Health, Bureau of Social Welfare and Public Health, Tokyo Metropolitan Government, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Shuzo Matsushita
- The Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shigeyoshi Harada
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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5
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He L, Zhou G, Sofiyev V, Garcia E, Nguyen N, Li KH, Gochin M. Targeting a Conserved Lysine in the Hydrophobic Pocket of HIV-1 gp41 Improves Small Molecule Antiviral Activity. Viruses 2022; 14:v14122703. [PMID: 36560708 PMCID: PMC9784957 DOI: 10.3390/v14122703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Human Immunodeficiency virus (HIV-1) fusion is mediated by glycoprotein-41, a protein that has not been widely exploited as a drug target. Small molecules directed at the gp41 ectodomain have proved to be poorly drug-like, having moderate efficacy, high hydrophobicity and/or high molecular weight. We recently investigated conversion of a fairly potent hydrophobic inhibitor into a covalent binder, by modifying it to react with a lysine residue on the protein. We demonstrated a 10-fold improvement in antiviral efficacy. Here, we continue this study, utilizing instead molecules with better inherent drug-like properties. Molecules possessing low to no antiviral activity as equilibrium binders were converted into µM inhibitors upon addition of an electrophilic warhead in the form of a sulfotetrafluorophenyl (STP) activated ester. We confirmed specificity for gp41 and for entry. The small size of the inhibitors described here offers an opportunity to expand their reach into neighboring pockets while retaining drug-likeness. STP esterification of equilibrium binders is a promising avenue to explore for inhibiting HIV-1 entry. Many gp41 targeting molecules studied over the years possess carboxylic acid groups which can be easily converted into the corresponding STP ester. It may be worth the effort to evaluate a library of such inhibitors as a way forward to small molecule inhibition of fusion of HIV and possibly other enveloped viruses.
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Affiliation(s)
- Li He
- Department of Basic Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Guangyan Zhou
- Department of Basic Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Vladimir Sofiyev
- Department of Basic Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Eddie Garcia
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Newton Nguyen
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Kathy H. Li
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
| | - Miriam Gochin
- Department of Basic Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
- Correspondence: ; Tel.: +1-707-638-5463
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6
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Klug YA, Schwarzer R, Ravula T, Rotem E, Ramamoorthy A, Shai Y. Structural and Mechanistic Evidence for Calcium Interacting Sites in the HIV Transmembrane Protein gp41 Involved in Membrane Fusion. Biochemistry 2022; 61:1915-1922. [PMID: 35994087 PMCID: PMC9454089 DOI: 10.1021/acs.biochem.2c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The HIV envelope protein gp160 comprises two subunits, gp120 and gp41, responsible for receptor binding and membrane fusion during viral entry, respectively. In the course of the membrane fusion process, gp41 undergoes a conformational change, leading to the formation of a six-helix bundle (SHB), which ultimately drives membrane fusion. The gp41 C-terminal and N-terminal heptad repeats (CHR and NHR) interact with one another to form the SHB, and this step can be targeted by peptide inhibitors, which are used in the clinic to mitigate HIV infection. Here, we discover the calcium interaction motifs (CIMs) in the gp41 CHR and NHR regions via NMR spectroscopy. We find that the assembly of the CHR-NHR SHB is facilitated in Ca2+-containing media and impaired in CIM mutants. Of note, the clinically approved, gp41-derived fusion inhibitor T20, which does not contain the CIM motif, exhibits reduced inhibitory efficiency when challenged with calcium. This finding could have important implications for the development of better fusion inhibitors for HIV.
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Affiliation(s)
- Yoel A. Klug
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7632701, Israel
| | - Roland Schwarzer
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7632701, Israel
- Institute
for Translational HIV Research, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany
| | - Thirupathi Ravula
- Biophysics
Program, Department of Chemistry, Macromolecular Science and Engineering,
Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Etai Rotem
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7632701, Israel
| | - Ayyalusamy Ramamoorthy
- Biophysics
Program, Department of Chemistry, Macromolecular Science and Engineering,
Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Yechiel Shai
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7632701, Israel
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7
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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: 0] [Impact Index Per Article: 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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8
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Jiang S, Tuzikov A, Andrianov A. Small-molecule HIV-1 entry inhibitors targeting the epitopes of broadly neutralizing antibodies. Cell Chem Biol 2022; 29:757-773. [PMID: 35353988 DOI: 10.1016/j.chembiol.2022.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/27/2022] [Accepted: 03/10/2022] [Indexed: 11/20/2022]
Abstract
Highly active antiretroviral therapy currently used for HIV/AIDS has significantly increased the life expectancy of HIV-infected individuals. It has also improved the quality of life, reduced mortality, and decreased the incidence of AIDS and HIV-related conditions. Currently, however, affected individuals are typically on a lifetime course of several therapeutic drugs, all with the potential for associated toxicity and emergence of resistance. This calls for development of novel, potent, and broad anti-HIV agents able to stop the spread of HIV/AIDS. Significant progress has been made toward identification of anti-HIV-1 broadly neutralizing antibodies (bNAbs). However, antibody-based drugs are costly to produce and store. Administration (by injection only) and other obstacles limit clinical use. In recent years, several highly promising small-molecule HIV-1 entry inhibitors targeting the epitopes of bNAbs have been developed. These newly developed compounds are the focus of the present article.
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Affiliation(s)
- Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 200032, China.
| | - Alexander Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Republic of Belarus
| | - Alexander Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Republic of Belarus.
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9
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Conformational Stabilization of Gp41-Mimetic Miniproteins Opens Up New Ways of Inhibiting HIV-1 Fusion. Int J Mol Sci 2022; 23:ijms23052794. [PMID: 35269936 PMCID: PMC8911282 DOI: 10.3390/ijms23052794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 12/20/2022] Open
Abstract
Inhibition of the HIV-1 fusion process constitutes a promising strategy to neutralize the virus at an early stage before it enters the cell. In this process, the envelope glycoprotein (Env) plays a central role by promoting membrane fusion. We previously identified a vulnerability at the flexible C-terminal end of the gp41 C-terminal heptad repeat (CHR) region to inhibition by a single-chain miniprotein (named covNHR-N) that mimics the first half of the gp41 N-terminal heptad repeat (NHR). The miniprotein exhibited low stability, moderate binding to its complementary CHR region, both as an isolated peptide and in native trimeric Envs, and low inhibitory activity against a panel of pseudoviruses. The addition of a disulfide bond stabilizing the miniprotein increased its inhibitory activity, without altering the binding affinity. Here, to further study the effect of conformational stability on binding and inhibitory potency, we additionally stabilized these miniproteins by engineering a second disulfide bond stapling their N-terminal end, The new disulfide-bond strongly stabilizes the protein, increases binding affinity for the CHR target and strongly improves inhibitory activity against several HIV-1 strains. Moreover, high inhibitory activity could be achieved without targeting the preserved hydrophobic pocket motif of gp41. These results may have implications in the discovery of new strategies to inhibit HIV targeting the gp41 CHR region.
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10
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Small-Molecule HIV Entry Inhibitors Targeting gp120 and gp41. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:27-43. [DOI: 10.1007/978-981-16-8702-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Huhmann S, Nyakatura EK, Rohrhofer A, Moschner J, Schmidt B, Eichler J, Roth C, Koksch B. Systematic Evaluation of Fluorination as Modification for Peptide-Based Fusion Inhibitors against HIV-1 Infection. Chembiochem 2021; 22:3443-3451. [PMID: 34605595 PMCID: PMC9297971 DOI: 10.1002/cbic.202100417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/04/2021] [Indexed: 01/01/2023]
Abstract
With the emergence of novel viruses, the development of new antivirals is more urgent than ever. A key step in human immunodeficiency virus type 1 (HIV-1) infection is six-helix bundle formation within the envelope protein subunit gp41. Selective disruption of bundle formation by peptides has been shown to be effective; however, these drugs, exemplified by T20, are prone to rapid clearance from the patient. The incorporation of non-natural amino acids is known to improve these pharmacokinetic properties. Here, we evaluate a peptide inhibitor in which a critical Ile residue is replaced by fluorinated analogues. We characterized the influence of the fluorinated analogues on the biophysical properties of the peptide. Furthermore, we show that the fluorinated peptides can block HIV-1 infection of target cells at nanomolar levels. These findings demonstrate that fluorinated amino acids are appropriate tools for the development of novel peptide therapeutics.
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Affiliation(s)
- Susanne Huhmann
- Freie Universität BerlinDepartment of Biology, Chemistry and PharmacyInstitute of Chemistry and BiochemistryArnimallee 2014195BerlinGermany
| | - Elisabeth K. Nyakatura
- Freie Universität BerlinDepartment of Biology, Chemistry and PharmacyInstitute of Chemistry and BiochemistryArnimallee 2014195BerlinGermany
- Antibody Engineering Tri-Institutional Therapeutics Discovery Institute417 East 68th Street, 19 Floor North, P: 646-888-2003New YorkNY 10021USA
| | - Anette Rohrhofer
- Institute of Clinical Microbiology and HygieneRegensburg University HospitalFranz-Josef-Strauß-Allee 1193053RegensburgGermany
| | - Johann Moschner
- Freie Universität BerlinDepartment of Biology, Chemistry and PharmacyInstitute of Chemistry and BiochemistryArnimallee 2014195BerlinGermany
| | - Barbara Schmidt
- Institute of Clinical Microbiology and HygieneRegensburg University HospitalFranz-Josef-Strauß-Allee 1193053RegensburgGermany
| | - Jutta Eichler
- Friedrich-Alexander-Universität Erlangen-NürnbergDepartment Chemie und PharmazieNikolaus-Fiebiger-Str. 1091058ErlangenGermany
| | - Christian Roth
- Max Planck Institute of Colloids and InterfacesBiomolecular SystemsArnimallee 2214195BerlinGermany
| | - Beate Koksch
- Freie Universität BerlinDepartment of Biology, Chemistry and PharmacyInstitute of Chemistry and BiochemistryArnimallee 2014195BerlinGermany
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12
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Abstract
Viral fusion glycoproteins catalyze membrane fusion during viral entry. Unlike most enzymes, however, they lack a conventional active site in which formation or scission of a specific covalent bond is catalyzed. Instead, they drive the membrane fusion reaction by cojoining highly regulated changes in conformation to membrane deformation. Despite the challenges in applying inhibitor design approaches to these proteins, recent advances in knowledge of the structures and mechanisms of viral fusogens have enabled the development of small-molecule inhibitors of both class I and class II viral fusion proteins. Here, we review well-validated inhibitors, including their discovery, targets, and mechanism(s) of action, while highlighting mechanistic similarities and differences. Together, these examples make a compelling case for small-molecule inhibitors as tools for probing the mechanisms of viral glycoprotein-mediated fusion and for viral glycoproteins as druggable targets.
