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Uygun ZO, Tasoglu S. Impedimetric antimicrobial peptide biosensor for the detection of human immunodeficiency virus envelope protein gp120. iScience 2024; 27:109190. [PMID: 38414859 PMCID: PMC10897921 DOI: 10.1016/j.isci.2024.109190] [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: 09/17/2023] [Revised: 10/07/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
This study presents the design and implementation of an antimicrobial peptide-based electrochemical impedance spectroscopy (EIS) based biosensor system. The biosensor consists of a gold coated carbon electrode with MXene and silver nanoparticles (AgNPs) for the label-free detection of the human immunodeficiency virus (HIV) envelope protein gp120. Scanning electron microscopy was used to confirm the presence and distribution of MXene and AgNPs on the biosensor surface. The employment of the antimicrobial peptide on the electrode surface minimized the denaturation of the biorecognition receptor to ensure reliable and stable performance. The biosensor exhibited a linear range of 10-4000 pg mL-1 for gp120 detection, demonstrating good repeatability in real samples. The limit of detection (LOD) and limit of quantification (LOQ) were also calculated as 0.05 pg mL-1 and 0.14 pg mL-1, respectively. This biosensing platform has promising applications in the detection of HIV in clinical and point-of-care settings.
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Affiliation(s)
- Zihni Onur Uygun
- Kafkas University, Faculty of Medicine, Department of Medical Biochemistry, Kars 36100, Türkiye
- Koç University, Koç University Translational Medicine Research Center (KUTTAM), Istanbul 34450, Türkiye
| | - Savas Tasoglu
- Koç University, Koç University Translational Medicine Research Center (KUTTAM), Istanbul 34450, Türkiye
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Istanbul 34450, Türkiye
- Koç University, Engineering Faculty, Department of Mechanical Engineering, Istanbul 34450, Türkiye
- Boğaziçi University, Boğaziçi Institute of Biomedical Engineering, Istanbul 34684, Türkiye
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2
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Zhang J, Han J, Li H, Li Z, Zou P, Li J, Zhao T, Che J, Yang Y, Yang M, Wang Y, Gong W, Li Z, Li L, Gao C, Xiao H. Lymphocyte Membrane- and 12p1-Dual-Functionalized Nanoparticles for Free HIV-1 Trapping and Precise siRNA Delivery into HIV-1-Infected Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300282. [PMID: 36755201 PMCID: PMC10074117 DOI: 10.1002/advs.202300282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Despite the success of small interfering RNA (siRNA) in clinical settings and its potential value in human immunodeficiency virus (HIV) therapy, the rapid clearance and absence of precise delivery to target cells still hinder the therapeutic effect of siRNA. Herein, a new system, which can escape immune recognition, has HIV-1 neutralizing capacity, and the ability to deliver siRNA specifically into HIV-1-infected cells, is constructed by functionalizing siRNA delivery lipid nanoparticles with the lymphocyte membrane and 12p1. The constructed system is shown to escape uptake by the mononuclear phagocyte system. The constructed system exhibits strong binding ability with gp120, thus displaying distinguished neutralizing breadth and potency. The constructed system neutralizes all tested HIV-1 pseudotyped viruses with a geometric mean 80% inhibitory concentration (IC80) of 29.75 µg mL-1 and inhibits X4-tropic HIV-1 with an IC80 of 64.20 µg mL-1 , and R5-tropic HIV-1 with an IC80 of 16.39 µg mL-1 . The new system also specifically delivers siRNA into the cytoplasm of HIV-1-infected cells and exhibits evident gene silencing of tat and rev. Therefore, this new system can neutralize HIV-1 and deliver siRNA selectively into HIV-1-infected cells and may be a promising therapeutic candidate for the precise therapy of HIV.
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Affiliation(s)
- Jinbang Zhang
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
- Pharmaceutical CollegeHenan UniversityKaifeng475001China
| | - Jingwan Han
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijing100071China
| | - Hui Li
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
- Pharmaceutical CollegeHenan UniversityKaifeng475001China
| | - Zhengyang Li
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijing100071China
- School of Public Health and Health ManagementGannan Medical UniversityGanzhou341000China
| | - Pengfei Zou
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
| | - Jiaxin Li
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
- Pharmaceutical CollegeHenan UniversityKaifeng475001China
| | - Te Zhao
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
| | - Junwei Che
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
| | - Yang Yang
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
| | - Meiyan Yang
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
| | - Yuli Wang
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
| | - Wei Gong
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
| | - Zhiping Li
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
| | - Lin Li
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijing100071China
| | - Chunsheng Gao
- State key Laboratory of Toxicology and Medical CountermeasureDepartment of PharmaceuticsBeijing Institute of Pharmacology and ToxicologyBeijing100039China
- Pharmaceutical CollegeHenan UniversityKaifeng475001China
| | - Haihua Xiao
- Institute of ChemistryChinese Academy of SciencesBeijing100190China
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Vivekanandan S, Vetrivel U, Hanna LE. Design of human immunodeficiency virus-1 neutralizing peptides targeting CD4-binding site: An integrative computational biologics approach. Front Med (Lausanne) 2022; 9:1036874. [DOI: 10.3389/fmed.2022.1036874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
Peptide therapeutics have recently gained momentum in antiviral therapy due to their increased potency and cost-effectiveness. Interaction of the HIV-1 envelope gp120 with the host CD4 receptor is a critical step for viral entry, and therefore the CD4-binding site (CD4bs) of gp120 is a potential hotspot for blocking HIV-1 infection. The present study aimed to design short peptides from well-characterized CD4bs targeting broadly neutralizing antibodies (bNAbs), which could be utilized as bNAb mimetics for viral neutralization. Co-crystallized structures of HIV-1 gp120 in complex with CD4bs-directed bNAbs were used to derive hexameric peptides using the Rosetta Peptiderive protocol. Based on empirical insights into co-crystallized structures, peptides derived from the heavy chain alone were considered. The peptides were docked with both HIV-1 subtype B and C gp120, and the stability of the peptide–antigen complexes was validated using extensive Molecular Dynamics (MD) simulations. Two peptides identified in the study demonstrated stable intermolecular interactions with SER365, GLY366, and GLY367 of the PHE43 cavity in the CD4 binding pocket, and with ASP368 of HIV-1 gp120, thereby mimicking the natural interaction between ASP368gp120 and ARG59CD4–RECEPTOR. Furthermore, the peptides featured favorable physico-chemical properties for virus neutralization suggesting that these peptides may be highly promising bNAb mimetic candidates that may be taken up for experimental validation.
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4
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Charlermroj R, Makornwattana M, Phuengwas S, Karoonuthaisiri N. A rapid colorimetric lateral flow test strip for detection of live Salmonella Enteritidis using whole phage as a specific binder. Front Microbiol 2022; 13:1008817. [PMID: 36246228 PMCID: PMC9556839 DOI: 10.3389/fmicb.2022.1008817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Specific antibodies are essential components of immunoassay, which can be applied for the detection of pathogens. However, producing an antibody specific to live bacterial pathogens by the classical method of immunizing animals with live pathogens can be impractical. Phage display technology is an effective alternative method to obtain antibodies with the desired specificity against selected antigenic molecules. In this study, we demonstrated the power of a microarray-based technique for obtaining specific phage-derived antibody fragments against Salmonella, an important foodborne pathogen. The selected phage-displayed antibody fragments were subsequently employed to develop a lateral flow test strip assay for the detection of live Salmonella. The test strips showed specificity to Salmonella Enteritidis without cross-reactivity to eight serovars of Salmonella or other bacteria strains. The test strip assay requires 15 min, whereas the conventional biochemical and serological confirmation test requires at least 24 h. The microarray screening technique for specific phage-based binders and the test strip method can be further applied to other foodborne pathogens.
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Affiliation(s)
- Ratthaphol Charlermroj
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
- *Correspondence: Ratthaphol Charlermroj,
| | - Manlika Makornwattana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sudtida Phuengwas
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
- International Joint Research Center on Food Security, Pathum Thani, Thailand
- Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
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5
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Peptide-Based HIV Entry Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:15-26. [DOI: 10.1007/978-981-16-8702-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Poh CL, Lalani S. Strategies to identify and develop antiviral peptides. VITAMINS AND HORMONES 2021; 117:17-46. [PMID: 34420580 DOI: 10.1016/bs.vh.2021.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The emergence and re-emergence of viral pathogens capable of causing epidemics or pandemics pose a serious healthcare burden. Small molecule antivirals used in conventional therapy have given rise to the severe problem of viral resistance against them. Peptides are generally considered safe, effective and are less likely to induce viral resistance. Antiviral peptides can be identified from screening of phage display of combinational peptide libraries, peptide array libraries or designed against viral targets. Limitations of peptides such as bioavailability can be improved with chemical modifications. Nanotechnology can further improve the stability of peptides in systemic circulation and enhance the antiviral activity of peptides, making them an appealing therapeutic option.
