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He L, McAndrew R, Barbu R, Gifford G, Halacoglu C, Drouin-Allaire C, Weber L, Kristensen LG, Gupta S, Chen Y, Petzold CJ, Allaire M, Li KH, Ralston CY, Gochin M. Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity. J Mol Biol 2024; 436:168650. [PMID: 38866091 PMCID: PMC11297672 DOI: 10.1016/j.jmb.2024.168650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.
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Affiliation(s)
- Li He
- Department of Foundational Biomedical Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Ryan McAndrew
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Razvan Barbu
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Grant Gifford
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Cari Halacoglu
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Camille Drouin-Allaire
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lindsey Weber
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Line G Kristensen
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
| | - Corie Y Ralston
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miriam Gochin
- Department of Foundational Biomedical Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA; Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA.
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2
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Si L, Meng K, Tian Z, Sun J, Li H, Zhang Z, Soloveva V, Li H, Fu G, Xia Q, Xiao S, Zhang L, Zhou D. Triterpenoids manipulate a broad range of virus-host fusion via wrapping the HR2 domain prevalent in viral envelopes. SCIENCE ADVANCES 2018; 4:eaau8408. [PMID: 30474060 PMCID: PMC6248931 DOI: 10.1126/sciadv.aau8408] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/24/2018] [Indexed: 05/19/2023]
Abstract
A trimer-of-hairpins motif has been identified in triggering virus-cell fusion within a variety of viral envelopes. Chemically manipulating such a motif represents current repertoire of viral fusion inhibitors. Here, we report that triterpenoids, a class of natural products, antagonize this trimer-of-hairpins via its constitutive heptad repeat-2 (HR2), a prevalent α-helical coil in class I viral fusion proteins. Triterpenoids inhibit the entry of Ebola, Marburg, HIV, and influenza A viruses with distinct structure-activity relationships. Specifically, triterpenoid probes capture the viral envelope via photocrosslinking HR2. Profiling the Ebola HR2-triterpenoid interactions using amino acid substitution, surface plasmon resonance, and nuclear magnetic resonance revealed six residues accessible to triterpenoids, leading to wrapping of the hydrophobic helix and blocking of the HR1-HR2 interaction critical in the trimer-of-hairpins formation. This finding was also observed in the envelopes of HIV and influenza A viruses and might potentially extend to a broader variety of viruses, providing a mechanistic insight into triterpenoid-mediated modulation of viral fusion.
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Affiliation(s)
- Longlong Si
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Kun Meng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Zhenyu Tian
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Jiaqi Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Huiqiang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Ziwei Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Veronica Soloveva
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Haiwei Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Ge Fu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Sulong Xiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
- Corresponding author.
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3
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Zhou G, Chu S, Nemati A, Huang C, Snyder BA, Ptak RG, Gochin M. Investigation of the molecular characteristics of bisindole inhibitors as HIV-1 glycoprotein-41 fusion inhibitors. Eur J Med Chem 2018; 161:533-542. [PMID: 30390441 DOI: 10.1016/j.ejmech.2018.10.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 11/20/2022]
Abstract
In previous work, we described 6-6'-bisindole compounds targeting a hydrophobic pocket on the N-heptad repeat region of viral glycoprotein-41 as effective inhibitors of HIV-1 fusion. Two promising compounds with sub-micromolar IC50's contained a benzoic acid group and a benzoic acid ester attached at the two indole nitrogens. Here we have conducted a thorough structure-activity relationship (SAR) study evaluating the contribution of each of the ring systems and various substituents to compound potency. Hydrophobicity, polarity and charge were varied to produce 35 new compounds that were evaluated in binding, cell-cell fusion and viral infectivity assays. We found that (a) activity based solely on increasing hydrophobic content plateaued at ∼ 200 nM; (b) the bisindole scaffold surpassed other heterocyclic ring systems in efficacy; (c) a polar interaction possibly involving Gln575 in the pocket could supplant less specific hydrophobic interactions; and (d) the benzoic acid ester moiety did not appear to form specific contacts with the pocket. The importance of this hydrophobic group to compound potency suggests a mechanism whereby it might interact with a tertiary component during fusion, such as membrane. A promising small molecule 10b with sub-μM activity was discovered with molecular weight <500 da and reduced logP compared to earlier compounds. The work provides insight into requirements for small molecule inhibition of HIV-1 fusion.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University-California, Vallejo, CA, 94592, USA
| | - Shidong Chu
- Department of Basic Sciences, Touro University-California, Vallejo, CA, 94592, USA
| | - Ariana Nemati
- Department of Basic Sciences, Touro University-California, Vallejo, CA, 94592, USA
| | - Chunsheng Huang
- Southern Research Institute, 431 Aviation Way, Frederick, MD, 21701, USA
| | - Beth A Snyder
- Southern Research Institute, 431 Aviation Way, Frederick, MD, 21701, USA
| | - Roger G Ptak
- Southern Research Institute, 431 Aviation Way, Frederick, MD, 21701, USA
| | - Miriam Gochin
- Department of Basic Sciences, Touro University-California, Vallejo, CA, 94592, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, CA, 94143, USA.