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Affiliation(s)
- Han-Yuan Liu
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Current affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Palo Alto, California 94305, USA;
| | - Priscilla L Yang
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Current affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Palo Alto, California 94305, USA;
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13
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Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods Enzymol 2021; 656:1-25. [PMID: 34325784 DOI: 10.1016/bs.mie.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Examination of complexes of proteins with biomolecular ligands reveals that proteins tend to interact with partners via folded sub-domains, in which the backbone possesses secondary structure. α-Helices comprising the largest class of protein secondary structures, play fundamental roles in a multitude of highly specific protein-protein and protein-nucleic acid interactions. We have demonstrated a unique strategy for stabilization of the α-helical conformation that involves replacement of one of the main chain i and i+4 hydrogen bonds in the target α-helix with a covalent bond. We termed this synthetic strategy a hydrogen bond surrogate (HBS) approach. Two salient features of this approach are: (1) the internal placement of the crosslink allows development of helices such that none of the solvent-exposed surfaces are blocked by the constraining element, i.e., all side chains of the constrained helices remain available for molecular recognition. (2) This approach can be deployed to constrain very short peptides (<10 amino acid residues) into highly stable α-helices. This chapter presents the biophysical basis for the development of the hydrogen bond surrogate approach, as well as methods for the synthesis and conformational analysis of the artificial helices.
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Affiliation(s)
- Ganesh S Jedhe
- Department of Chemistry, New York University, New York, NY, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, United States.
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14
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Zhou G, He L, Li KH, Pedroso CCS, Gochin M. A targeted covalent small molecule inhibitor of HIV-1 fusion. Chem Commun (Camb) 2021; 57:4528-4531. [PMID: 33956029 DOI: 10.1039/d1cc01013a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a low molecular weight covalent inhibitor targeting a conserved lysine residue within the hydrophobic pocket of HIV-1 glycoprotein-41. The inhibitor bound selectively to the hydrophobic pocket and exhibited an order of magnitude enhancement of anti-fusion activity against HIV-1 compared to its non-covalent counterpart. The findings represent a significant advance in the quest to obtain non-peptide fusion inhibitors.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA.
| | - Li He
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA.
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
| | - Cássio C S Pedroso
- Lawrence Berkeley National Laboratory, The Molecular Foundry, 1 Cyclotron Road, 67R5114, Berkeley, CA 94720, USA
| | - Miriam Gochin
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA. and Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
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15
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Serrão VHB, Cook JD, Lee JE. Snapshot of an influenza virus glycoprotein fusion intermediate. Cell Rep 2021; 35:109152. [PMID: 34010634 DOI: 10.1016/j.celrep.2021.109152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/31/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Enveloped virus entry requires the fusion of cellular and viral membranes, a process directed by their viral fusion glycoproteins. Our current knowledge of this process has been shaped by structural studies of the pre- and post-fusion conformations of these viral fusogens. These structural snapshots have revealed the start and end states necessary for fusion, but the dynamics of the intermediate conformations have remained unclear. Using the influenza C virus hemagglutinin-esterase-fusion glycoprotein as a model, we report the structural and biophysical characterization of a trapped intermediate. Crystallographic studies revealed a structural reorganization of the C terminus to create a second chain reversal region, resulting in the N and C termini being positioned in opposing directions. Intrinsic tryptophan fluorescence and bimane-induced quenching measurements suggest intermediate formation is mediated by conserved hydrophobic residues. Our study reveals a late-stage extended intermediate structural event. This work adds to our understanding of virus cell fusion.
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Affiliation(s)
- Vitor Hugo B Serrão
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
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16
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Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci 2021; 7:607323. [PMID: 33614705 PMCID: PMC7886686 DOI: 10.3389/fmolb.2020.607323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022] Open
Abstract
Two new computational approaches are described to aid in the design of new peptide-based drugs by evaluating ensembles of protein structures from their dynamics and through the assessing of structures using empirical contact potential. These approaches build on the concept that conformational variability can aid in the binding process and, for disordered proteins, can even facilitate the binding of more diverse ligands. This latter consideration indicates that such a design process should be less restrictive so that multiple inhibitors might be effective. The example chosen here focuses on proteins/peptides that bind to hemagglutinin (HA) to block the large-scale conformational change for activation. Variability in the conformations is considered from sets of experimental structures, or as an alternative, from their simple computed dynamics; the set of designe peptides/small proteins from the David Baker lab designed to bind to hemagglutinin, is the large set considered and is assessed with the new empirical contact potentials.
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Affiliation(s)
- Robert L. Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Kannan Sankar
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Kejue Jia
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Eshel Faraggi
- Research and Information Systems, LLC, Indianapolis, IN, United States
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, IN, United States
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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17
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Su B, Yao C, Zhao QX, Cai WP, Wang M, Lu HZ, Chen YY, Liu L, Wang H, He Y, Zheng YH, Li LH, Chen JF, Yu JH, Zhu B, Zhao M, Sun YT, Lun WH, Xia W, Sun LJ, Dai LL, Jiang TY, Wang MX, Zheng QS, Peng HY, Wang Y, Lu RJ, Hu JH, Xing H, Shao YM, Xie D, Zhang T, Zhang FJ, Wu H. Efficacy and safety of the long-acting fusion inhibitor albuvirtide in antiretroviral-experienced adults with human immunodeficiency virus-1: interim analysis of the randomized, controlled, phase 3, non-inferiority TALENT study. Chin Med J (Engl) 2020; 133:2919-2927. [PMID: 33252379 PMCID: PMC7752691 DOI: 10.1097/cm9.0000000000001273] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Albuvirtide is a once-weekly injectable human immunodeficiency virus (HIV)-1 fusion inhibitor. We present interim data for a phase 3 trial assessing the safety and efficacy of albuvirtide plus lopinavir-ritonavir in HIV-1-infected adults already treated with antiretroviral drugs. METHODS We carried out a 48-week, randomized, controlled, open-label non-inferiority trial at 12 sites in China. Adults on the World Health Organization (WHO)-recommended first-line treatment for >6 months with a plasma viral load >1000 copies/mL were enrolled and randomly assigned (1:1) to receive albuvirtide (once weekly) plus ritonavir-boosted lopinavir (ABT group) or the WHO-recommended second-line treatment (NRTI group). The primary endpoint was the proportion of patients with a plasma viral load below 50 copies/mL at 48 weeks. Non-inferiority was prespecified with a margin of 12%. RESULTS At the time of analysis, week 24 data were available for 83 and 92 patients, and week 48 data were available for 46 and 50 patients in the albuvirtide and NRTI groups, respectively. At 48 weeks, 80.4% of patients in the ABT group and 66.0% of those in the NRTI group had HIV-1 RNA levels below 50 copies/mL, meeting the criteria for non-inferiority. For the per-protocol population, the superiority of albuvirtide over NRTI was demonstrated. The frequency of grade 3 to 4 adverse events was similar in the two groups; the most common adverse events were diarrhea, upper respiratory tract infections, and grade 3 to 4 increases in triglyceride concentration. Renal function was significantly more impaired at 12 weeks in the patients of the NRTI group who received tenofovir disoproxil fumarate than in those of the ABT group. CONCLUSIONS The TALENT study is the first phase 3 trial of an injectable long-acting HIV drug. This interim analysis indicates that once-weekly albuvirtide in combination with ritonavir-boosted lopinavir is well tolerated and non-inferior to the WHO-recommended second-line regimen in patients with first-line treatment failure. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02369965; https://www.clinicaltrials.gov.Chinese Clinical Trial Registry No. ChiCTR-TRC-14004276; http://www.chictr.org.cn/enindex.aspx.
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Affiliation(s)
- Bin Su
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Cheng Yao
- Frontier Biotechnologies Inc., Nanjing, Jiangsu 211122, China
| | - Qing-Xia Zhao
- Department of Infectious Diseases, Infectious Disease Hospital of Henan Province, Zhengzhou, Henan 450061, China
| | - Wei-Ping Cai
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Min Wang
- Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, Hunan 410005, China
| | - Hong-Zhou Lu
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yuan-Yuan Chen
- Department of Infectious Diseases, Infectious Disease Hospital of Henan Province, Zhengzhou, Henan 450061, China
| | - Li Liu
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Hui Wang
- Department of Infectious Diseases, National Clinical Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong 518112, China
| | - Yun He
- Department of Infectious Diseases, National Clinical Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong 518112, China
| | - Yu-Huang Zheng
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Ling-Hua Li
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Jin-Feng Chen
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Jian-Hua Yu
- Department of Infectious Diseases, Xixi Hospital of Hangzhou, Hangzhou, Zhejiang 310023, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Min Zhao
- National Clinical Research Center for Infectious Diseases, the Fifth Medical Center of PLA General Hospital, Beijing 100039, China
| | - Yong-Tao Sun
- Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Wen-Hui Lun
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Wei Xia
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Li-Jun Sun
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Li-Li Dai
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Tai-Yi Jiang
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Mei-Xia Wang
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Qing-Shan Zheng
- Center for Drug Clinical Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hai-Yan Peng
- Beijing Co-CRO Medical Development Co., Ltd., Beijing 100711, China
| | - Yao Wang
- Beijing Co-CRO Medical Development Co., Ltd., Beijing 100711, China
| | - Rong-Jian Lu
- Frontier Biotechnologies Inc., Nanjing, Jiangsu 211122, China
| | - Jian-Hua Hu
- Frontier Biotechnologies Inc., Nanjing, Jiangsu 211122, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yi-Ming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dong Xie
- Frontier Biotechnologies Inc., Nanjing, Jiangsu 211122, China
| | - Tong Zhang
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Fu-Jie Zhang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Hao Wu
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
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18
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Kobayakawa T, Ebihara K, Tsuji K, Kawada T, Fujino M, Honda Y, Ohashi N, Murakami T, Tamamura H. Bivalent HIV-1 fusion inhibitors based on peptidomimetics. Bioorg Med Chem 2020; 28:115812. [PMID: 33157478 DOI: 10.1016/j.bmc.2020.115812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Membrane fusion is a valid target for inhibition of HIV-1 replication. A 34-mer fragment peptide (C34), which is contained in the HIV-1 envelope protein gp41, has significant anti-HIV activity. Previously, a dimeric derivative of C34 linked by a disulfide bridge at its C-terminus was found to have more potent anti-HIV activity than the C34 peptide monomer. To date, several peptidomimetic small inhibitors have been reported, but most have lower potency than peptide derivatives related to C34. In the present study we applied this dimerization concept to these peptidomimetic small inhibitors and designed several bivalent peptidomimetic HIV-1 fusion inhibitors. The importance of the length of linkers crosslinking two peptidomimetic compounds was demonstrated and several potent bivalent inhibitors containing tethered peptidomimetics were produced.