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Affiliation(s)
- Chit Laa Poh
- Centre for Virus and Vaccine Research, Sunway University, Subang Jaya, Selangor, Malaysia.
| | - Salima Lalani
- Centre for Virus and Vaccine Research, Sunway University, Subang Jaya, Selangor, Malaysia; Department of Biological Sciences, Sunway University, Subang Jaya, Selangor, Malaysia
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7
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Agarwal G, Gabrani R. Identification of Peptide Binders to Truncated Recombinant Chikungunya Virus Envelope Protein 2 Using Phage Display Technology and Their In Silico Characterization. Protein Pept Lett 2021; 28:508-519. [PMID: 33121397 DOI: 10.2174/0929866527666201029144245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/08/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
AIM To identify and characterize peptide binders to truncated recombinant chikungunya virus envelope protein 2. BACKGROUND Despite extensive research on the chikungunya virus (CHIKV), the specific antiviral treatment's unavailability has stressed the need for the urgent development of therapeutics. The Envelope protein 2 (E2) of CHIKV that displays putative receptor binding sites and specific epitopes for virus neutralizing antibodies is a critical target for the therapeutic intervention. OBJECTIVE The study aims to identify the unique peptides that can bind to truncated E2 protein of CHIKV and further explore their properties as potential therapeutic candidate. METHODS A stretch of CHIKV-E2 (rE2), which is prominently exposed on the surface of virion, was used as bait protein to identify peptide binders to the CHIKV-rE2 using a 12-mer phage display peptide library. Three rounds of biopanning yielded several peptide binders to CHIKV-rE2 and their binding affinities were compared by phage ELISA. Additionally, a fully flexible-blind docking simulation investigated the possible binding modes of the selected peptides. Furthermore, the selected peptides were characterized and their ADMET properties were explored in silico. RESULTS Five peptides were identified as potential binders based on their robust reactivity to the bait protein. The selected peptides appeared to interact with the crucial residues that were notably exposed on the surface of E1-E2 trimeric structure. The explored in silico studies suggested their non-allergenicity, non-toxicity and likeliness to be antiviral. CONCLUSION The potential binding peptides of CHIKV-rE2 protein were identified using phage display technology and characterized in silico. The selected peptides could be further used for the development of therapeutics against the CHIKV infection.>.
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Affiliation(s)
- Garima Agarwal
- Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, UP 201309, India
| | - Reema Gabrani
- Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, UP 201309, India
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8
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Ding Y, Ting JP, Liu J, Al-Azzam S, Pandya P, Afshar S. Impact of non-proteinogenic amino acids in the discovery and development of peptide therapeutics. Amino Acids 2020; 52:1207-1226. [PMID: 32945974 PMCID: PMC7544725 DOI: 10.1007/s00726-020-02890-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/05/2020] [Indexed: 12/14/2022]
Abstract
With the development of modern chemistry and biology, non-proteinogenic amino acids (NPAAs) have become a powerful tool for developing peptide-based drug candidates. Drug-like properties of peptidic medicines, due to the smaller size and simpler structure compared to large proteins, can be changed fundamentally by introducing NPAAs in its sequence. While peptides composed of natural amino acids can be used as drug candidates, the majority have shown to be less stable in biological conditions. The impact of NPAA incorporation can be extremely beneficial in improving the stability, potency, permeability, and bioavailability of peptide-based therapies. Conversely, undesired effects such as toxicity or immunogenicity should also be considered. The impact of NPAAs in the development of peptide-based therapeutics is reviewed in this article. Further, numerous examples of peptides containing NPAAs are presented to highlight the ongoing development in peptide-based therapeutics.
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Affiliation(s)
- Yun Ding
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Joey Paolo Ting
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Shams Al-Azzam
- Professional Scientific Services, Eurofins Lancaster Laboratories, Lancaster, PA, 17605, USA
| | - Priyanka Pandya
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA.
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Pattnaik GP, Chakraborty H. Entry Inhibitors: Efficient Means to Block Viral Infection. J Membr Biol 2020; 253:425-444. [PMID: 32862236 PMCID: PMC7456447 DOI: 10.1007/s00232-020-00136-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
The emerging and re-emerging viral infections are constant threats to human health and wellbeing. Several strategies have been explored to develop vaccines against these viral diseases. The main effort in the journey of development of vaccines is to neutralize the fusion protein using antibodies. However, significant efforts have been made in discovering peptides and small molecules that inhibit the fusion between virus and host cell, thereby inhibiting the entry of viruses. This class of inhibitors is called entry inhibitors, and they are extremely efficient in reducing viral infection as the entry of the virus is considered as the first step of infection. Nevertheless, these inhibitors are highly selective for a particular virus as antibody-based vaccines. The recent COVID-19 pandemic lets us ponder to shift our attention towards broad-spectrum antiviral agents from the so-called ‘one bug-one drug’ approach. This review discusses peptide and small molecule-based entry inhibitors against class I, II, and III viruses and sheds light on broad-spectrum antiviral agents.
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Affiliation(s)
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768 019, India. .,Centre of Excellence in Natural Products and Therapeutics, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768 019, India.
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10
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Wang Z, Kennedy PG, Dupree C, Wang M, Lee C, Pointon T, Langford TD, Graner MW, Yu X. Antibodies from Multiple Sclerosis Brain Identified Epstein-Barr Virus Nuclear Antigen 1 & 2 Epitopes which Are Recognized by Oligoclonal Bands. J Neuroimmune Pharmacol 2020; 16:567-580. [PMID: 32808238 PMCID: PMC7431217 DOI: 10.1007/s11481-020-09948-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/27/2020] [Indexed: 12/30/2022]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system (CNS), the etiology of which is poorly understood. The most common laboratory abnormality associated with MS is increased intrathecal immunoglobulin G (IgG) synthesis and the presence of oligoclonal bands (OCBs) in the brain and cerebrospinal fluid (CSF). However, the major antigenic targets of these antibody responses are unknown. The risk of MS is increased after infectious mononucleosis (IM) due to EBV infection, and MS patients have higher serum titers of anti-EBV antibodies than control populations. Our goal was to identify disease-relevant epitopes of IgG antibodies in MS; to do so, we screened phage-displayed random peptide libraries (12-mer) with total IgG antibodies purified from the brain of a patient with acute MS. We identified and characterized the phage peptides for binding specificity to intrathecal IgG from patients with MS and from controls by ELISA, phage-mediated Immuno-PCR, and isoelectric focusing. We identified two phage peptides that share sequence homologies with EBV nuclear antigens 1 and 2 (EBNA1 and EBNA2), respectively. The specificity of the EBV epitopes found by panning with MS brain IgG was confirmed by ELISA and competitive inhibition assays. Using a highly sensitive phage-mediated immuno-PCR assay, we determined specific bindings of the two EBV epitopes to IgG from CSF from 46 MS and 5 inflammatory control (IC) patients. MS CSF IgG have significantly higher bindings to EBNA1 epitope than to EBNA2 epitope, whereas EBNA1 and EBNA2 did not significantly differ in binding to IC CSF IgG. Further, the EBNA1 epitope was recognized by OCBs from multiple MS CSF as shown in blotting assays with samples separated by isoelectric focusing. The EBNA1 epitope is reactive to MS intrathecal antibodies corresponding to oligoclonal bands. This reinforces the potential role of EBV in the etiology of MS. Antibodies purified from an MS brain plaque were panned by phage display peptide libraries to discern potential antigens. Phage displaying peptide sequences resembling Epstein-Barr Virus Nuclear Antigens 1 & 2 (EBNA1 & 2) epitopes were identified. Antibodies from sera and CSF from other MS patients also reacted to those epitopes. ![]()
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Affiliation(s)
- Zhe Wang
- National Engineering Research Center for Protein Drugs, Beijing, 102206, China
| | - Peter Ge Kennedy
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Cecily Dupree
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Min Wang
- Immunoah Therapeutics, Inc., 12635 East Montview Boulevard, Aurora, CO, 80045, USA
| | - Catherin Lee
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tiffany Pointon
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - T Dianne Langford
- Lewis Katz School of Medicine, Temple University, 3500 N. Broad St, Philadelphia, PA, 19140, USA
| | - Michael W Graner
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Xiaoli Yu
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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11
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Su X, Wang Q, Wen Y, Jiang S, Lu L. Protein- and Peptide-Based Virus Inactivators: Inactivating Viruses Before Their Entry Into Cells. Front Microbiol 2020; 11:1063. [PMID: 32523582 PMCID: PMC7261908 DOI: 10.3389/fmicb.2020.01063] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Infectious diseases caused by human immunodeficiency virus (HIV) and other highly pathogenic enveloped viruses, have threatened the global public health. Most antiviral drugs act as passive defenders to inhibit viral replication inside the cell, while a few of them function as gate keepers to combat viruses outside the cell, including fusion inhibitors, e.g., enfuvirtide, and receptor antagonists, e.g., maraviroc, as well as virus inactivators (including attachment inhibitors). Different from fusion inhibitors and receptor antagonists that must act in the presence of target cells, virus inactivators can actively inactivate cell-free virions in the blood, through interaction with one or more sites in the envelope glycoproteins (Envs) on virions. Notably, a number of protein- and peptide-based virus inactivators (PPVIs) under development are expected to have a better utilization rate than the current antiviral drugs and be safer for in vivo human application than the chemical-based virus inactivators. Here we have highlighted recent progress in developing PPVIs against several important enveloped viruses, including HIV, influenza virus, Zika virus (ZIKV), dengue virus (DENV), and herpes simplex virus (HSV), and the potential use of PPVIs for urgent treatment of infection by newly emerging or re-emerging viruses.