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4
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Wang C, Zhao L, Xia S, Zhang T, Cao R, Liang G, Li Y, Meng G, Wang W, Shi W, Zhong W, Jiang S, Liu K. De Novo Design of α-Helical Lipopeptides Targeting Viral Fusion Proteins: A Promising Strategy for Relatively Broad-Spectrum Antiviral Drug Discovery. J Med Chem 2018; 61:8734-8745. [PMID: 30192544 PMCID: PMC7075651 DOI: 10.1021/acs.jmedchem.8b00890] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/19/2022]
Abstract
Class I enveloped viruses share similarities in their apparent use of a hexameric coiled-coil assembly to drive the merging of virus and host cell membranes. Inhibition of coiled coil-mediated interactions using bioactive peptides that replicate an α-helical chain from the viral fusion machinery has significant antiviral potential. Here, we present the construction of a series of lipopeptides composed of a de novo heptad repeat sequence-based α-helical peptide plus a hydrocarbon tail. Promisingly, the constructs adopted stable α-helical conformations and exhibited relatively broad-spectrum antiviral activities against Middle East respiratory syndrome coronavirus (MERS-CoV) and influenza A viruses (IAVs). Together, these findings reveal a new strategy for relatively broad-spectrum antiviral drug discovery by relying on the tunability of the α-helical coiled-coil domains present in all class I fusion proteins and the amphiphilic nature of the individual helices from this multihelix motif.
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Affiliation(s)
- Chao Wang
- State
Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Lei Zhao
- State
Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Shuai Xia
- Key
Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic
Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, 130 Dong An Road, Shanghai 200032, China
| | - Tianhong Zhang
- State
Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Ruiyuan Cao
- State
Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Guodong Liang
- State
Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Yue Li
- Key Laboratory
of Structure-Based Drug Design & Discovery of the Ministry of
Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Guangpeng Meng
- Key Laboratory
of Structure-Based Drug Design & Discovery of the Ministry of
Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Weicong Wang
- Department
of Clinical Trial Center, China National Clinical Research Center
for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Weiguo Shi
- State
Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Wu Zhong
- State
Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Shibo Jiang
- Key
Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic
Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, 130 Dong An Road, Shanghai 200032, China
- Lindsley
F. Kimball Research Institute, New York
Blood Center, New York, New York 10065, United
States
| | - Keliang Liu
- State
Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Tai-Ping Road, Beijing 100850, China
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5
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Sofiyev V, Kaur H, Snyder BA, Hogan PA, Ptak RG, Hwang P, Gochin M. Enhanced potency of bivalent small molecule gp41 inhibitors. Bioorg Med Chem 2017; 25:408-420. [PMID: 27908751 PMCID: PMC5260928 DOI: 10.1016/j.bmc.2016.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/31/2016] [Accepted: 11/03/2016] [Indexed: 11/28/2022]
Abstract
Low molecular weight peptidomimetic inhibitors with hydrophobic pocket binding properties and moderate fusion inhibitory activity against HIV-1 gp41-mediated cell fusion were elaborated by increasing the available surface area for interacting with the heptad repeat-1 (HR1) coiled coil on gp41. Two types of modifications were tested: 1) increasing the overall hydrophobicity of the molecules with an extension that could interact in the HR1 groove, and 2) forming symmetrical dimers with two peptidomimetic motifs that could potentially interact simultaneously in two hydrophobic pockets on the HR1 trimer. The latter approach was more successful, yielding 40-60times improved potency against HIV fusion over the monomers. Biophysical characterization, including equilibrium binding studies by fluorescence and kinetic analysis by Surface Plasmon Resonance, revealed that inhibitor potency was better correlated to off-rates than to binding affinity. Binding and kinetic data could be fit to a model of bidentate interaction of dimers with the HR1 trimer as an explanation for the slow off-rate, albeit with minimal cooperativity due to the highly flexible ligand structures. The strong cooperativity observed in fusion inhibitory activity of the dimers implied accentuated potency due to the transient nature of the targeted intermediate. Optimization of monomer, dimer or higher order structures has the potential to lead to highly potent non-peptide fusion inhibitors by targeting multiple hydrophobic pockets.