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Affiliation(s)
- Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kento Ebihara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kohei Tsuji
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuma Kawada
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yuzuna Honda
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Nami Ohashi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Tsutomu Murakami
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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19
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Nishimura Y, Francis JN, Donau OK, Jesteadt E, Sadjadpour R, Smith AR, Seaman MS, Welch BD, Martin MA, Kay MS. Prevention and treatment of SHIVAD8 infection in rhesus macaques by a potent d-peptide HIV entry inhibitor. Proc Natl Acad Sci U S A 2020; 117:22436-22442. [PMID: 32820072 PMCID: PMC7486783 DOI: 10.1073/pnas.2009700117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cholesterol-PIE12-trimer (CPT31) is a potent d-peptide HIV entry inhibitor that targets the highly conserved gp41 N-peptide pocket region. CPT31 exhibited strong inhibitory breadth against diverse panels of primary virus isolates. In a simian-HIV chimeric virus AD8 (SHIVAD8) macaque model, CPT31 prevented infection from a single high-dose rectal challenge. In chronically infected animals, CPT31 monotherapy rapidly reduced viral load by ∼2 logs before rebound occurred due to the emergence of drug resistance. In chronically infected animals with viremia initially controlled by combination antiretroviral therapy (cART), CPT31 monotherapy prevented viral rebound after discontinuation of cART. These data establish CPT31 as a promising candidate for HIV prevention and treatment.
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Affiliation(s)
- Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - J Nicholas Francis
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
- Navigen, Inc., Salt Lake City, UT 84108
| | - Olivia K Donau
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Eric Jesteadt
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Reza Sadjadpour
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Amanda R Smith
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | | | - Malcolm A Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892;
| | - Michael S Kay
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112;
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20
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Shao J, Zeng D, Tian S, Liu G, Fu J. Identification of the natural product berberine as an antiviral drug. AMB Express 2020; 10:164. [PMID: 32897426 PMCID: PMC7479080 DOI: 10.1186/s13568-020-01088-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/28/2022] Open
Abstract
Drugs targeting the fusion process of viral entry into host cells have been approved for clinical use in the treatment of AIDS. There remains a great need to improve the use of existing drugs for HIV therapy. Berberine is traditionally used to treat diarrhea, bacillary dysentery, and gastroenteritis in clinics, here our research shows that berberine is effective in inhibiting HIV-1 entry. Native polyacrylamide gel electrophoresis studies reveal that berberine can directly bind to both N36 and C34 to form a novel N36-berberine-C34 complex and effectively block the six-helix bundle formation between the N-terminal heptad repeat peptide N36 and the C-terminal heptad repeat peptide C34. Circular dichroism experiments show that binding of berberine produces conformational changes that damages the secondary structures of 6-HB. Computer-aided molecular docking studies suggest a hydrogen bond with T-639 and two polar bonds with Q-563 and T-639 are established, involving the oxygen atom and the C=O group of the indole ring. Berberine completely inhibits six HIV-1 clade B isolates and exhibits antiviral activities in a concentration-dependent manner with IC50 values varying from 5.5 to 10.25 µg/ml. This compound-peptide interaction may represent a mechanism of action of antiviral activities of berberine. As a summary, these studies successfully identify compound berberine as a potential candidate drug for HIV-1 treatment. As a summary, antiviral activity of berberine in combination with its use in clinical practice, this medicine can be used as a potential clinically anti-HIV drug.
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21
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Zhou G, Chu S, Kohli A, Szoka FC, Gochin M. Biophysical studies of HIV-1 glycoprotein-41 interactions with peptides and small molecules - Effect of lipids and detergents. Biochim Biophys Acta Gen Subj 2020; 1864:129724. [PMID: 32889078 DOI: 10.1016/j.bbagen.2020.129724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND The hydrophobic pocket (HP) of HIV-1 glycoprotein-41 ectodomain is defined by two chains of the N-heptad repeat trimer, within the protein-protein interface that mediates 6HB formation. It is a potential target for inhibitors of viral fusion, but its hydrophobic nature and proximity to membrane in situ has precluded ready analysis of inhibitor interactions. METHODS We evaluated the sensitivity of 19F NMR and fluorescence for detecting peptide and small molecule binding to the HP and explored the effect of non-denaturing detergent or phospholipid as cosolvents and potential mimics of the membrane environment surrounding gp41. RESULTS Chemical shifts of aromatic fluorines were found to be sensitive to changes in the hydrogen bonding network that occurred when inhibitors transitioned from solvent into the HP or into ordered detergent micelles. Fluorescence intensities and emission maxima of autofluorescent compounds responded to changes in the local environment. CONCLUSIONS Gp41 - ligand binding occurred under all conditions, but was diminished in the presence of detergents. NMR and fluorescence studies revealed that dodecylphosphocholine (DPC) was a poor substitute for membrane in this system, while liposomes could mimic the membrane surroundings. GENERAL SIGNIFICANCE Our findings suggest that development of high potency small molecule binders to the HP may be frustrated by competition between binding to the HP and binding to the bilayer membrane.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America
| | - Shidong Chu
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America
| | - Aditya Kohli
- Department of Bioengineering and Therapeutic Sciences, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America
| | - Francis C Szoka
- Department of Bioengineering and Therapeutic Sciences, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America; Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America
| | - Miriam Gochin
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America; Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America.
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22
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Jurado S, Moog C, Cano-Muñoz M, Schmidt S, Laumond G, Ruocco V, Standoli S, Polo-Megías D, Conejero-Lara F, Morel B. Probing Vulnerability of the gp41 C-Terminal Heptad Repeat as Target for Miniprotein HIV Inhibitors. J Mol Biol 2020; 432:5577-5592. [PMID: 32822695 DOI: 10.1016/j.jmb.2020.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022]
Abstract
One of the therapeutic strategies in HIV neutralization is blocking membrane fusion. In this process, tight interaction between the N-terminal and C-terminal heptad-repeat (NHR and CHR) regions of gp41 is essential to promote membranes apposition and merging. We have previously developed single-chain proteins (named covNHR) that accurately mimic the complete gp41 NHR region in its trimeric conformation. They tightly bind CHR-derived peptides and show a potent and broad HIV inhibitory activity in vitro. However, the extremely high binding affinity (sub-picomolar) is not in consonance with their inhibitory activity (nanomolar), likely due to partial or temporal accessibility of their target in the virus. Here, we have designed and characterized two single-chain covNHR miniproteins each encompassing one of the two halves of the NHR region and containing two of the four sub-pockets of the NHR crevice. The two miniproteins fold as trimeric helical bundles as expected but while the C-terminal covNHR (covNHR-C) miniprotein is highly stable, the N-terminal counterpart (covNHR-N) shows only marginal stability that could be improved by engineering an internal disulfide bond. Both miniproteins bind their respective complementary CHR peptides with moderate (micromolar) affinity. Moreover, the covNHR-N miniproteins can access their target in the context of trimeric native envelope proteins and show significant inhibitory activity for several HIV pseudoviruses. In contrast, covNHR-C cannot bind its target sequence and neither inhibits HIV, indicating a higher vulnerability of C-terminal part of CHR. These results may guide the development of novel HIV inhibitors targeting the gp41 CHR region.
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Affiliation(s)
- Samuel Jurado
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Christiane Moog
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Sylvie Schmidt
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Géraldine Laumond
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Valentina Ruocco
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Sara Standoli
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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23
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Polyethylene Glycol 40-Modified Peptide with High Therapeutic Efficacy in Simian-Human Immunodeficiency Virus-Acutely Infected Rhesus Monkeys. J Virol 2020; 94:JVI.00386-20. [PMID: 32404523 DOI: 10.1128/jvi.00386-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/03/2020] [Indexed: 01/09/2023] Open
Abstract
Anti-human immunodeficiency virus type 1 (anti-HIV-1) fusion peptides have been studied for nearly 2 decades, but few candidates have found useful clinical applications. One factor underlying the failure of such agents to reach the clinic is their poor pharmacokinetic properties, and many efforts have been made to overcome this problem. In this study, we modified C34, a peptide inhibitor of HIV-1 fusion, at its conserved glycosylation site using polyethylene glycols (PEGs) of different molecular weights. PEG40-NC, a conjugate of C34 and branched PEG 40 kDa (PEG40), which has been previously shown to improve the pharmacokinetic profiles of proteins, showed a significantly extended half-life (t 1/2; 10.39 h in rats), which compensated for decreased in vitro activity (50% effective concentration [EC50] of 18.51 nM). PEG40-NC also showed a mechanism of action similar to that of C34. PEG40-NC monotherapy in acutely simian-human immunodeficiency virus (SHIV)-infected rhesus monkeys significantly suppressed viral load compared with a control treatment. Efficacy was linked to the extended half-life and lymphatic exposure conferred by attached PEG40. These results highlight the potential of further clinical investigations of PEG40-NC in combination with antiretroviral therapy or other anti-HIV agents.IMPORTANCE Poor pharmacokinetics have severely hindered the clinical use of anti-HIV peptides. Different small molecules, such as lipid, cholesterol, and small PEG, were designed to modify peptides to improve their pharmacokinetics. In this study, we incorporated large branched PEG to anti-HIV peptide and obtained a conjugate with extended half-life and improved in vivo efficacy. The strategy we developed in this study can also be applicable for the development of other peptide candidates.