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Affiliation(s)
- Xiaojie Su
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yumei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
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12
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Agarwal G, Gabrani R. Antiviral Peptides: Identification and Validation. Int J Pept Res Ther 2020; 27:149-168. [PMID: 32427225 PMCID: PMC7233194 DOI: 10.1007/s10989-020-10072-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/30/2020] [Accepted: 05/08/2020] [Indexed: 12/26/2022]
Abstract
Despite rapid advances in the human healthcare, the infection caused by certain viruses results in high morbidity and mortality accentuate the importance for development of new antivirals. The existing antiviral drugs are limited, due to their inadequate response, increased rate of resistance and several adverse side effects. Therefore, one of the newly emerging field “peptide-based therapeutics” against viruses is being explored and seems promising. Over the last few years, a lot of scientific effort has been made for the identification of novel and potential peptide-based therapeutics using various advanced technologies. Consequently, there are more than 60 approved peptide drugs available for sale in the market of United States, Europe, Japan, and some Asian countries. Moreover, the number of peptide drugs undergoing the clinical trials is rising gradually year by year. The peptide-based antiviral therapeutics have been approved for the Human immunodeficiency virus (HIV), Influenza virus and Hepatitis virus (B and C). This review enlightens the various peptide sources and the different approaches that have contributed to the search of potential antiviral peptides. These include computational approaches, natural and biological sources (library based high throughput screening) for the identification of lead peptide molecules against their target. Further the applications of few advanced techniques based on combinatorial chemistry and molecular biology have been illustrated to measure the binding parameters such as affinity and kinetics of the screened interacting partners. The employment of these advanced techniques can contribute to investigate antiviral peptide therapeutics for emerging infections.
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Affiliation(s)
- Garima Agarwal
- Department of Biotechnology, Center for Emerging Diseases, Jaypee Institute of Information Technology, Noida, UP 201309 India
| | - Reema Gabrani
- Department of Biotechnology, Center for Emerging Diseases, Jaypee Institute of Information Technology, Noida, UP 201309 India
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13
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Pu J, Wang Q, Xu W, Lu L, Jiang S. Development of Protein- and Peptide-Based HIV Entry Inhibitors Targeting gp120 or gp41. Viruses 2019; 11:v11080705. [PMID: 31374953 PMCID: PMC6722851 DOI: 10.3390/v11080705] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
Application of highly active antiretroviral drugs (ARDs) effectively reduces morbidity and mortality in HIV-infected individuals. However, the emergence of multiple drug-resistant strains has led to the increased failure of ARDs, thus calling for the development of anti-HIV drugs with targets or mechanisms of action different from those of the current ARDs. The first peptide-based HIV entry inhibitor, enfuvirtide, was approved by the U.S. FDA in 2003 for treatment of HIV/AIDS patients who have failed to respond to the current ARDs, which has stimulated the development of several series of protein- and peptide-based HIV entry inhibitors in preclinical and clinical studies. In this review, we highlighted the properties and mechanisms of action for those promising protein- and peptide-based HIV entry inhibitors targeting the HIV-1 gp120 or gp41 and discussed their advantages and disadvantages, compared with the current ARDs.
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Affiliation(s)
- Jing Pu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Qian Wang
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Wei Xu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Lu Lu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China.
| | - Shibo Jiang
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China.
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
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14
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de la Guardia C, Quijada M, Lleonart R. Phage-Displayed Peptides Selected to Bind Envelope Glycoprotein Show Antiviral Activity against Dengue Virus Serotype 2. Adv Virol 2017; 2017:1827341. [PMID: 29081802 PMCID: PMC5610824 DOI: 10.1155/2017/1827341] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/26/2017] [Indexed: 02/06/2023] Open
Abstract
Dengue virus is a growing public health threat that affects hundreds of million peoples every year and leave huge economic and social damage. The virus is transmitted by mosquitoes and the incidence of the disease is increasing, among other causes, due to the geographical expansion of the vector's range and the lack of effectiveness in public health interventions in most prevalent countries. So far, no highly effective vaccine or antiviral has been developed for this virus. Here we employed phage display technology to identify peptides able to block the DENV2. A random peptide library presented in M13 phages was screened with recombinant dengue envelope and its fragment domain III. After four rounds of panning, several binding peptides were identified, synthesized, and tested against the virus. Three peptides were able to block the infectivity of the virus while not being toxic to the target cells. Blind docking simulations were done to investigate the possible mode of binding, showing that all peptides appear to bind domain III of the protein and may be mostly stabilized by hydrophobic interactions. These results are relevant to the development of novel therapeutics against this important virus.
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Affiliation(s)
- Carolina de la Guardia
- Center of Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Building 219, Ciudad del Saber, Apartado 0843-01103, Panamá, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Mario Quijada
- Center of Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Building 219, Ciudad del Saber, Apartado 0843-01103, Panamá, Panama
| | - Ricardo Lleonart
- Center of Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Building 219, Ciudad del Saber, Apartado 0843-01103, Panamá, Panama
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15
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Acharya K, Rashad AA, Moraca F, Klasse PJ, Moore JP, Abrams C, Chaiken I. Recognition of HIV-inactivating peptide triazoles by the recombinant soluble Env trimer, BG505 SOSIP.664. Proteins 2017; 85:843-851. [PMID: 28056499 DOI: 10.1002/prot.25238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/18/2016] [Indexed: 11/08/2022]
Abstract
Peptide triazole (PT) antagonists interact with gp120 subunits of HIV-1 Env trimers to block host cell receptor interactions, trigger gp120 shedding, irreversibly inactivate virus and inhibit infection. Despite these enticing functions, understanding the structural mechanism of PT-Env trimer encounter has been limited. In this work, we combined competition interaction analysis and computational simulation to demonstrate PT binding to the recombinant soluble trimer, BG505 SOSIP.664, a stable variant that resembles native virus spikes in binding to CD4 receptor as well as known conformationally-dependent Env antibodies. Binding specificity and computational modeling fit with encounter through complementary PT pharmacophore Ile-triazolePro-Trp interaction with a 2-subsite cavity in the Env gp120 subunit of SOSIP trimer similar to that in monomeric gp120. These findings argue that PTs are able to recognize and bind a closed prefusion state of Env trimer upon HIV-1 encounter. The results provide a structural model of how PTs exert their function on virion trimeric spike protein and a platform to inform future antagonist design. Proteins 2017; 85:843-851. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kriti Acharya
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania, 19102
| | - Adel A Rashad
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania, 19102
| | - Francesca Moraca
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania, 19104
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065
| | - Cameron Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania, 19104
| | - Irwin Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania, 19102
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16
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Gao P, Sun L, Zhou J, Li X, Zhan P, Liu X. Discovery of novel anti-HIV agents via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry-based approach. Expert Opin Drug Discov 2016; 11:857-71. [PMID: 27400283 DOI: 10.1080/17460441.2016.1210125] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In recent years, a variety of new synthetic methodologies and concepts have been proposed in the search for new pharmaceutical lead structures and optimization. Notably, the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry approach has drawn great attention and has become a powerful tool for the generation of privileged medicinal skeletons in the discovery of anti-HIV agents. This is due to the high degree of reliability, complete specificity (chemoselectivity and regioselectivity), mild conditions, and the biocompatibility of the reactants. AREAS COVERED Herein, the authors describe the progress thus far on the discovery of novel anti-HIV agents via the CuAAC click chemistry-based approach. EXPERT OPINION CuAAC click chemistry is a proven protocol for synthesizing triazole products which could serve as basic pharmacophores, act as replacements of traditional scaffold or substituent modification, be a linker of dual-target or dual-site inhibitors and more for the discovery of novel anti-HIV agents. What's more, it also provides convenience and feasibility for dynamic combinatorial chemistry and in situ screening. It is envisioned that click chemistry will draw more attention and make more contributions in anti-HIV drug discovery in the future.
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Affiliation(s)
- Ping Gao
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Lin Sun
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Junsu Zhou
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Xiao Li
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
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17
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Bailey LD, Kalyana Sundaram RV, Li H, Duffy C, Aneja R, Rosemary Bastian A, Holmes AP, Kamanna K, Rashad AA, Chaiken I. Disulfide Sensitivity in the Env Protein Underlies Lytic Inactivation of HIV-1 by Peptide Triazole Thiols. ACS Chem Biol 2015; 10:2861-73. [PMID: 26458166 DOI: 10.1021/acschembio.5b00381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the mode of action underlying lytic inactivation of HIV-1 virions by peptide triazole thiol (PTT), in particular the relationship between gp120 disulfides and the C-terminal cysteine-SH required for virolysis. Obligate PTT dimer obtained by PTT SH cross-linking and PTTs with serially truncated linkers between pharmacophore isoleucine-ferrocenyltriazole-proline-tryptophan and cysteine-SH were synthesized. PTT variants showed loss of lytic activity but not binding and infection inhibition upon SH blockade. A disproportionate loss of lysis activity vs binding and infection inhibition was observed upon linker truncation. Molecular docking of PTT onto gp120 argued that, with sufficient linker length, the peptide SH could approach and disrupt several alternative gp120 disulfides. Inhibition of lysis by gp120 mAb 2G12, which binds at the base of the V3 loop, as well as disulfide mutational effects, argued that PTT-induced disruption of the gp120 disulfide cluster at the base of the V3 loop is an important step in lytic inactivation of HIV-1. Further, PTT-induced lysis was enhanced after treating virus with reducing agents dithiothreitol and tris (2-carboxyethyl)phosphine. Overall, the results are consistent with the view that the binding of PTT positions the peptide SH group to interfere with conserved disulfides clustered proximal to the CD4 binding site in gp120, leading to disulfide exchange in gp120 and possibly gp41, rearrangement of the Env spike, and ultimately disruption of the viral membrane. The dependence of lysis activity on thiol-disulfide interaction may be related to intrinsic disulfide exchange susceptibility in gp120 that has been reported previously to play a role in HIV-1 cell infection.