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Affiliation(s)
- Vladimir Sofiyev
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, United States
| | - Hardeep Kaur
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, United States
| | - Beth A Snyder
- Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, United States
| | - Priscilla A Hogan
- Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, United States
| | - Roger G Ptak
- Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, United States
| | - Peter Hwang
- Department of Biophysics and Biochemistry, University of California San Francisco, CA 94143, United States
| | - Miriam Gochin
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94143, United States.
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6
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Yi HA, Fochtman BC, Rizzo RC, Jacobs A. Inhibition of HIV Entry by Targeting the Envelope Transmembrane Subunit gp41. Curr HIV Res 2016; 14:283-94. [PMID: 26957202 DOI: 10.2174/1570162x14999160224103908] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 09/23/2015] [Accepted: 09/30/2015] [Indexed: 11/22/2022]
Abstract
BACKGROUND The transmembrane subunit of the HIV envelope protein, gp41 is a vulnerable target to inhibit HIV entry. There is one fusion inhibitor T20 (brand name: Fuzeon, generic name: enfuvirtide) available by prescription. However, it has several drawbacks such as a high level of development of drug resistance, a short-half life in vivo, rapid renal clearance, low oral bioavailability, and it is only used as a salvage therapy. Therefore, investigators have been studying a variety of different modalities to attempt to overcome these limitations. METHODS Comprehensive literature searches were performed on HIV gp41, inhibition mechanisms, and inhibitors. The latest structural information was collected, and multiple inhibition strategies targeting gp41 were reviewed. RESULTS Many of the recent advances in inhibitors were peptide-based. Several creative modification strategies have also been performed to improve inhibitory efficacy of peptides and to overcome the drawbacks of T20 treatment. Small compounds have also been an area of intense research. There is a wide variety in development from those identified by virtual screens targeting specific regions of the protein to natural products. Finally, broadly neutralizing antibodies have also been important area of research. The inaccessible nature of the target regions for antibodies is a challenge, however, extensive efforts to develop better neutralizing antibodies are ongoing. CONCLUSION The fusogenic protein, gp41 has been extensively studied as a promising target to inhibit membrane fusion between the virus and target cells. At the same time, it is a challenging target because the vulnerable conformations of the protein are exposed only transiently. However, advances in biochemical, biophysical, structural, and immunological studies are coming together to move the field closer to an understanding of gp41 structure and function that will lead to the development of novel drugs and vaccines.
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Affiliation(s)
| | | | | | - Amy Jacobs
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA.
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7
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Abstract
Virus-cell fusion is the primary means by which the human immunodeficiency virus-1 (HIV) delivers its genetic material into the human T-cell host. Fusion is mediated in large part by the viral glycoprotein 41 (gp41) which advances through four distinct conformational states: (i) native, (ii) pre-hairpin intermediate, (iii) fusion active (fusogenic), and (iv) post-fusion. The pre-hairpin intermediate is a particularly attractive step for therapeutic intervention given that gp41 N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR) domains are transiently exposed prior to the formation of a six-helix bundle required for fusion. Most peptide-based inhibitors, including the FDA-approved drug T20, target the intermediate and there are significant efforts to develop small molecule alternatives. Here, we review current approaches to studying interactions of inhibitors with gp41 with an emphasis on atomic-level computer modeling methods including molecular dynamics, free energy analysis, and docking. Atomistic modeling yields a unique level of structural and energetic detail, complementary to experimental approaches, which will be important for the design of improved next generation anti-HIV drugs.