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Radwan A, Mahrous GM. Docking studies and molecular dynamics simulations of the binding characteristics of waldiomycin and its methyl ester analog to Staphylococcus aureus histidine kinase. PLoS One 2020; 15:e0234215. [PMID: 32502195 PMCID: PMC7274439 DOI: 10.1371/journal.pone.0234215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/20/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial histidine kinases (HKs) are considered attractive drug targets because of their ability to govern adaptive responses coupled with their ubiquity. There are several classes of HK inhibitors; however, they suffer from drug resistance, poor bioavailability, and a lack of selectivity. The 3D structure of Staphylococcus aureus HK was not isolated in high-resolution coordinates, precluding further disclosure of structure-dependent binding to the specific antibiotics. To elucidate structure-dependent binding, the 3D structure of the catalytic domain WalK of S. aureus HK was constructed using homology modeling to investigate the WalK-ligand binding mechanisms through molecular docking studies and molecular dynamics simulations. The binding free energies of the waldiomycin and its methyl ester analog were calculated using molecular mechanics/generalized born surface area scoring. The key residues for protein-ligand binding were postulated. The structural divergence responsible for the 7.4-fold higher potency of waldiomycin than that of its ester analog was clearly observed. The optimized 3D macromolecule-ligand binding modes shed light on the S. aureus HK/WalK-ligand interactions that afford a means to assess binding affinity to design new HK/WalK inhibitors.
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Affiliation(s)
- Awwad Radwan
- Kayyali Chair, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Gamal M. Mahrous
- Kayyali Chair, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Jurado S, Cano-Muñoz M, Polo-Megías D, Conejero-Lara F, Morel B. Thermodynamic dissection of the interface between HIV-1 gp41 heptad repeats reveals cooperative interactions and allosteric effects. Arch Biochem Biophys 2020; 688:108401. [PMID: 32376316 DOI: 10.1016/j.abb.2020.108401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/03/2020] [Accepted: 04/27/2020] [Indexed: 11/27/2022]
Abstract
HIV-1 glycoprotein 41 (gp41) mediates fusion between virus and target cells by folding into a fusion active state, in which the C-terminal heptad repeat (CHR) regions associate externally to the N-terminal heptad repeat (NHR) trimer and form a very stable six-helix bundle coiled-coil structure. Therefore, interfering with the NHR-CHR interaction of gp41 is a promising therapeutic approach against HIV-1. However, a full understanding of the molecular and mechanistic details of this interaction is still incomplete. Here, we use single-chain, chimeric proteins (named covNHR) that reproduce accurately the CHR-NHR interactions to analyze the binding thermodynamics of several peptides with different length from the CHR region. The results indicate that cooperative binding involving two or more pockets of the NHR groove is necessary to obtain relevant affinities and that the binding energy is broadly distributed along the interface, underlining a crucial role of a middle pocket to achieve tight binding. In contrast, targeting only the deep hydrophobic pocket is insufficient to achieve significant affinity. Moreover, calorimetry experiments in combination with limited proteolysis performed using a mutant with occluded binding in the N-terminal pocket reveal the existence of an allosteric communication between the different regions. This study is the first detailed thermodynamic dissection of the NHR-CHR interaction in gp41 and contributes therefore to a better understanding of HIV fusion. These results are relevant for the development of potential fusion inhibitors.
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Affiliation(s)
- Samuel Jurado
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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Joshi VR, Newman RM, Pack ML, Power KA, Munro JB, Okawa K, Madani N, Sodroski JG, Schmidt AG, Allen TM. Gp41-targeted antibodies restore infectivity of a fusion-deficient HIV-1 envelope glycoprotein. PLoS Pathog 2020; 16:e1008577. [PMID: 32392227 PMCID: PMC7241850 DOI: 10.1371/journal.ppat.1008577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/21/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
The HIV-1 envelope glycoprotein (Env) mediates viral entry via conformational changes associated with binding the cell surface receptor (CD4) and coreceptor (CCR5/CXCR4), resulting in subsequent fusion of the viral and cellular membranes. While the gp120 Env surface subunit has been extensively studied for its role in viral entry and evasion of the host immune response, the gp41 transmembrane glycoprotein and its role in natural infection are less well characterized. Here, we identified a primary HIV-1 Env variant that consistently supports >300% increased viral infectivity in the presence of autologous or heterologous HIV-positive plasma. However, in the absence of HIV-positive plasma, viruses with this Env exhibited reduced infectivity that was not due to decreased CD4 binding. Using Env chimeras and sequence analysis, we mapped this phenotype to a change Q563R, in the gp41 heptad repeat 1 (HR1) region. We demonstrate that Q563R reduces viral infection by disrupting formation of the gp41 six-helix bundle required for virus-cell membrane fusion. Intriguingly, antibodies that bind cluster I epitopes on gp41 overcome this inhibitory effect, restoring infectivity to wild-type levels. We further demonstrate that the Q563R change increases HIV-1 sensitivity to broadly neutralizing antibodies (bNAbs) targeting the gp41 membrane-proximal external region (MPER). In summary, we identify an HIV-1 Env variant with impaired infectivity whose Env functionality is restored through the binding of host antibodies. These data contribute to our understanding of gp41 residues involved in membrane fusion and identify a mechanism by which host factors can alleviate a viral defect.
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Affiliation(s)
- Vinita R. Joshi
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruchi M. Newman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Melissa L. Pack
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Karen A. Power
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ken Okawa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Joseph G. Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Todd M. Allen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
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Design, synthesis and biological evaluation of novel 5-((substituted quinolin-3-yl/1-naphthyl) methylene)-3-substituted imidazolidin-2,4-dione as HIV-1 fusion inhibitors. Bioorg Chem 2020; 99:103782. [PMID: 32229348 DOI: 10.1016/j.bioorg.2020.103782] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/19/2020] [Accepted: 03/19/2020] [Indexed: 01/16/2023]
Abstract
A series of novel 5-(substituted quinolin-3-yl or 1-naphthyl)methylene)-3-substituted imidazolidin-2,4-dione 9-26 was designed and synthesized. The prepared compounds were identified using 1H NMR, 13C NMR as well as elemental analyses. The inhibitory activity of 9-26 on HIV-1IIIB replication in MT-2 cells was evaluated. Some derivatives showed good to excellent anti-HIV activities as compounds 13, 18, 19, 20, 22 and 23. They showed EC50 of 0.148, 0.460, 0.332, 0.50, 0.271 and 0.420 μM respectively being more potent than compound I (EC50 = 0.70 μM) and II ( EC50 = 2.40 μM) as standards. The inhibitory activity of 9-26 on infected primary HIV-1 domain, 92US657 (clade B, R5) was investigated. All the tested compounds consistently inhibited infection of this virus with EC50 from 0.520 to 11.857 μM. Results from SAR studies showed that substitution on ring A with 6/7/8-methyl group resulted in significant increase in the inhibitory activity against HIV-1IIIB infection (5- >300 times) compared to the unsubstituted analog 9. The cytotoxicity of these compounds on MT-2 cells was tested and their CC50 values ranged from 11 to 85 μM with selectivity indexes ranged from 0.53 to 166. The docking study revealed nice fitting of the new compounds into the hydrophobic pocket of HIV-1 gp41 and higher affinity than NB-64. Compound 13, the most active in preventing HIV-1IIIB infection, adopted a similar orientation to compound IV. Molecular docking analysis of the new compounds revealed hydrogen bonding interactions between the imidazolidine-2,4-dione ring and LYS574 which were missed in the weakly active derivatives.
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Yu D, Su Y, Ding X, Zhu Y, Qin B, Chong H, Cui S, He Y. Structural and Functional Characterization of the Secondary Mutation N126K Selected by Various HIV-1 Fusion Inhibitors. Viruses 2020; 12:v12030326. [PMID: 32197300 PMCID: PMC7150849 DOI: 10.3390/v12030326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/15/2020] [Accepted: 03/03/2020] [Indexed: 01/15/2023] Open
Abstract
Peptides derived from the C-terminal heptad repeat (CHR) region of HIV-1 gp41 is potent viral membrane fusion inhibitors, such as the first clinically approved peptide drug T20 and a group of newly-designed peptides. The resistance profiles of various HIV-1 fusion inhibitors were previously characterized, and the secondary mutation N126K in the gp41 CHR was routinely identified during the in vitro and in vivo selections. In this study, the functional and structural relevance of the N126K mutation has been characterized from multiple angles. First, we show that a single N126K mutation across several HIV-1 isolates conferred mild to moderate cross-resistances. Second, the N126K mutation exerted different effects on Env-mediated HIV-1 entry and cell-cell fusion. Third, the N126K mutation did not interfere with the expression and processing of viral Env glycoproteins, but it disrupted the Asn126-based glycosylation site in gp41. Fourth, the N126K mutation was verified to enhance the thermal stability of 6-HB conformation. Fifth, we determined the crystal structure of a 6-HB bearing the N126K mutation, which revealed the interhelical and intrahelical interactions underlying the increased thermostability. Therefore, our data provide new information to understand the mechanism of HIV-1 gp41-mediated cell fusion and its resistance mode to viral fusion inhibitors.