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Affiliation(s)
- Lauren D. Bailey
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Ramalingam Venkat Kalyana Sundaram
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
- School
of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Huiyuan Li
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Caitlin Duffy
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Rachna Aneja
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | | | - Andrew P. Holmes
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Kantharaju Kamanna
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Adel A. Rashad
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Irwin Chaiken
- Department
of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
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18
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Peptide triazole inactivators of HIV-1: how do they work and what is their potential? Future Med Chem 2015; 7:2305-10. [PMID: 26599515 DOI: 10.4155/fmc.15.152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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19
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Chen J, Kovacs JM, Peng H, Rits-Volloch S, Lu J, Park D, Zablowsky E, Seaman MS, Chen B. HIV-1 ENVELOPE. Effect of the cytoplasmic domain on antigenic characteristics of HIV-1 envelope glycoprotein. Science 2015; 349:191-5. [PMID: 26113642 DOI: 10.1126/science.aaa9804] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/08/2015] [Indexed: 12/20/2022]
Abstract
A major goal for HIV-1 vaccine development is the production of an immunogen to mimic native, functional HIV-1 envelope trimeric spikes (Env) on the virion surface. We lack a reliable description of a native, functional trimer, however, because of inherent instability and heterogeneity in most preparations. We describe here two conformationally homogeneous Envs derived from difficult-to-neutralize primary isolates. All their non-neutralizing epitopes are fully concealed and independent of their proteolytic processing. Most broadly neutralizing antibodies (bnAbs) recognize these native trimers. Truncation of their cytoplasmic tail has little effect on membrane fusion, but it diminishes binding to trimer-specific bnAbs while exposing non-neutralizing epitopes. These results yield a more accurate antigenic picture than hitherto possible of a genuinely untriggered and functional HIV-1 Env; they can guide effective vaccine development.
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Affiliation(s)
- Jia Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA. Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA
| | - James M Kovacs
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA. Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sophia Rits-Volloch
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jianming Lu
- Codex BioSolutions, Inc., 401 Professional Drive, Gaithersburg, MD 20879, USA
| | - Donghyun Park
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Elise Zablowsky
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA. Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA.
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20
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Rosemary Bastian A, Nangarlia A, Bailey LD, Holmes A, Kalyana Sundaram RV, Ang C, Moreira DRM, Freedman K, Duffy C, Contarino M, Abrams C, Root M, Chaiken I. Mechanism of multivalent nanoparticle encounter with HIV-1 for potency enhancement of peptide triazole virus inactivation. J Biol Chem 2014; 290:529-43. [PMID: 25371202 DOI: 10.1074/jbc.m114.608315] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Entry of HIV-1 into host cells remains a compelling yet elusive target for developing agents to prevent infection. A peptide triazole (PT) class of entry inhibitor has previously been shown to bind to HIV-1 gp120, suppress interactions of the Env protein at host cell receptor binding sites, inhibit cell infection, and cause envelope spike protein breakdown, including gp120 shedding and, for some variants, virus membrane lysis. We found that gold nanoparticle-conjugated forms of peptide triazoles (AuNP-PT) exhibit substantially more potent antiviral effects against HIV-1 than corresponding peptide triazoles alone. Here, we sought to reveal the mechanism of potency enhancement underlying nanoparticle conjugate function. We found that altering the physical properties of the nanoparticle conjugate, by increasing the AuNP diameter and/or the density of PT conjugated on the AuNP surface, enhanced potency of infection inhibition to impressive picomolar levels. Further, compared with unconjugated PT, AuNP-PT was less susceptible to reduction of antiviral potency when the density of PT-competent Env spikes on the virus was reduced by incorporating a peptide-resistant mutant gp120. We conclude that potency enhancement of virolytic activity and corresponding irreversible HIV-1 inactivation of PTs upon AuNP conjugation derives from multivalent contact between the nanoconjugates and metastable Env spikes on the HIV-1 virus. The findings reveal that multispike engagement can exploit the metastability built into virus the envelope to irreversibly inactivate HIV-1 and provide a conceptual platform to design nanoparticle-based antiviral agents for HIV-1 specifically and putatively for metastable enveloped viruses generally.
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Affiliation(s)
- Arangassery Rosemary Bastian
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, the School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104
| | - Aakansha Nangarlia
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, the School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104
| | - Lauren D Bailey
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
| | - Andrew Holmes
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
| | - R Venkat Kalyana Sundaram
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, the School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104
| | - Charles Ang
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, the School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104
| | - Diogo R M Moreira
- the Fundação Oswaldo Cruz, Centro de Pesquisas Goncalo Moniz, Salvador-BA 40296-710, Brazil
| | - Kevin Freedman
- the Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, and
| | - Caitlin Duffy
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
| | - Mark Contarino
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
| | - Cameron Abrams
- the Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, and
| | - Michael Root
- the Department of Biochemistry and Molecular Biology, Jefferson University, Philadelphia, Pennsylvania 19107
| | - Irwin Chaiken
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102,
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21
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A phage-displayed peptide recognizing porcine aminopeptidase N is a potent small molecule inhibitor of PEDV entry. Virology 2014; 456-457:20-7. [PMID: 24889221 PMCID: PMC7112085 DOI: 10.1016/j.virol.2014.01.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 12/28/2013] [Accepted: 01/16/2014] [Indexed: 12/21/2022]
Abstract
Three phage-displayed peptides designated H, S and F that recognize porcine aminopeptidase N (pAPN), the cellular receptor of porcine transmissible gastroenteritis virus (TGEV) were able to inhibit cell infection by TGEV. These same peptides had no inhibitory effects on infection of Vero cells by porcine epidemic diarrhea virus (PEDV). However, when PEDV, TGEV and porcine pseudorabies virus were incubated with peptide H (HVTTTFAPPPPR), only infection of Vero cells by PEDV was inhibited. Immunofluoresence assays indicated that inhibition of PEDV infection by peptide H was independent of pAPN. Western blots demonstrated that peptide H interacted with PEDV spike protein and that pre-treatment of PEDV with peptide H led to a higher inhibition than synchronous incubation with cells. These results indicate direct interaction with the virus is necessary to inhibit infectivity. Temperature shift assays demonstrated that peptide H inhibited pre-attachment of the virus to the cells.
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22
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Roitburd-Berman A, Dela G, Kaplan G, Lewis GK, Gershoni JM. Allosteric induction of the CD4-bound conformation of HIV-1 Gp120. Retrovirology 2013; 10:147. [PMID: 24304511 PMCID: PMC4235218 DOI: 10.1186/1742-4690-10-147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/25/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND HIV-1 infection of target cells is mediated via the binding of the viral envelope protein, gp120, to the cell surface receptor CD4. This interaction leads to conformational rearrangements in gp120 forming or revealing CD4 induced (CD4i) epitopes which are critical for the subsequent recognition of the co-receptor required for viral entry. The CD4-bound state of gp120 has been considered a potential immunogen for HIV-1 vaccine development. Here we report on an alternative means to induce gp120 into the CD4i conformation. RESULTS Combinatorial phage display peptide libraries were screened against HIV-1 gp120 and short (14aa) peptides were selected that bind the viral envelope and allosterically induce the CD4i conformation. The lead peptide was subsequently systematically optimized for higher affinity as well as more efficient inductive activity. The peptide:gp120 complex was scrutinized with a panel of neutralizing anti-gp120 monoclonal antibodies and CD4 itself, illustrating that peptide binding does not interfere with or obscure the CD4 binding site. CONCLUSIONS Two surfaces of gp120 are considered targets for the development of cross neutralizing antibodies against HIV-1; the CD4 binding site and CD4i epitopes. By implementing novel peptides that allosterically induce the CD4i epitopes we have generated a viral envelope that presents both of these surfaces simultaneously.
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Affiliation(s)
| | | | | | | | - Jonathan M Gershoni
- Department of Cell Research and Immunology, George S, Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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23
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Li H, Aneja R, Chaiken I. Click chemistry in peptide-based drug design. Molecules 2013; 18:9797-817. [PMID: 23959192 PMCID: PMC4155329 DOI: 10.3390/molecules18089797] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 12/27/2022] Open
Abstract
Click chemistry is an efficient and chemoselective synthetic method for coupling molecular fragments under mild reaction conditions. Since the advent in 2001 of methods to improve stereochemical conservation, the click chemistry approach has been broadly used to construct diverse chemotypes in both chemical and biological fields. In this review, we discuss the application of click chemistry in peptide-based drug design. We highlight how triazoles formed by click reactions have been used for mimicking peptide and disulfide bonds, building secondary structural components of peptides, linking functional groups together, and bioconjugation. The progress made in this field opens the way for synthetic approaches to convert peptides with promising functional leads into structure-minimized and more stable forms.
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Affiliation(s)
- Huiyuan Li
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, 245 N 15th Street, New College Building, Room 11102, Philadelphia, PA 19102, USA.
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24
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Emileh A, Tuzer F, Yeh H, Umashankara M, Moreira DRM, Lalonde JM, Bewley CA, Abrams CF, Chaiken IM. A model of peptide triazole entry inhibitor binding to HIV-1 gp120 and the mechanism of bridging sheet disruption. Biochemistry 2013; 52:2245-61. [PMID: 23470147 DOI: 10.1021/bi400166b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Peptide triazole (PT) entry inhibitors prevent HIV-1 infection by blocking the binding of viral gp120 to both the HIV-1 receptor and the coreceptor on target cells. Here, we used all-atom explicit solvent molecular dynamics (MD) to propose a model for the encounter complex of the peptide triazoles with gp120. Saturation transfer difference nuclear magnetic resonance (STD NMR) and single-site mutagenesis experiments were performed to test the simulation results. We found that docking of the peptide to a conserved patch of residues lining the "F43 pocket" of gp120 in a bridging sheet naïve gp120 conformation of the glycoprotein led to a stable complex. This pose prevents formation of the bridging sheet minidomain, which is required for receptor-coreceptor binding, providing a mechanistic basis for dual-site antagonism of this class of inhibitors. Burial of the peptide triazole at the gp120 inner domain-outer domain interface significantly contributed to complex stability and rationalizes the significant contribution of hydrophobic triazole groups to peptide potency. Both the simulation model and STD NMR experiments suggest that the I-X-W [where X is (2S,4S)-4-(4-phenyl-1H-1,2,3-triazol-1-yl)pyrrolidine] tripartite hydrophobic motif in the peptide is the major contributor of contacts at the gp120-PT interface. Because the model predicts that the peptide Trp side chain hydrogen bonding with gp120 S375 contributes to the stability of the PT-gp120 complex, we tested this prediction through analysis of peptide binding to gp120 mutant S375A. The results showed that a peptide triazole KR21 inhibits S375A with 20-fold less potency than WT, consistent with predictions of the model. Overall, the PT-gp120 model provides a starting point for both the rational design of higher-affinity peptide triazoles and the development of structure-minimized entry inhibitors that can trap gp120 into an inactive conformation and prevent infection.
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Affiliation(s)
- Ali Emileh
- Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
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25
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Kamanna K, Aneja R, Duffy C, Kubinski P, Moreira DR, Bailey LD, McFadden K, Schön A, Holmes A, Tuzer F, Contarino M, Freire E, Chaiken IM. Non-natural peptide triazole antagonists of HIV-1 envelope gp120. ChemMedChem 2013; 8:322-8. [PMID: 23239505 PMCID: PMC3810028 DOI: 10.1002/cmdc.201200422] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/08/2012] [Indexed: 11/06/2022]
Abstract
We investigated the derivation of non-natural peptide triazole dual receptor site antagonists of HIV-1 Env gp120 to establish a pathway for developing peptidomimetic antiviral agents. Previously we found that the peptide triazole HNG-156 [R-I-N-N-I-X-W-S-E-A-M-M-CONH(2), in which X=ferrocenyltriazole-Pro (FtP)] has nanomolar binding affinity to gp120, inhibits gp120 binding to CD4 and the co-receptor surrogate mAb 17b, and has potent antiviral activity in cell infection assays. Furthermore, truncated variants of HNG-156, typified by UM-24 (Cit-N-N-I-X-W-S-CONH(2)) and containing the critical central stereospecific (L)X-(L)W cluster, retain the functional characteristics of the parent peptide triazole. In the current work, we examined the possibility of replacing natural with unnatural residue components in UM-24 to the greatest extent possible. The analogue with the critical "hot spot" residue Trp 6 replaced with L-3-benzothienylalanine (Bta) (KR-41), as well as a completely non-natural analogue containing D-amino acid substitutions outside the central cluster (KR-42, (D)Cit-(D)N-(D)N-(D)I-X-Bta-(D)S-CONH(2)), retained the dual receptor site antagonism/antiviral activity signature. The results define differential functional roles of subdomains within the peptide triazole and provide a structural basis for the design of metabolically stable peptidomimetic inhibitors of HIV-1 Env gp120.
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Affiliation(s)
- Kantharaju Kamanna
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Rachna Aneja
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Caitlin Duffy
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Pamela Kubinski
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Diogo Rodrigo Moreira
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Lauren D Bailey
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Karyn McFadden
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218 (USA)
| | - Andrew Holmes
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Ferit Tuzer
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Mark Contarino
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218 (USA)
| | - Irwin M Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245N, 15 Street, New College Building, Room 11302, Philadelphia, PA, 19102 (USA)
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26
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Tuzer F, Madani N, Kamanna K, Zentner I, LaLonde J, Holmes A, Upton E, Rajagopal S, McFadden K, Contarino M, Sodroski J, Chaiken I. HIV-1 Env gp120 structural determinants for peptide triazole dual receptor site antagonism. Proteins 2012; 81:271-90. [PMID: 23011758 DOI: 10.1002/prot.24184] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/18/2012] [Accepted: 09/03/2012] [Indexed: 11/09/2022]
Abstract
Despite advances in HIV therapy, viral resistance and side-effects with current drug regimens require targeting new components of the virus. Dual antagonist peptide triazoles (PT) are a novel class of HIV-1 inhibitors that specifically target the gp120 component of the viral spike and inhibit its interaction with both of its cell surface protein ligands, namely the initial receptor CD4 and the co-receptor (CCR5/CXCR4), thus preventing viral entry. Following an initial survey of 19 gp120 alanine mutants by ELISA, we screened 11 mutants for their importance in binding to, and inhibition by the PT KR21 using surface plasmon resonance. Key mutants were purified and tested for their effects on the peptide's affinity and its ability to inhibit binding of CD4 and the co-receptor surrogate mAb 17b. Effects of the mutations on KR21 viral neutralization were measured by single-round cell infection assays. Two mutations, D474A and T257A, caused large-scale loss of KR21 binding, as well as losses in both CD4/17b and viral inhibition by KR21. A set of other Ala mutants revealed more moderate losses in direct binding affinity and inhibition sensitivity to KR21. The cluster of sensitive residues defines a PT functional epitope. This site is in a conserved region of gp120 that overlaps the CD4 binding site and is distant from the co-receptor/17b binding site, suggesting an allosteric mode of inhibition for the latter. The arrangement and sequence conservation of the residues in the functional epitope explain the breadth of antiviral activity, and improve the potential for rational inhibitor development.
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Affiliation(s)
- Ferit Tuzer
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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27
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Delhalle S, Schmit JC, Chevigné A. Phages and HIV-1: from display to interplay. Int J Mol Sci 2012; 13:4727-4794. [PMID: 22606007 PMCID: PMC3344243 DOI: 10.3390/ijms13044727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/26/2012] [Accepted: 03/30/2012] [Indexed: 11/16/2022] Open
Abstract
The complex hide-and-seek game between HIV-1 and the host immune system has impaired the development of an efficient vaccine. In addition, the high variability of the virus impedes the long-term control of viral replication by small antiviral drugs. For more than 20 years, phage display technology has been intensively used in the field of HIV-1 to explore the epitope landscape recognized by monoclonal and polyclonal HIV-1-specific antibodies, thereby providing precious data about immunodominant and neutralizing epitopes. In parallel, biopanning experiments with various combinatorial or antibody fragment libraries were conducted on viral targets as well as host receptors to identify HIV-1 inhibitors. Besides these applications, phage display technology has been applied to characterize the enzymatic specificity of the HIV-1 protease. Phage particles also represent valuable alternative carriers displaying various HIV-1 antigens to the immune system and eliciting antiviral responses. This review presents and summarizes the different studies conducted with regard to the nature of phage libraries, target display mode and biopanning procedures.
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Affiliation(s)
- Sylvie Delhalle
- Laboratory of Retrovirology, CRP-Sante, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg; E-Mails: (J.-C.S.); (A.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +352-26970211; Fax: +352-26970221
| | - Jean-Claude Schmit
- Laboratory of Retrovirology, CRP-Sante, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg; E-Mails: (J.-C.S.); (A.C.)
- Service National des Maladies Infectieuses, Centre Hospitalier Luxembourg, 4, rue E. Barblé, L-1210 Luxembourg, Luxembourg
| | - Andy Chevigné
- Laboratory of Retrovirology, CRP-Sante, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg; E-Mails: (J.-C.S.); (A.C.)
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28
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Antiviral breadth and combination potential of peptide triazole HIV-1 entry inhibitors. Antimicrob Agents Chemother 2011; 56:1073-80. [PMID: 22083481 DOI: 10.1128/aac.05555-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first stage of human immunodeficiency virus type 1 (HIV-1) infection involves the fusion of viral and host cellular membranes mediated by viral envelope glycoprotein gp120. Inhibitors that specifically target gp120 are gaining increased attention as therapeutics or preventatives to prevent the spread of HIV-1. One promising new group of inhibitors is the peptide triazoles, which bind to gp120 and simultaneously block its interaction with both CD4 and the coreceptor. In this study, we assessed the most potent peptide triazole, HNG-156, for inhibitory breadth, cytotoxicity, and efficacy, both alone and in combination with other antiviral compounds, against HIV-1. HNG-156 inhibited a panel of 16 subtype B and C isolates of HIV-1 in a single-round infection assay. Inhibition of cell infection by replication-competent clinical isolates of HIV-1 was also observed with HNG-156. We found that HNG-156 had a greater than predicted effect when combined with several other entry inhibitors or the reverse transcriptase inhibitor tenofovir. Overall, we find that HNG-156 is noncytotoxic, has a broad inhibition profile, and provides a positive combination with several inhibitors of the HIV-1 life cycle. These results support the pursuit of efficacy and toxicity analyses in more advanced cell and animal models to develop peptide triazole family inhibitors of HIV-1 into antagonists of HIV-1 infection.
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29
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Celigoy J, Ramirez B, Tao L, Rong L, Yan L, Feng YR, Quinnan GV, Broder CC, Caffrey M. Probing the HIV gp120 envelope glycoprotein conformation by NMR. J Biol Chem 2011; 286:23975-81. [PMID: 21592971 DOI: 10.1074/jbc.m111.251025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The HIV envelope glycoprotein gp120 plays a critical role in virus entry, and thus, its structure is of extreme interest for the development of novel therapeutics and vaccines. To date, high resolution structural information about gp120 in complex with gp41 has proven intractable. In this study, we characterize the structural properties of gp120 in the presence and absence of gp41 domains by NMR. Using the peptide probe 12p1 (sequence, RINNIPWSEAMM), which was identified previously as an entry inhibitor that binds to gp120, we identify atoms of 12p1 in close contact with gp120 in the monomeric and trimeric states. Interestingly, the binding mode of 12p1 with gp120 is similar for clades B and C. In addition, we show a subtle difference in the binding mode of 12p1 in the presence of gp41 domains, i.e. the trimeric state, which we interpret as small differences in the gp120 structure in the presence of gp41.