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Affiliation(s)
- Danwei Yu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yang Su
- Department of Lab Medicine, Institute of Hematology, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Xiaohui Ding
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuanmei Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Huihui Chong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Correspondence: ; Tel.: +86-10-67870275
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29
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Lin M, Da LT. Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry. J Chem Inf Model 2019; 60:162-174. [DOI: 10.1021/acs.jcim.9b00746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mengna Lin
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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The Tryptophan-Rich Motif of HIV-1 gp41 Can Interact with the N-Terminal Deep Pocket Site: New Insights into the Structure and Function of gp41 and Its Inhibitors. J Virol 2019; 94:JVI.01358-19. [PMID: 31619552 DOI: 10.1128/jvi.01358-19] [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: 08/14/2019] [Accepted: 10/09/2019] [Indexed: 11/20/2022] Open
Abstract
Refolding of the HIV-1 gp41 N- and C-terminal heptad repeats (NHR and CHR, respectively) into a six-helix bundle (6-HB) juxtaposes viral and cellular membranes for fusion. The CHR-derived peptide T20 is the only clinically approved viral fusion inhibitor and has potent anti-HIV activity; however, its mechanism of action is not fully understood. In this study, we surprisingly found that T20 disrupted the α-helical conformation of the NHR-derived peptide N54 through its C-terminal tryptophan-rich motif (TRM) and that synthetic short peptides containing the TRM sequence, TRM8 and TRM12, disrupted the N54 helix in a dose-dependent manner. Interestingly, TRM8 efficiently interfered with the secondary structures of three overlapping NHR peptides (N44, N38, and N28) and interacted with N28, which contains mainly the deep NHR pocket-forming sequence, with high affinity, suggesting that TRM targeted the NHR pocket site to mediate the disruption. Unlike TRM8, the short peptide corresponding to the pocket-binding domain (PBD) of the CHR helix had no such disruptive effect, and the CHR peptide C34 could form a stable 6-HB with the NHR helix; however, addition of the TRM to the C terminus of C34 resulted in a peptide (C46) that destroyed the NHR helix. Although the TRM peptides alone had no anti-HIV activity and could not block the formation of 6-HB conformation, substitution of the TRM for the PBD in C34 resulted in a mutant inhibitor (C34TRM) with high binding and inhibitory capacities. Combined, the present data inform a new mode of action of T20 and the structure-function relationship of gp41.IMPORTANCE The HIV-1 Env glycoprotein mediates membrane fusion and is conformationally labile. Despite extensive efforts, the structural property of the native fusion protein gp41 is largely unknown, and the mechanism of action of the gp41-derived fusion inhibitor T20 remains elusive. Here, we report that T20 and its C-terminal tryptophan-rich motif (TRM) can efficiently impair the conformation of the gp41 N-terminal heptad repeat (NHR) coiled coil by interacting with the deep NHR pocket site. The TRM sequence has been verified to possess the ability to replace the pocket-binding domain of C34, a fusion inhibitor peptide with high anti-HIV potency. Therefore, our studies have not only facilitated understanding of the mechanism of action of T20 and developed novel HIV-1 fusion inhibitors but also provided new insights into the structural property of the prefusion state of gp41.
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Hu Y, Zhao T, Zhang N, Zhang Y, Cheng L. A Review of Recent Advances and Research on Drug Target Identification Methods. Curr Drug Metab 2019; 20:209-216. [PMID: 30251599 DOI: 10.2174/1389200219666180925091851] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/01/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND From a therapeutic viewpoint, understanding how drugs bind and regulate the functions of their target proteins to protect against disease is crucial. The identification of drug targets plays a significant role in drug discovery and studying the mechanisms of diseases. Therefore the development of methods to identify drug targets has become a popular issue. METHODS We systematically review the recent work on identifying drug targets from the view of data and method. We compiled several databases that collect data more comprehensively and introduced several commonly used databases. Then divided the methods into two categories: biological experiments and machine learning, each of which is subdivided into different subclasses and described in detail. RESULTS Machine learning algorithms are the majority of new methods. Generally, an optimal set of features is chosen to predict successful new drug targets with similar properties. The most widely used features include sequence properties, network topological features, structural properties, and subcellular locations. Since various machine learning methods exist, improving their performance requires combining a better subset of features and choosing the appropriate model for the various datasets involved. CONCLUSION The application of experimental and computational methods in protein drug target identification has become increasingly popular in recent years. Current biological and computational methods still have many limitations due to unbalanced and incomplete datasets or imperfect feature selection methods.
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Affiliation(s)
- Yang Hu
- School of Life Science and Technology, Department of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Tianyi Zhao
- School of Life Science and Technology, Department of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Ningyi Zhang
- School of Life Science and Technology, Department of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Ying Zhang
- Department of Pharmacy, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin 150088, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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32
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Zhu H, Mathew E, Connelly SM, Zuber J, Sullivan M, Piepenbrink MS, Kobie JJ, Dumont ME. Identification of variant HIV envelope proteins with enhanced affinities for precursors to anti-gp41 broadly neutralizing antibodies. PLoS One 2019; 14:e0221550. [PMID: 31504041 PMCID: PMC6736307 DOI: 10.1371/journal.pone.0221550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/09/2019] [Indexed: 11/19/2022] Open
Abstract
HIV envelope protein (Env) is the sole target of broadly neutralizing antibodies (BNAbs) that are capable of neutralizing diverse strains of HIV. While BNAbs develop spontaneously in a subset of HIV-infected patients, efforts to design an envelope protein-based immunogen to elicit broadly neutralizing antibody responses have so far been unsuccessful. It is hypothesized that a primary barrier to eliciting BNAbs is the fact that HIV envelope proteins bind poorly to the germline-encoded unmutated common ancestor (UCA) precursors to BNAbs. To identify variant forms of Env with increased affinities for the UCA forms of BNAbs 4E10 and 10E8, which target the Membrane Proximal External Region (MPER) of Env, libraries of randomly mutated Env variants were expressed in a yeast surface display system and screened using fluorescence activated cell sorting for cells displaying variants with enhanced abilities to bind the UCA antibodies. Based on analyses of individual clones obtained from the screen and on next-generation sequencing of sorted libraries, distinct but partially overlapping sets of amino acid substitutions conferring enhanced UCA antibody binding were identified. These were particularly enriched in substitutions of arginine for highly conserved tryptophan residues. The UCA-binding variants also generally exhibited enhanced binding to the mature forms of anti-MPER antibodies. Mapping of the identified substitutions into available structures of Env suggest that they may act by destabilizing both the initial pre-fusion conformation and the six-helix bundle involved in fusion of the viral and cell membranes, as well as providing new or expanded epitopes with increased accessibility for the UCA antibodies.
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Affiliation(s)
- Hong Zhu
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Elizabeth Mathew
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Sara M. Connelly
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Jeffrey Zuber
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Mark Sullivan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Michael S. Piepenbrink
- Infectious Diseases Division, University of Rochester Medical Center, Rochester, NY United States of America
| | - James J. Kobie
- Infectious Diseases Division, University of Rochester Medical Center, Rochester, NY United States of America
| | - Mark E. Dumont
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
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33
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Qiu J, Liang T, Wu J, Yu F, He X, Tian Y, Xie L, Jiang S, Liu S, Li L. N-Substituted Pyrrole Derivative 12m Inhibits HIV-1 Entry by Targeting Gp41 of HIV-1 Envelope Glycoprotein. Front Pharmacol 2019; 10:859. [PMID: 31427969 PMCID: PMC6688628 DOI: 10.3389/fphar.2019.00859] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 07/05/2019] [Indexed: 11/13/2022] Open
Abstract
The combination of three or more antiviral agents that act on different targets is known as highly active antiretroviral therapy (HAART), which is widely used to control HIV infection. However, because drug resistance and adverse effects occur after long-term administration, an increasing number of HIV/AIDS patients do not tolerate HAART. It is necessary to continue developing novel anti-HIV drugs, particularly HIV entry/fusion inhibitors. Our group previously identified a small-molecule compound, NB-64, with weak anti-HIV activity. Here, we found that N-substituted pyrrole derivative 12m (NSPD-12m), which was derived from NB-64, had strong anti-HIV-1 activity, and NSPD-12m-treated cells showed good viability. The mechanism of action of NSPD-12m might be targeting the gp41 transmembrane subunit of the HIV envelope glycoprotein, thus inhibiting HIV entry. Site-directed mutagenesis confirmed that a positively charged lysine residue (K574) located in the gp41 pocket region is pivotal for the binding of NSPD-12m to gp41. These findings suggest that NSPD-12m can serve as a lead compound to develop novel virus entry inhibitors.
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Affiliation(s)
- Jiayin Qiu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.,School of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Pharmacy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Taizhen Liang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Junyan Wu
- Department of Pharmacy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fei Yu
- College of Life Sciences, Agricultural University of Hebei, Baoding, China.,Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoyang He
- Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Lan Xie
- Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Lin Li
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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34
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Singleton CD, Humby MS, Yi HA, Rizzo RC, Jacobs A. Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry. J Virol 2019; 93:e00676-19. [PMID: 31092576 PMCID: PMC6639268 DOI: 10.1128/jvi.00676-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/31/2022] Open
Abstract
A key step in the Ebola virus (EBOV) replication cycle involves conformational changes in viral glycoprotein 2 (GP2) which facilitate host-viral membrane fusion and subsequent release of the viral genome. Ebola GP2 plays a critical role in virus entry and has similarities in mechanism and structure to the HIV gp41 protein for which inhibitors have been successfully developed. In this work, a putative binding pocket for the C-terminal heptad repeat in the N-terminal heptad repeat trimer was targeted for identification of small molecules that arrest EBOV-host membrane fusion. Two computational structure-based virtual screens of ∼1.7 M compounds were performed (DOCK program) against a GP2 five-helix bundle, resulting in 165 commercially available compounds purchased for experimental testing. Based on assessment of inhibitory activity, cytotoxicity, and target specificity, four promising candidates emerged with 50% inhibitory concentration values in the 3 to 26 μM range. Molecular dynamics simulations of the two most potent candidates in their DOCK-predicted binding poses indicate that the majority of favorable interactions involve seven highly conserved residues that can be used to guide further inhibitor development and refinement targeting EBOV.IMPORTANCE The most recent Ebola virus disease outbreak, from 2014 to 2016, resulted in approximately 28,000 individuals becoming infected, which led to over 12,000 causalities worldwide. The particularly high pathogenicity of the virus makes paramount the identification and development of promising lead compounds to serve as inhibitors of Ebola infection. To limit viral load, the virus-host membrane fusion event can be targeted through the inhibition of the class I fusion glycoprotein of Ebolavirus In the current work, several promising small-molecule inhibitors that target the glycoprotein GP2 were identified through systematic application of structure-based computational and experimental drug design procedures.