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Affiliation(s)
- Jessica Celigoy
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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30
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Caffrey M. HIV envelope: challenges and opportunities for development of entry inhibitors. Trends Microbiol 2011; 19:191-7. [PMID: 21377881 PMCID: PMC3071980 DOI: 10.1016/j.tim.2011.02.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 01/29/2011] [Accepted: 02/03/2011] [Indexed: 01/24/2023]
Abstract
The HIV envelope proteins glycoprotein 120 (gp120) and glycoprotein 41 (gp41) play crucial roles in HIV entry, therefore they are of extreme interest in the development of novel therapeutics. Studies using diverse methods, including structural biology and mutagenesis, have resulted in a detailed model for envelope-mediated entry, which consists of multiple conformations, each a potential target for therapeutic intervention. In this review, the challenges, strategies and progress to date for developing novel entry inhibitors directed at disrupting HIV gp120 and gp41 function are discussed.
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Affiliation(s)
- Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL 60607, USA.
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31
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Umashankara M, McFadden K, Zentner I, Schön A, Rajagopal S, Tuzer F, Kuriakose SA, Contarino M, Lalonde J, Freire E, Chaiken I. The active core in a triazole peptide dual-site antagonist of HIV-1 gp120. ChemMedChem 2011; 5:1871-9. [PMID: 20677318 DOI: 10.1002/cmdc.201000222] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In an effort to identify broadly active inhibitors of HIV-1 entry into host cells, we previously reported a family of dodecamer triazole-peptide conjugates with nanomolar affinity for the viral surface protein gp120. This peptide class exhibits potent antiviral activity and the capacity to simultaneously inhibit interaction of the viral envelope protein with both CD4 and co-receptor. In this investigation, we minimized the structural complexity of the lead triazole inhibitor HNG-156 (peptide 1) to explore the limits of the pharmacophore that enables dual antagonism and to improve opportunities for peptidomimetic design. Truncations of both carboxy- and amino-terminal residues from the parent 12-residue peptide 1 were found to have minimal effects on both affinity and antiviral activity. In contrast, the central triazole(Pro)-Trp cluster at residues 6 and 7 with ferrocenyl-triazole(Pro) (Ftp) was found to be critical for bioactivity. Amino-terminal residues distal to the central triazole(Pro)-Trp sequence tolerated decreasing degrees of side chain variation upon approaching the central cluster. A peptide fragment containing residues 3-7 (Asn-Asn-Ile-Ftp-Trp) exhibited substantial direct binding affinity, antiviral potency, dual receptor site antagonism, and induction of gp120 structuring, all properties that define the functional signature of the parent compound 1. This active core contains a stereochemically specific hydrophobic triazole(Pro)-Trp cluster, with a short N-terminal peptide extension providing groups for potential main chain and side chain hydrogen bonding. The results of this work argue that the pharmacophore for dual antagonism is structurally limited, thereby enhancing the potential to develop minimized peptidomimetic HIV-1 entry inhibitors that simultaneously suppress binding of envelope protein to both of its host cell receptors. The results also argue that the target epitope on gp120 is relatively small, pointing to a localized allosteric inhibition site in the HIV-1 envelope that could be targeted for small-molecule inhibitor discovery.
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Affiliation(s)
- Muddegowda Umashankara
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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32
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Cerutti N, Mendelow BV, Napier GB, Papathanasopoulos MA, Killick M, Khati M, Stevens W, Capovilla A. Stabilization of HIV-1 gp120-CD4 receptor complex through targeted interchain disulfide exchange. J Biol Chem 2010; 285:25743-52. [PMID: 20538591 PMCID: PMC2919137 DOI: 10.1074/jbc.m110.144121] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 06/09/2010] [Indexed: 12/17/2022] Open
Abstract
HIV-1 enters cells via interaction between the trimeric envelope (Env) glycoprotein gp120/gp41 and the host cell surface receptor molecule CD4. The requirement of CD4 for viral entry has rationalized the development of recombinant CD4-based proteins as competitive viral attachment inhibitors and immunotherapeutic agents. In this study, we describe a novel recombinant CD4 protein designed to bind gp120 through a targeted disulfide-exchange mechanism. According to structural models of the gp120-CD4 receptor complex, substitution of Ser(60) on the CD4 domain 1 alpha-helix with Cys positions a thiol in proximity of the gp120 V1/V2 loop disulfide (Cys(126)-Cys(196)), satisfying the stereochemical and geometric conditions for redox exchange between CD4 Cys(60) and gp120 Cys(126), and the consequent formation of an interchain disulfide bond. In this study, we provide experimental evidence for this effect by describing the expression, purification, refolding, receptor binding and antiviral activity analysis of a recombinant two-domain CD4 variant containing the S60C mutation (2dCD4-S60C). We show that 2dCD4-S60C binds HIV-1 gp120 with a significantly higher affinity than wild-type protein under conditions that facilitate disulfide exchange and that this translates into a corresponding increase in the efficacy of CD4-mediated viral entry inhibition. We propose that targeted redox exchange between conserved gp120 disulfides and nucleophilic moieties positioned strategically on CD4 (or CD4-like scaffolds) conceptualizes a new strategy in the development of high affinity HIV-1 Env ligands, with important implications for therapy and vaccine development. More generally, this chalcogen substitution approach provides a general means of stabilizing receptor-ligand complexes where the structural and biophysical conditions for disulfide exchange are satisfied.
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Affiliation(s)
- Nichole Cerutti
- Elevation Biotech, 8 Blackwood Avenue, Parktown 2193, Johannesburg, and
| | - Barry V. Mendelow
- From the Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg
| | - Grant B. Napier
- Elevation Biotech, 8 Blackwood Avenue, Parktown 2193, Johannesburg, and
| | - Maria A. Papathanasopoulos
- From the Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg
- Elevation Biotech, 8 Blackwood Avenue, Parktown 2193, Johannesburg, and
| | - Mark Killick
- Elevation Biotech, 8 Blackwood Avenue, Parktown 2193, Johannesburg, and
| | - Makobetsa Khati
- the Council for Scientific and Industrial Research, P. O. Box 395, Pretoria 0001, South Africa
| | - Wendy Stevens
- From the Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg
| | - Alexio Capovilla
- From the Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg
- Elevation Biotech, 8 Blackwood Avenue, Parktown 2193, Johannesburg, and
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33
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Development of a Novel Bioinformatics Tool for In Silico Validation of Protein Interactions. J Biomed Biotechnol 2010; 2010:670125. [PMID: 20625507 PMCID: PMC2896714 DOI: 10.1155/2010/670125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 03/10/2010] [Accepted: 03/30/2010] [Indexed: 11/17/2022] Open
Abstract
Protein interactions are crucial in most biological processes. Several in silico methods have been recently developed to predict them. This paper describes a bioinformatics method that combines sequence similarity and structural information to support experimental studies on protein interactions. Given a target protein, the approach selects the most likely interactors among the candidates revealed by experimental techniques, but not yet in vivo validated. The sequence and the structural information of the in vivo confirmed proteins and complexes are exploited to evaluate the candidate interactors. Finally, a score is calculated to suggest the most likely interactors of the target protein. As an example, we searched for GRB2 interactors. We ranked a set of 46 candidate interactors by the presented method. These candidates were then reduced to 21, through a score threshold chosen by means of a cross-validation strategy. Among them, the isoform 1 of MAPK14 was in silico confirmed as a GRB2 interactor. Finally, given a set of already confirmed interactors of GRB2, the accuracy and the precision of the approach were 75% and 86%, respectively. In conclusion, the proposed method can be conveniently exploited to select the proteins to be experimentally investigated within a set of potential interactors.
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34
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Gopi H, Cocklin S, Pirrone V, McFadden K, Tuzer F, Zentner I, Ajith S, Baxter S, Jawanda N, Krebs FC, Chaiken IM. Introducing metallocene into a triazole peptide conjugate reduces its off-rate and enhances its affinity and antiviral potency for HIV-1 gp120. J Mol Recognit 2009; 22:169-74. [PMID: 18498083 DOI: 10.1002/jmr.892] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this work, we identified a high affinity and potency metallocene-containing triazole peptide conjugate that suppresses the interactions of HIV-1 envelope gp120 at both its CD4 and co-receptor binding sites. The ferrocene-peptide conjugate, HNG-156, was formed by an on-resin copper-catalysed [2+3] cycloaddition reaction. Surface plasmon resonance interaction analysis revealed that, compared to a previously reported phenyl-containing triazole conjugate HNG-105 (105), peptide 156 had a higher direct binding affinity for several subtypes of HIV-1 gp120 due mainly to the decreased dissociation rate of the conjugate-gp120 complex. The ferrocene triazole conjugate bound to gp120 of both clade A (92UG037-08) and clade B (YU-2 and SF162) virus subtypes with nanomolar KD in direct binding and inhibited the binding of gp120 to soluble CD4 and to antibodies that bind to HIV-1YU-2 gp120 at both the CD4 binding site and CD4-induced binding sites. HNG-156 showed a close-to nanomolar IC50 for inhibiting cell infection by HIV-1BaL whole virus. The dual receptor site antagonist activity and potency of HNG-156 make it a promising viral envelope inhibitor lead for developing anti-HIV-1 treatments.
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Affiliation(s)
- Hosahudya Gopi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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35
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Kaushik-Basu N, Basu A, Harris D. Peptide inhibition of HIV-1: current status and future potential. BioDrugs 2008; 22:161-75. [PMID: 18481899 DOI: 10.2165/00063030-200822030-00003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
More than 2 decades of intensive research has focused on defining replication mechanisms of HIV type 1 (HIV-1), the etiologic agent of AIDS. The delineation of strategies for combating this viral infection has yielded many innovative approaches toward this end. HIV-1 is a lentivirus in the family retroviridae that is relatively small with regard to both structure and genome size, having a diploid RNA genome of approximately 9 kb, with only three major genes and several gene products resulting from alternate splicing and translational frameshifting. Most marketed drugs for treating AIDS are inhibitors of HIV-1 reverse transcriptase or protease enzymes, but new targets include the integrase enzyme, cell surface interactions that facilitate viral entry, and also virus particle maturation and assembly. The emergence of drug-resistant variants of HIV-1 has been the main impediment to successful treatment of AIDS. Thus, there is a pressing need to develop novel treatment strategies targeting multiple stages of the virus life-cycle. Research efforts aimed at developing successful means for combating HIV-1 infection have included development of peptide inhibitors of HIV-1. This article summarizes past and current endeavors in the development of peptides that inhibit replication of HIV-1 and the role of peptide inhibitors in the search for new anti-HIV drugs.
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Affiliation(s)
- Neerja Kaushik-Basu
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA.
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36
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Gopi H, Umashankara M, Pirrone V, LaLonde J, Madani N, Tuzer F, Baxter S, Zentner I, Cocklin S, Jawanda N, Miller SR, Schön A, Klein JC, Freire E, Krebs FC, Smith AB, Sodroski J, Chaiken I. Structural determinants for affinity enhancement of a dual antagonist peptide entry inhibitor of human immunodeficiency virus type-1. J Med Chem 2008; 51:2638-47. [PMID: 18402432 PMCID: PMC2921370 DOI: 10.1021/jm070814r] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-activity correlations were investigated for substituted peptide conjugates that function as dual receptor site antagonists of HIV-1 gp120. A series of peptide conjugates were constructed via click reaction of both aryl and alkyl acetylenes with an internally incorporated azidoproline 6 derived from the parent peptide 1 (12p1, RINNIPWSEAMM). Compared to 1, many of these conjugates were found to exhibit several orders of magnitude increase in both affinity for HIV-1 gp120 and inhibition potencies at both the CD4 and coreceptor binding sites of gp120. We sought to determine structural factors in the added triazole grouping responsible for the increased binding affinity and antiviral activity of the dual inhibitor conjugates. We measured peptide conjugate potencies in both kinetic and cell infection assays. High affinity was sterically specific, being exhibited by the cis- but not the trans-triazole. The results demonstrate that aromatic, hydrophobic, and steric features in the residue 6 side-chain are important for increased affinity and inhibition. Optimizing these features provides a basis for developing gp120 dual inhibitors into peptidomimetic and increasingly smaller molecular weight entry antagonist leads.
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Affiliation(s)
- Hosahudya Gopi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - M. Umashankara
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, and Center for Molecular Therapeutics, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Judith LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA
| | - Navid Madani
- Dana-Farber Cancer Institute, Division of AIDS, Harvard Medical School, Boston, MA 02115
| | - Ferit Tuzer
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Sabine Baxter
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Isaac Zentner
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Simon Cocklin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Navneet Jawanda
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Shendra R. Miller
- Department of Microbiology and Immunology, and Center for Molecular Therapeutics, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Jeffrey C. Klein
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Fred C. Krebs
- Department of Microbiology and Immunology, and Center for Molecular Therapeutics, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Joseph Sodroski
- Dana-Farber Cancer Institute, Division of AIDS, Harvard Medical School, Boston, MA 02115
| | - Irwin Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
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McFadden K, Cocklin S, Gopi H, Baxter S, Ajith S, Mahmood N, Shattock R, Chaiken I. A recombinant allosteric lectin antagonist of HIV-1 envelope gp120 interactions. Proteins 2007; 67:617-29. [PMID: 17348010 DOI: 10.1002/prot.21295] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The first, critical stage of HIV-1 infection is fusion of viral and host cellular membranes initiated by a viral envelope glycoprotein gp120. We evaluated the potential to form a chimeric protein entry inhibitor that combines the action of two gp120-targeting molecules, an allosteric peptide inhibitor 12p1 and a higher affinity carbohydrate-binding protein cyanovirin (CVN). In initial mixing experiments, we demonstrated that the inhibitors do not interfere with each other and instead show functional synergy in inhibiting viral cell infection. Based on this, we created a chimera, termed L5, with 12p1 fused to the C-terminal domain of CVN through a linker of five penta-peptide repeats. L5 revealed the same broad specificity as CVN for gp120 from a variety of clades and tropisms. By comparison to CVN, the L5 chimera exhibited substantially increased inhibition of gp120 binding to receptor CD4, coreceptor surrogate mAb 17b and gp120 antibody F105. These binding inhibition effects by the chimera reflected both the high affinity of the CVN domain and the allosteric action of the 12p1 domain. The results open up the possibility to form high potency chimeras, as well as noncovalent mixtures, as leads for HIV-1 envelope antagonism that can overcome potency limits and potential virus mutational resistance for either 12p1 or CVN alone.
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Affiliation(s)
- Karyn McFadden
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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Cao J, Liao XL, Wu SM, Zhao P, Zhao LJ, Wu WB, Qi ZT. Selection of a phage-displayed peptide recognized by monoclonal antibody directed blocking the site of hepatitis C virus E2 for human CD81. J Microbiol Methods 2007; 68:601-4. [PMID: 17178166 DOI: 10.1016/j.mimet.2006.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Revised: 11/14/2006] [Accepted: 11/17/2006] [Indexed: 11/24/2022]
Abstract
The human CD81 (hCD81) molecule has been identified as a putative receptor for hepatitis C virus (HCV). HCV envelope glycoprotein 2 (E2) most likely plays a pivotal role in binding to host cells by interacting with the hCD81 molecule. In this study, a phage-displayed peptide library was used to select small peptides with anti-hCD81 monoclonal antibody JS-81. The output/input ratio of phages increased about 91 fold after the third round of selection. Eight of the 30 phage clones selected from the phage library showed specific binding to the anti-hCD81 by enzyme linked immunosorbent assay (ELISA). Competitive inhibition test further demonstrated that HCV E2 could significantly inhibit the binding of a positive phage clone to anti-hCD81 JS-81. Exogenous small peptide ATWVCGPCT contained by the positive phage clones showed aligned with the hCD81 sequence from 153-161 by sequence analyses. These results suggest that the selected ATWVCGPCT is a novel hCD81-like small peptide, which can block the binding site of HCV E2 for hCD81. It may be of further application on development of antiviral agents targeting the stage of HCV entry.
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Affiliation(s)
- J Cao
- Department of Microbiology, State Key Laboratory of Medical Immunology, Second Military Medical University, Shanghai 200433, China.
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39
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Cocklin S, Gopi H, Querido B, Nimmagadda M, Kuriakose S, Cicala C, Ajith S, Baxter S, Arthos J, Martín-García J, Chaiken IM. Broad-spectrum anti-human immunodeficiency virus (HIV) potential of a peptide HIV type 1 entry inhibitor. J Virol 2007; 81:3645-8. [PMID: 17251295 PMCID: PMC1866025 DOI: 10.1128/jvi.01778-06] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The AIDS epidemic continues to spread at an alarming rate worldwide, especially in developing countries. One approach to solving this problem is the generation of anti-human immunodeficiency virus (HIV) compounds with inhibition spectra broad enough to include globally prevailing forms of the virus. We have examined the HIV type 1 (HIV-1) envelope specificity of a recently identified entry inhibitor candidate, HNG-105, using surface plasmon resonance spectroscopy and pseudovirus inhibition assays. The combined results suggest that the HNG-105 molecule may be effective across the HIV-1 subtypes, and they highlight its potential as a lead for developing therapeutic and microbicidal agents to help combat the spread of AIDS.
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Affiliation(s)
- Simon Cocklin
- Drexel University College of Medicine, 11313 New College Building, 245 N. 15th St., Philadelphia, PA 19102, USA.
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40
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Gopi HN, Tirupula KC, Baxter S, Ajith S, Chaiken IM. Click chemistry on azidoproline: high-affinity dual antagonist for HIV-1 envelope glycoprotein gp120. ChemMedChem 2006; 1:54-7. [PMID: 16892335 DOI: 10.1002/cmdc.200500037] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hosahudya N Gopi
- Department of Biochemistry and Molecular Biology and A. J. Drexel Institute of Basic and Applied Protein Science, 11102 New College Building, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102, USA
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41
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Affiliation(s)
- Keith Bupp
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Pisacataway, New Jersey 08854, USA
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42
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Sun W, Hu Y, Gong J, Zhu C, Zhu B. Identification of beta-lactamase inhibitory peptide using yeast two-hybrid system. BIOCHEMISTRY (MOSCOW) 2006; 70:753-60. [PMID: 16097938 DOI: 10.1007/s10541-005-0180-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Random oligonucleotide fragments were designed and amplified by PCR and fused with the activating domain of pGAD424 to construct a random peptide library. The DNA fragment encoding beta-lactamase was fused with the binding domain of pGBT9(+2). Subsequently, using yeast two-hybrid system we found two positive clones encoding peptides P1 and P2 that have the ability to bind beta-lactamase in vivo. The genes encoding P1 and P2 were cloned into pGEX-4T-1. GST-peptide fusion proteins were expressed in Escherichia coli and isolated by glutathione-Sepharose 4B affinity chromatography. Finally, P1 and P2 were cleaved from the fusion protein with thrombin and purified by ultrafiltration. Inhibition assay of peptides with beta-lactamase in vitro indicated that only P1 has the ability to inhibit beta-lactamase.