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Affiliation(s)
- Courtney D Singleton
- Department of Molecular & Cellular Pharmacology, Stony Brook University, Stony Brook, New York, USA
| | - Monica S Humby
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, State University of New York (SUNY) at Buffalo, Buffalo, New York, USA
| | - Hyun Ah Yi
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, State University of New York (SUNY) at Buffalo, Buffalo, New York, USA
| | - Robert C Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Amy Jacobs
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, State University of New York (SUNY) at Buffalo, Buffalo, New York, USA
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Xu W, Pu J, Su S, Hua C, Su X, Wang Q, Jiang S, Lu L. Revisiting the mechanism of enfuvirtide and designing an analog with improved fusion inhibitory activity by targeting triple sites in gp41. AIDS 2019; 33:1545-1555. [PMID: 30932963 DOI: 10.1097/qad.0000000000002208] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To revisit the mechanism of action of enfuvirtide (T20) and based on the newly defined mechanism, design an analogous peptide of T20 with improved antiviral activity. DESIGN We compared the inhibitory activity of T20 with that of T1144 on six-helix bundle (6HB) formation at different time after coculture of HIV type 1 (HIV-1) envelope (Env)-expressing Chinese hamster ovary (CHO-Env) cells and CD4-expressing MT-2 cells at 31.5 °C and with that of T20-SF, an analogous peptide of T20 with an additional tryptophan-rich motif, on hemolysis mediated by FP-P, which contains fusion peptide and fusion peptide (FP) proximal region (FPPR), and HIV-1 infection. METHODS Inhibitory activity of peptides on 6HB formation was tested in a temperature-controlled cell-cell fusion assay by flow cytometry using 6HB-specific mAb 2G8; on HIV-1 infection and fusion was assessed by p24 and cell-cell fusion assays. Interaction between different peptides or peptide and antibody was evaluated by ELISA. RESULTS T20 could inhibit 6HB formation at early, but not late, stage of HIV-1 fusion, whereas T1144 was effective at both stages. T20-SF is much more effective than T20 in binding to FP-P and inhibiting infection of HIV-1, including T20-resistant strains, and FP-P-mediated hemolysis. CONCLUSION Results suggest that T20 has a double-target mechanism, by which its N-terminal and C-terminal portions bind to N-terminal heptad repeat and FPPR, respectively. T20-SF designed based on this new mechanism exhibits significantly improved anti-HIV-1 activity because it targets the triple sites in gp41, including N-terminal heptad repeat, FPPR, and fusion peptide. Thus, this study provides clues for designing novel HIV fusion inhibitors with improved antiviral activity.
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Chen G, Cook JD, Ye W, Lee JE, Sidhu SS. Optimization of peptidic HIV-1 fusion inhibitor T20 by phage display. Protein Sci 2019; 28:1501-1512. [PMID: 31228294 PMCID: PMC6635768 DOI: 10.1002/pro.3669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 11/06/2022]
Abstract
The HIV fusion inhibitor T20 has been approved to treat those living with HIV/AIDS, but treatment gives rise to resistant viruses. Using combinatorial phage-displayed libraries, we applied a saturation scan approach to dissect the entire T20 sequence for binding to a prefusogenic five-helix bundle (5HB) mimetic of HIV-1 gp41. Our data set compares all possible amino acid substitutions at all positions, and affords a complete view of the complex molecular interactions governing the binding of T20 to 5HB. The scan of T20 revealed that 12 of its 36 positions were conserved for 5HB binding, which cluster into three epitopes: hydrophobic epitopes at the ends and a central dyad of hydrophilic residues. The scan also revealed that the T20 sequence was highly adaptable to mutations at most positions, demonstrating a striking structural plasticity that allows multiple amino acid substitutions at contact points to adapt to conformational changes, and also at noncontact points to fine-tune the interface. Based on the scan result and structural knowledge of the gp41 fusion intermediate, a library was designed with tailored diversity at particular positions of T20 and was used to derive a variant (T20v1) that was found to be a highly effective inhibitor of infection by multiple HIV-1 variants, including a common T20-escape mutant. These findings show that the plasticity of the T20 functional sequence space can be exploited to develop variants that overcome resistance of HIV-1 variants to T20 itself, and demonstrate the utility of saturation scanning for rapid epitope mapping and protein engineering.
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Affiliation(s)
- Gang Chen
- Banting and Best Department of Medical Research, The Terrence Donnelly Center for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioM5S 3E1Canada
- Department of Molecular GeneticsUniversity of TorontoTorontoOntarioM5S 1A8Canada
| | - Jonathan D. Cook
- Department of Laboratory Medicine and Pathobiology, Faculty of MedicineUniversity of TorontoTorontoOntarioM5S 1A8Canada
| | - Wei Ye
- Banting and Best Department of Medical Research, The Terrence Donnelly Center for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioM5S 3E1Canada
- Department of Molecular GeneticsUniversity of TorontoTorontoOntarioM5S 1A8Canada
| | - Jeffrey E. Lee
- Department of Laboratory Medicine and Pathobiology, Faculty of MedicineUniversity of TorontoTorontoOntarioM5S 1A8Canada
| | - Sachdev S. Sidhu
- Banting and Best Department of Medical Research, The Terrence Donnelly Center for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioM5S 3E1Canada
- Department of Molecular GeneticsUniversity of TorontoTorontoOntarioM5S 1A8Canada
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Kobayakawa T, Ebihara K, Honda Y, Fujino M, Nomura W, Yamamoto N, Murakami T, Tamamura H. Dimeric C34 Derivatives Linked through Disulfide Bridges as New HIV-1 Fusion Inhibitors. Chembiochem 2019; 20:2101-2108. [PMID: 31012222 DOI: 10.1002/cbic.201900187] [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: 03/25/2019] [Indexed: 11/12/2022]
Abstract
C34, a 34-mer fragment peptide, is contained in the HIV-1 envelope protein gp41. A dimeric derivative of C34 linked through a disulfide bridge at its C terminus was synthesized and found to display potent anti-HIV activity, comparable with that of a previously reported PEGylated dimer of C34REG. The reduction in the size of the linker moiety for dimerization was thus successful, and this result might shed some light on the mechanism of the suppression of six-helix bundle formation by these C34 dimeric derivatives. Addition of a Gly-Cys(CH2 CONH2 )-Gly-Gly motif at the N-terminal position of a C34 monomeric derivative significantly increased the anti-HIV-1 activity. This moiety functions as a new pharmacophore, and this might provide a useful insight into the design of potent HIV-1 fusion inhibitors.
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Affiliation(s)
- Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Kento Ebihara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Yuzuna Honda
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Wataru Nomura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Naoki Yamamoto
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Tsutomu Murakami
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
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Conserved Residue Asn-145 in the C-Terminal Heptad Repeat Region of HIV-1 gp41 is Critical for Viral Fusion and Regulates the Antiviral Activity of Fusion Inhibitors. Viruses 2019; 11:v11070609. [PMID: 31277353 PMCID: PMC6669600 DOI: 10.3390/v11070609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 06/29/2019] [Accepted: 06/29/2019] [Indexed: 12/21/2022] Open
Abstract
Entry of HIV-1 into target cells is mediated by its envelope (Env) glycoprotein composed of the receptor binding subunit gp120 and the fusion protein gp41. Refolding of the gp41 N- and C-terminal heptad repeats (NHR and CHR) into a six-helix bundle (6-HB) conformation drives the viral and cellular membranes in close apposition and generates huge amounts of energy to overcome the kinetic barrier leading to membrane fusion. In this study, we focused on characterizing the structural and functional properties of a single Asn-145 residue, which locates at the middle CHR site of gp41 and is extremely conserved among all the HIV-1, HIV-2, and simian immunodeficiency virus (SIV) isolates. By mutational analysis, we found that Asn-145 plays critical roles for Env-mediated cell-cell fusion and HIV-1 entry. As determined by circular dichroism (CD) spectroscopy and isothermal titration calorimetry (ITC), the substitution of Asn-145 with alanine (N145A) severely impaired the interactions between the NHR and CHR helices. Asn-145 was also verified to be important for the antiviral activity of CHR-derived peptide fusion inhibitors and served as a turn-point for the inhibitory potency. Intriguingly, Asn-145 could regulate the functionality of the M-T hook structure at the N-terminus of the inhibitors and displayed comparable activities with the C-terminal IDL anchor. Crystallographic studies further demonstrated the importance of Asn-145-mediated interhelical and intrahelical interactions in the 6-HB structure. Combined, the present results have provided valuable information for the structure-function relationship of HIV-1 gp41 and the structure-activity relationship of gp41-dependent fusion inhibitors.
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Gorai B, Das S, Maiti PK. Prediction and validation of HIV-1 gp41 ecto-transmembrane domain post-fusion trimeric structure using molecular modeling. J Biomol Struct Dyn 2019; 38:2592-2603. [DOI: 10.1080/07391102.2019.1635916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Biswajit Gorai
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka, India
| | - Satyabrata Das
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka, India
| | - Prabal K. Maiti
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka, India
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Jurado S, Cano-Muñoz M, Morel B, Standoli S, Santarossa E, Moog C, Schmidt S, Laumond G, Cámara-Artigas A, Conejero-Lara F. Structural and Thermodynamic Analysis of HIV-1 Fusion Inhibition Using Small gp41 Mimetic Proteins. J Mol Biol 2019; 431:3091-3106. [PMID: 31255705 DOI: 10.1016/j.jmb.2019.06.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 11/25/2022]
Abstract
Development of effective inhibitors of the fusion between HIV-1 and the host cell membrane mediated by gp41 continues to be a grand challenge due to an incomplete understanding of the molecular and mechanistic details of the fusion process. We previously developed single-chain, chimeric proteins (named covNHR) that accurately mimic the N-heptad repeat (NHR) region of gp41 in a highly stable coiled-coil conformation. These molecules bind strongly to peptides derived from the gp41 C-heptad repeat (CHR) and are potent and broad HIV-1 inhibitors. Here, we investigated two covNHR variants differing in two mutations, V10E and Q123R (equivalent to V38E and Q40R in gp41 sequence) that reproduce the effect of HIV-1 mutations associated with resistance to fusion inhibitors, such as T20 (enfuvirtide). A detailed calorimetric analysis of the binding between the covNHR proteins and CHR peptides (C34 and T20) reveals drastic changes in affinity due to the mutations as a result of local changes in interactions at the site of T20 resistance. The crystallographic structure of the covNHR:C34 complex shows a virtually identical CHR-NHR binding interface to that of the post-fusion structure of gp41 and underlines an important role of buried interfacial water molecules in binding affinity and in development of resistance against CHR peptides. Despite the great difference in affinity, both covNHR variants demonstrate strong inhibitory activity for a wide variety of HIV-1 strains. These properties support the high potential of these covNHR proteins as new potent HIV-1 inhibitors. Our results may guide future inhibition approaches.