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Affiliation(s)
- Wei Sun
- School of Medicine, Tongji University, Shanghai, 200092, China.
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43
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Gardiner L, Coyle BJ, Chan WC, Soultanas P. Discovery of antagonist peptides against bacterial helicase-primase interaction in B. stearothermophilus by reverse yeast three-hybrid. ACTA ACUST UNITED AC 2005; 12:595-604. [PMID: 15911380 PMCID: PMC3035177 DOI: 10.1016/j.chembiol.2005.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 03/21/2005] [Accepted: 04/04/2005] [Indexed: 11/28/2022]
Abstract
Developing small-molecule antagonists against protein-protein interactions will provide powerful tools for mechanistic/functional studies and the discovery of new antibacterials. We have developed a reverse yeast three-hybrid approach that allows high-throughput screening for antagonist peptides against essential protein-protein interactions. We have applied our methodology to the essential bacterial helicase-primase interaction in Bacillus stearothermophilus and isolated a unique antagonist peptide. This peptide binds to the primase, thus excluding the helicase and inhibiting an essential interaction in bacterial DNA replication. We provide proof of principle that our reverse yeast three-hybrid method is a powerful "one-step" screen tool for direct high-throughput antagonist peptide selection against any protein-protein interaction detectable by traditional yeast two-hybrid systems. Such peptides will provide useful "leads" for the development of new antibacterials.
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Affiliation(s)
- Laurence Gardiner
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Barry J. Coyle
- Institute of Infection, Immunity, & Inflammation, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Weng C. Chan
- Institute of Infection, Immunity, & Inflammation, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Panos Soultanas
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- Correspondence:
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44
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Loregian A, Palù G. Disruption of protein-protein interactions: towards new targets for chemotherapy. J Cell Physiol 2005; 204:750-62. [PMID: 15880642 DOI: 10.1002/jcp.20356] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein-protein interactions play a key role in various mechanisms of cellular growth and differentiation, and in the replication of pathogen organisms in host cells. Thus, inhibition of these interactions is a promising novel approach for rational drug design against a wide number of cellular and microbial targets. In the past few years, attempts to inhibit protein-protein interactions using antibodies, peptides, and synthetic or natural small molecules have met with varying degrees of success, and these will be the focus of this review.
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Affiliation(s)
- Arianna Loregian
- Department of Histology, Microbiology, and Medical Biotechnologies, University of Padova, Italy.
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45
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Huang CC, Stricher F, Martin L, Decker JM, Majeed S, Barthe P, Hendrickson WA, Robinson J, Roumestand C, Sodroski J, Wyatt R, Shaw GM, Vita C, Kwong PD. Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth. Structure 2005; 13:755-68. [PMID: 15893666 DOI: 10.1016/j.str.2005.03.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 03/12/2005] [Accepted: 03/14/2005] [Indexed: 11/22/2022]
Abstract
The binding surface on CD4 for the HIV-1 gp120 envelope glycoprotein has been transplanted previously onto a scorpion-toxin scaffold. Here, we use X-ray crystallography to characterize atomic-level details of gp120 with this transplant, CD4M33. Despite known envelope flexibility, the conformation of gp120 induced by CD4M33 was so similar to that induced by CD4 that localized measures were required to distinguish ligand-induced differences from lattice variation. To investigate relationships between structure, function, and mimicry, an F23 analog of CD4M33 was devised. Structural and thermodynamic analyses showed F23 to be a better molecular mimic of CD4 than CD4M33. F23 also showed increased neutralization breadth, against diverse isolates of HIV-1, HIV-2, and SIVcpz. Our results lend insight into the stability of the CD4 bound conformation of gp120, define measures that quantify molecular mimicry as a function of evolutionary distance, and suggest how such evaluations might be useful in developing mimetic antagonists with increased neutralization breadth.
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Affiliation(s)
- Chih-chin Huang
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland 20892, USA
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46
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Abstract
New ligands for a variety of biological targets can be selected from biological or synthetic combinatorial peptide libraries. The use of different libraries to select novel peptides with potential therapeutic applications is reviewed. The possible combination of molecular diversity provided by combinatorial libraries and a rational approach derived from computational modeling is also considered. Advantages and disadvantages of different approaches are compared. Possible strategies to bypass loss of peptide bioactivity in the transition from ligand selection to in vivo use are discussed.
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Affiliation(s)
- Chiara Falciani
- Department of Molecular Biology, University of Siena, I-53100 Siena, Italy
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47
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Aytuna AS, Gursoy A, Keskin O. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 2005; 21:2850-5. [PMID: 15855251 DOI: 10.1093/bioinformatics/bti443] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Elucidation of the full network of protein-protein interactions is crucial for understanding of the principles of biological systems and processes. Thus, there is a need for in silico methods for predicting interactions. We present a novel algorithm for automated prediction of protein-protein interactions that employs a unique bottom-up approach combining structure and sequence conservation in protein interfaces. RESULTS Running the algorithm on a template dataset of 67 interfaces and a sequentially non-redundant dataset of 6170 protein structures, 62 616 potential interactions are predicted. These interactions are compared with the ones in two publicly available interaction databases (Database of Interacting Proteins and Biomolecular Interaction Network Database) and also the Protein Data Bank. A significant number of predictions are verified in these databases. The unverified ones may correspond to (1) interactions that are not covered in these databases but known in literature, (2) unknown interactions that actually occur in nature and (3) interactions that do not occur naturally but may possibly be realized synthetically in laboratory conditions. Some unverified interactions, supported significantly with studies found in the literature, are discussed. AVAILABILITY http://gordion.hpc.eng.ku.edu.tr/prism CONTACT agursoy@ku.edu.tr; okeskin@ku.edu.tr.
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Affiliation(s)
- A Selim Aytuna
- Koc University, Center for Computational Biology and Bioinformatics, College of Engineering, Rumelifeneri Yolu 34450 Sariyer, Istanbul, Turkey
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48
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Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, Harrison SC. Structure of an unliganded simian immunodeficiency virus gp120 core. Nature 2005; 433:834-41. [PMID: 15729334 DOI: 10.1038/nature03327] [Citation(s) in RCA: 443] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Accepted: 12/22/2004] [Indexed: 01/18/2023]
Abstract
Envelope glycoproteins of human and simian immunodeficiency virus (HIV and SIV) undergo a series of conformational changes when they interact with receptor (CD4) and co-receptor on the surface of a potential host cell, leading ultimately to fusion of viral and cellular membranes. Structures of fragments of gp120 and gp41 from the envelope protein are known, in conformations corresponding to their post-attachment and postfusion states, respectively. We report the crystal structure, at 4 A resolution, of a fully glycosylated SIV gp120 core, in a conformation representing its prefusion state, before interaction with CD4. Parts of the protein have a markedly different organization than they do in the CD4-bound state. Comparison of the unliganded and CD4-bound structures leads to a model for events that accompany receptor engagement of an envelope glycoprotein trimer. The two conformations of gp120 also present distinct antigenic surfaces. We identify the binding site for a compound that inhibits viral entry.
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Affiliation(s)
- Bing Chen
- Children's Hospital Laboratory of Molecular Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
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49
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Desjobert C, de Soultrait VR, Faure A, Parissi V, Litvak S, Tarrago-Litvak L, Fournier M. Identification by phage display selection of a short peptide able to inhibit only the strand transfer reaction catalyzed by human immunodeficiency virus type 1 integrase. Biochemistry 2004; 43:13097-105. [PMID: 15476403 DOI: 10.1021/bi049385e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human immunodeficiency virus type 1 integrase catalyzes the integration of proviral DNA into the infected cell genome, so it is an important potential target for antiviral drug design. In an attempt to search for peptides that specifically interact with integrase (IN) and inhibit its function, we used an in vitro selection procedure, the phage display technique. A phage display library of random heptapeptides was used to screen for potential peptide ligands of HIV-1 IN. Several phage clones were identified that specifically bound IN. Two of the selected peptides (FHNHGKQ and HLEHLLF) exhibited a high affinity for IN and were chemically synthesized. High affinity was confirmed by a displacement assay which showed that these two synthetic peptides were able to compete with the phages expressing the corresponding peptide. These agents were assayed on the in vitro IN activities. While none of them inhibited the 3'-processing reaction, the FHNHGKQ peptide was found to be an inhibitor of the strand transfer reaction. Despite its high affinity for IN, the HLEHLLF peptide selected and assayed under the same conditions was unable to inhibit this reaction. We showed that the FHNHGKQ peptide inhibits specifically the strand transfer activity by competing with the target DNA for binding to IN. These IN-binding agents could be used as a base for developing new anti-integrase compounds as well as for structural studies of the still unknown three-dimensional structure of the entire integrase molecule.
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Affiliation(s)
- Cecile Desjobert
- UMR-5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France.
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50
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Smith AB, Chruma JJ, Han Q, Barbosa J. Complestatin synthetic studies; the effect of the amino acid configuration on peptide backbone conformation in the common western BCD macrocycle. Bioorg Med Chem Lett 2004; 14:1697-702. [PMID: 15026053 DOI: 10.1016/j.bmcl.2004.01.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Accepted: 01/20/2004] [Indexed: 11/28/2022]
Abstract
The synthesis and structural analysis, involving X-ray crystallographic, nuclear magnetic resonance, and computational studies of four diastereomers of the common western BCD diarylether macrocycle of the complestatins, a family of HIV entry inhibitors, has been achieved exploiting a ruthenium-promoted intramolecular S(N)Ar reaction. The stereogenicity of the individual phenylglycines (residues C and D) results in remarkable effects on the backbone conformation.
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Affiliation(s)
- Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
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