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Affiliation(s)
- Samuel Jurado
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Sara Standoli
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Elisabetta Santarossa
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Christiane Moog
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Sylvie Schmidt
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Géraline Laumond
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento, 04120 Almeria, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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Design and Characterization of Cholesterylated Peptide HIV-1/2 Fusion Inhibitors with Extremely Potent and Long-Lasting Antiviral Activity. J Virol 2019; 93:JVI.02312-18. [PMID: 30867304 DOI: 10.1128/jvi.02312-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 12/11/2022] Open
Abstract
HIV infection requires lifelong treatment with multiple antiretroviral drugs in a combination, which ultimately causes cumulative toxicities and drug resistance, thus necessitating the development of novel antiviral agents. We recently found that enfuvirtide (T-20)-based lipopeptides conjugated with fatty acids have dramatically increased in vitro and in vivo anti-HIV activities. Herein, a group of cholesterol-modified fusion inhibitors were characterized with significant findings. First, novel cholesterylated inhibitors, such as LP-83 and LP-86, showed the most potent activity in inhibiting divergent human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus (SIV). Second, the cholesterylated inhibitors were highly active to inhibit T-20-resistant mutants that still conferred high resistance to the fatty acid derivatives. Third, the cholesterylated inhibitors had extremely potent activity to block HIV envelope (Env)-mediated cell-cell fusion, especially a truncated minimum lipopeptide (LP-95), showing a greatly increased potency relative to its inhibition on virus infection. Fourth, the cholesterylated inhibitors efficiently bound to both the cellular and viral membranes to exert their antiviral activities. Fifth, the cholesterylated inhibitors displayed low cytotoxicity and binding capacity with human serum albumin. Sixth, we further demonstrated that LP-83 exhibited extremely potent and long-lasting anti-HIV activity in rhesus monkeys. Taken together, the present results help our understanding on the mechanism of action of lipopeptide-based viral fusion inhibitors and facilitate the development of novel anti-HIV drugs.IMPORTANCE The peptide drug enfuvirtide (T-20) remains the only membrane fusion inhibitor available for treatment of viral infection, which is used in combination therapy of HIV-1 infection; however, it exhibits relatively low antiviral activity and a genetic barrier to inducing resistance, calling for the continuous development for novel anti-HIV agents. In this study, we report cholesterylated fusion inhibitors showing the most potent and broad anti-HIV activities to date. The new inhibitors have been comprehensively characterized for their modes of action and druggability, including small size, low cytotoxicity, binding ability to human serum albumin (HSA), and, especially, extremely potent and long-lasting antiviral activity in rhesus monkeys. Therefore, the present studies have provided new drug candidates for clinical development, which can also be used as tools to probe the mechanisms of viral entry and inhibition.
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Gomes B, Sanna G, Madeddu S, Hollmann A, Santos NC. Combining 25-Hydroxycholesterol with an HIV Fusion Inhibitor Peptide: Interaction with Biomembrane Model Systems and Human Blood Cells. ACS Infect Dis 2019; 5:582-591. [PMID: 30816690 DOI: 10.1021/acsinfecdis.8b00321] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The fusion between the viral and the target cell membrane is a crucial step in the life cycle of enveloped viruses. The blocking of this process is a well-known therapeutic approach that led to the development of the fusion inhibitor peptide enfuvirtide, clinically used against human immunodeficiency virus (HIV) type 1. Despite this significant advance on viral treatment, the appearance of resistance has limited its clinical use. Such a limitation has led to the development of other fusion inhibitor peptides, such as C34, that present the same structural domain as enfuvirtide (heptad repeat sequence) but have different functional domains (pocket-binding domain in the case of C34 and lipid-binding domain in the case of enfuvirtide). Recently, the antiviral properties of 25-hydroxycholesterol were demonstrated, which boosted the interest in this oxysterol. The combination of two distinct antiviral molecules, C34 and 25-hydroxycholesterol, may help to suppress the emergence of resistant viruses. In this work, we characterized the interaction of the C34-25-hydroxycholesterol conjugate with biomembrane model systems and human blood cells. Lipid vesicles and monolayers with defined lipid compositions were used as biomembrane model systems. The conjugate interacts preferentially with membranes rich in sphingomyelin (a lipid enriched in lipid rafts) and presents a poor partition to membranes composed solely of phosphatidylcholine and cholesterol. We hypothesize that cholesterol causes a repulsive effect that is overcome in the presence of sphingomyelin. Importantly, the peptide shows a preference for human peripheral blood mononuclear cells relative to erythrocytes, which shows its potential to target CD4+ cells. Antiviral activity results against different wild-type and drug-resistant HIV strains further demonstrated the potential of C34-HC as a good candidate for future studies.
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Affiliation(s)
- Bárbara Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Giusepinna Sanna
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliary, Cagliari 09123, Italy
| | - Silvia Madeddu
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliary, Cagliari 09123, Italy
| | - Axel Hollmann
- Laboratory of Bioactive Compounds, CIBAAL−University of Santiago del Estero and CONICET, Santiago del Estero, Argentina
- Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, University of Quilmes, Bernal B1876BXD, Argentina
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
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Conformational Differences between Functional Human Immunodeficiency Virus Envelope Glycoprotein Trimers and Stabilized Soluble Trimers. J Virol 2019; 93:JVI.01709-18. [PMID: 30429345 DOI: 10.1128/jvi.01709-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/07/2018] [Indexed: 01/11/2023] Open
Abstract
Binding to the receptor CD4 triggers entry-related conformational changes in the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) trimer, (gp120/gp41)3 Soluble versions of HIV-1 Env trimers (sgp140 SOSIP.664) stabilized by a gp120-gp41 disulfide bond and a change (I559P) in gp41 have been structurally characterized. Here, we use cross-linking/mass spectrometry to evaluate the conformations of functional membrane Env and sgp140 SOSIP.664. Differences were detected in the gp120 trimer association domain and C terminus and in the gp41 heptad repeat 1 (HR1) region. Whereas the membrane Env trimer exposes the gp41 HR1 coiled coil only after CD4 binding, the sgp140 SOSIP.664 HR1 coiled coil was accessible to the gp41 HR2 peptide even in the absence of CD4. Our results delineate differences in both gp120 and gp41 subunits between functional membrane Env and the sgp140 SOSIP.664 trimer and provide distance constraints that can assist validation of candidate structural models of the native HIV-1 Env trimer.IMPORTANCE HIV-1 envelope glycoprotein spikes mediate the entry of the virus into host cells and are a major target for vaccine-induced antibodies. Soluble forms of the envelope glycoproteins that are stable and easily produced have been characterized extensively and are being considered as vaccines. Here, we present evidence that these stabilized soluble envelope glycoproteins differ in multiple respects from the natural HIV-1 envelope glycoproteins. By pinpointing these differences, our results can guide the improvement of envelope glycoprotein preparations to achieve greater similarity to the viral envelope glycoprotein spike, potentially increasing their effectiveness as a vaccine.
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Pattnaik GP, Chakraborty H. Coronin 1 derived tryptophan-aspartic acid containing peptides inhibit membrane fusion. Chem Phys Lipids 2018; 217:35-42. [DOI: 10.1016/j.chemphyslip.2018.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 11/16/2022]
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Xu X, Li L, Liu Z, Yao X, Zhang X, Liu S, Liu L. Investigation of the inhibition effect of arachidonic acid on the core structure of the HIV-1 gp41. J Pharm Biomed Anal 2018; 161:377-382. [PMID: 30199809 DOI: 10.1016/j.jpba.2018.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 08/31/2018] [Accepted: 09/02/2018] [Indexed: 11/29/2022]
Abstract
The gp41 transmembrane domain of the envelope glycoprotein of the human immunodeficiency virus (HIV) modulates the conformation of the viral envelope spike. During the HIV fusion process, C-terminal heptad repeat (CHR, C34) wrap antiparallel to the N-terminal heptad repeat (NHR, N36) helices to form a stable six-helix bundle (6-HB) core structure, which brings the viral and cell membranes into close proximity for fusion. Therefore, inhibiting the formation of 6-HB is considered to be a key activity of an effective HIV-1 fusion inhibitor. The level of arachidonic acid (AA) is increased in HIV infected patients. Our study provides a new insight into the functional role of AA during the formation of HIV-1 gp41 6-HB. Native polyacrylamide gel electrophoresis (N-PAGE), enzyme-linked-immunosorbent serologic assay (ELISA) and circular dichroism (CD) spectroscopy were used to investigate the inhibition of AA for the formation of 6-HB. Molecular docking technique was adopted to explore the underlying mechanism. HIV-1 JR-FL (R5 strain) Envelope was adopted to determine the inhibition effect of AA. AA is shown to interfere with the formation of α-helical complexes of N36 and C34 by N-PAGE, ELISA and CD spectroscopy. The isotherm titration microcalorimetry (ITC) results indicate there is a single class of binding site on N36. ΔH and ΔS are -12.43 kJ mol-1 and 70.07 J mol-1 K-1, respectively, indicating hydrophobic interaction and electrostatic forces are the main acting forces. The molecular docking results manifest that AA interacts with the hydrophobic residues (Trp-571, Leu-568, Val-570 and Leu-576) and ionic interactions occur between Arg-579 and the -COOH of AA. The inhibitory activity of AA on HIV-1 JR-FL is quantified by 50% effective concentration (EC50) and 90% effective concentration (EC90), which are 31.42 ± 1.08 and 133.47 ± 18.10 μg mL-1, respectively. All the results indicate that AA is able to inhibit the formation of 6-HB but cannot disrupt the preformed 6-HB. Therefore, AA is a potential inhibitor for the viral fusion/entry.
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Affiliation(s)
- Xiaoying Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Department of Pharmacy, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Lin Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaojun Yao
- Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xuanxuan Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Lihong Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
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Zhou G, Chu S, Nemati A, Huang C, Snyder BA, Ptak RG, Gochin M. Investigation of the molecular characteristics of bisindole inhibitors as HIV-1 glycoprotein-41 fusion inhibitors. Eur J Med Chem 2018; 161:533-542. [PMID: 30390441 DOI: 10.1016/j.ejmech.2018.10.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 11/20/2022]
Abstract
In previous work, we described 6-6'-bisindole compounds targeting a hydrophobic pocket on the N-heptad repeat region of viral glycoprotein-41 as effective inhibitors of HIV-1 fusion. Two promising compounds with sub-micromolar IC50's contained a benzoic acid group and a benzoic acid ester attached at the two indole nitrogens. Here we have conducted a thorough structure-activity relationship (SAR) study evaluating the contribution of each of the ring systems and various substituents to compound potency. Hydrophobicity, polarity and charge were varied to produce 35 new compounds that were evaluated in binding, cell-cell fusion and viral infectivity assays. We found that (a) activity based solely on increasing hydrophobic content plateaued at ∼ 200 nM; (b) the bisindole scaffold surpassed other heterocyclic ring systems in efficacy; (c) a polar interaction possibly involving Gln575 in the pocket could supplant less specific hydrophobic interactions; and (d) the benzoic acid ester moiety did not appear to form specific contacts with the pocket. The importance of this hydrophobic group to compound potency suggests a mechanism whereby it might interact with a tertiary component during fusion, such as membrane. A promising small molecule 10b with sub-μM activity was discovered with molecular weight <500 da and reduced logP compared to earlier compounds. The work provides insight into requirements for small molecule inhibition of HIV-1 fusion.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University-California, Vallejo, CA, 94592, USA
| | - Shidong Chu
- Department of Basic Sciences, Touro University-California, Vallejo, CA, 94592, USA
| | - Ariana Nemati
- Department of Basic Sciences, Touro University-California, Vallejo, CA, 94592, USA
| | - Chunsheng Huang
- Southern Research Institute, 431 Aviation Way, Frederick, MD, 21701, USA
| | - Beth A Snyder
- Southern Research Institute, 431 Aviation Way, Frederick, MD, 21701, USA
| | - Roger G Ptak
- Southern Research Institute, 431 Aviation Way, Frederick, MD, 21701, USA
| | - Miriam Gochin
- Department of Basic Sciences, Touro University-California, Vallejo, CA, 94592, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, CA, 94143, USA.
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Structural and Functional Characterization of Membrane Fusion Inhibitors with Extremely Potent Activity against Human Immunodeficiency Virus Type 1 (HIV-1), HIV-2, and Simian Immunodeficiency Virus. J Virol 2018; 92:JVI.01088-18. [PMID: 30089693 DOI: 10.1128/jvi.01088-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/01/2018] [Indexed: 12/28/2022] Open
Abstract
T-20 (enfuvirtide) is the only membrane fusion inhibitor available for the treatment of viral infection; however, it has low anti-human immunodeficiency virus (anti-HIV) activity and a low genetic barrier for drug resistance. We recently reported that T-20 sequence-based lipopeptides possess extremely potent in vitro and in vivo efficacies (X. Ding, Z. Zhang, H. Chong, Y. Zhu, H. Wei, X. Wu, J. He, X. Wang, Y. He, 2017, J Virol 91:e00831-17, https://doi.org/10.1128/JVI.00831-17; H. Chong, J. Xue, Y. Zhu, Z. Cong, T. Chen, Y. Guo, Q. Wei, Y. Zhou, C. Qin, Y. He, 2018, J Virol 92:e00775-18, https://doi.org/10.1128/JVI.00775-18). Here, we focused on characterizing the structure-activity relationships of the T-20 derivatives. First, a novel lipopeptide termed LP-52 was generated with improved target-binding stability and anti-HIV activity. Second, a large panel of truncated lipopeptides was characterized, revealing a 21-amino-acid sequence core structure. Third, it was surprisingly found that the addition of the gp41 pocket-binding residues in the N terminus of the new inhibitors resulted in increased binding but decreased antiviral activities. Fourth, while LP-52 showed the most potent activity in inhibiting divergent HIV-1 subtypes, its truncated versions, such as LP-55 (25-mer) and LP-65 (24-mer), still maintained their potencies at very low picomolar concentrations; however, both the N- and C-terminal motifs of LP-52 played crucial roles in the inhibition of T-20-resistant HIV-1 mutants, HIV-2, and simian immunodeficiency virus (SIV) isolates. Fifth, we verified that LP-52 can bind to target cell membranes and human serum albumin and has low cytotoxicity and a high genetic barrier to inducing drug resistance.IMPORTANCE Development of novel membrane fusion inhibitors against HIV and other enveloped viruses is highly important in terms of the peptide drug T-20, which remains the only one for clinical use, even if it is limited by large dosages and resistance. Here, we report a novel T-20 sequence-based lipopeptide showing extremely potent and broad activities against HIV-1, HIV-2, SIV, and T-20-resistant mutants, as well as an extremely high therapeutic selectivity index and genetic resistance barrier. The structure-activity relationship (SAR) of the T-20 derivatives has been comprehensively characterized, revealing a critical sequence core structure and the target sites of viral vulnerability that do not include the gp41 pocket. The results also suggest that membrane-anchored inhibitors possess unique modes of action relative to unconjugated peptides. Combined, our series studies have not only provided drug candidates for clinical development but also offered important tools to elucidate the mechanisms of viral fusion and inhibition.
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Guo Y, Fu L, Fan X, Shi X. Stapled SC34EK fusion inhibitors with high potency against HIV-1 and improved protease resistance. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.03.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yu D, Ding X, Liu Z, Wu X, Zhu Y, Wei H, Chong H, Cui S, He Y. Molecular mechanism of HIV-1 resistance to sifuvirtide, a clinical trial-approved membrane fusion inhibitor. J Biol Chem 2018; 293:12703-12718. [PMID: 29929981 DOI: 10.1074/jbc.ra118.003538] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/13/2018] [Indexed: 12/25/2022] Open
Abstract
Host cell infection with HIV-1 requires fusion of viral and cell membranes. Sifuvirtide (SFT) is a peptide-based HIV-1 fusion inhibitor approved for phase III clinical trials in China. Here, we focused on characterizing HIV-1 variants highly resistant to SFT to gain insight into the molecular resistance mechanism. Three primary substitutions (V38A, A47I, and Q52R) located at the inhibitor-binding site of HIV-1's envelope protein (Env) and one secondary substitution (N126K) located at the C-terminal heptad repeat region of the viral protein gp41, which is part of the envelope, conferred high SFT resistance and cross-resistance to the anti-HIV-1 drug T20 and the template peptide C34. Interestingly, SFT's resistance profile could be dramatically improved with an M-T hook structure-modified SFT (MTSFT) and with short-peptide inhibitors that mainly target the gp41 pocket (2P23 and its lipid derivative LP-19). We found that the V38A and Q52R substitutions reduce the binding stabilities of SFT, C34, and MTSFT, but they had no effect on the binding of 2P23 and LP-19; in sharp contrast, the A47I substitution enhanced fusion inhibitor binding. Furthermore, the primary resistance substitutions impaired Env-mediated membrane fusion and cell entry and changed the conformation of the gp41 core structure. Importantly, whereas the V38A and Q52R substitutions disrupted the N-terminal helix of gp41, a single A47I substitution greatly enhanced its thermostability. Taken together, our results provide crucial structural insights into the mechanism of HIV-1 resistance to gp41-dependent fusion inhibitors, which may inform the development of additional anti-HIV drugs.
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Affiliation(s)
- Danwei Yu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China; Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaohui Ding
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China; Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zixuan Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China; Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiyuan Wu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China; Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuanmei Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China; Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Huanmian Wei
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China; Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Huihui Chong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China; Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Sheng Cui
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China
| | - Yuxian He
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Beijing 100730, China; Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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Miranda PO, Cubitt B, Jacob NT, Janda KD, de la Torre JC. Mining a Kröhnke Pyridine Library for Anti-Arenavirus Activity. ACS Infect Dis 2018; 4:815-824. [PMID: 29405696 DOI: 10.1021/acsinfecdis.7b00236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Several arenaviruses cause hemorrhagic fever (HF) disease in humans and represent important public health problems in their endemic regions. In addition, evidence indicates that the worldwide-distributed prototypic arenavirus lymphocytic choriomeningitis virus is a neglected human pathogen of clinical significance. There are no licensed arenavirus vaccines, and current antiarenavirus therapy is limited to an off-label use of ribavirin that is only partially effective. Therefore, there is an unmet need for novel therapeutics to combat human pathogenic arenaviruses, a task that will be facilitated by the identification of compounds with antiarenaviral activity that could serve as probes to identify arenavirus-host interactions suitable for targeting, as well as lead compounds to develop future antiarenaviral drugs. Screening of a combinatorial library of Krönhke pyridines identified compound KP-146 [(5-(5-(2,3-dihydrobenzo[ b][1,4] dioxin-6-yl)-4'-methoxy-[1,1'-biphenyl]-3-yl)thiophene-2-carboxamide] as having strong anti-lymphocytic choriomeningitis virus (LCMV) activity in cultured cells. KP-146 did not inhibit LCMV cell entry but rather interfered with the activity of the LCMV ribonucleoprotein (vRNP) responsible for directing virus RNA replication and gene transcription, as well as with the budding process mediated by the LCMV matrix Z protein. LCMV variants with increased resistance to KP-146 did not emerge after serial passages in the presence of KP-146. Our findings support the consideration of Kröhnke pyridine scaffold as a valuable source to identify compounds that could serve as tools to dissect arenavirus-host interactions, as well as lead candidate structures to develop antiarenaviral drugs.
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