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8
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Chu S, Gochin M. Identification of fragments targeting an alternative pocket on HIV-1 gp41 by NMR screening and similarity searching. Bioorg Med Chem Lett 2013; 23:5114-8. [PMID: 23932360 DOI: 10.1016/j.bmcl.2013.07.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/02/2013] [Accepted: 07/16/2013] [Indexed: 01/12/2023]
Abstract
The HIV-1 envelope glycoprotein gp41 fusion intermediate is a promising drug target for inhibiting viral entry. However, drug development has been impeded by challenges inherent in mediating the underlying protein-protein interaction. Here we report on the identification of fragments that bind to a C-terminal sub-pocket adjacent to the well-known hydrophobic pocket on the NHR coiled coil. Using a specifically designed assay and ligand-based NMR screening of a fragment library, we identified a thioenylaminopyrazole compound with a dissociation constant of ~500 μM. Interaction with the C-terminal sub-pocket was confirmed by paramagnetic relaxation enhancement NMR experiments, which also yielded the binding mode. Shape-based similarity searching detected additional phenylpyrazole and phenyltriazole fragments within the library, enriching the hit rate over random screening, and revealing molecular features required for activity. Discovery of the novel scaffolds and binding mechanism suggests avenues for extending the interaction surface and improving the potency of a hydrophobic pocket binding inhibitor.
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Affiliation(s)
- Shidong Chu
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Mare Island, Vallejo, CA 94592, USA
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9
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Wang C, Shi W, Cai L, Lu L, Wang Q, Zhang T, Li J, Zhang Z, Wang K, Xu L, Jiang X, Jiang S, Liu K. Design, synthesis, and biological evaluation of highly potent small molecule-peptide conjugates as new HIV-1 fusion inhibitors. J Med Chem 2013; 56:2527-39. [PMID: 23458727 DOI: 10.1021/jm3018964] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The small molecule fusion inhibitors N-(4-carboxy-3-hydroxyphenyl)-2,5-dimethylpyrrole (NB-2) and N-(3-carboxy-4-hydroxyphenyl)-2,5-dimethylpyrrole (A12) target a hydrophobic pocket of HIV-1 gp41 and have moderate anti-HIV-1 activity. In this paper, we report the design, synthesis, and structure-activity relationship of a group of hybrid molecules in which the pocket-binding domain segment of the C34 peptide was replaced with NB-2 and A12 derivatives. In addition, the synergistic effect between the small molecule and peptide moieties was analyzed, and lead compounds with a novel scaffold were discovered. We found that either the nonpeptide or peptide part alone showed weak activity against HIV-1-mediated cell-cell fusion, but the conjugates properly generated a strong synergistic effect. Among them, conjugates Aoc-βAla-P26 and Noc-βAla-P26 exhibited a low nanomolar IC50 in the cell-cell fusion assay and effectively inhibited T20-sensitive and -resistant HIV-1 strains. Furthermore, the new molecules exhibited better stability against proteinase K digestion than T20 and C34.
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Affiliation(s)
- Chao Wang
- Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing 100850, China
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10
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Gochin M. A suite of modular fluorescence assays interrogate the human immunodeficiency virus glycoprotein-41 coiled coil and assist in determining binding mechanism of low molecular weight fusion inhibitors. Assay Drug Dev Technol 2012; 10:407-16. [PMID: 22897493 DOI: 10.1089/adt.2012.464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Several different segments of the gp41 N-heptad repeat coiled coil have been constructed using N-terminal bipyridyl modification of composite peptides and inducing trimerization by adding ferrous ions. These metallopeptides act as receptors in fluorescence-binding assays with corresponding fluorescently labeled C-peptide probes. The Fe(II) coordination complex quenches C-peptide fluorescence upon binding, and reversal of quenching by a small molecule inhibitor can be used to obtain the inhibitor-binding constant. A total of 10 peptide pairs targeting 25-46 residue segments of the coiled coil were constructed, with C-peptide probes of different lengths and binding affinities. The result is a suite of assays for exploring binding in the mM to nM range to any desired region of the coiled coil, including the hydrophobic pocket (HP), extended regions on either side of the pocket, or a region associated with T20 resistance mutations. These assays are high-throughput ready, and could be used to discover novel compounds binding along various regions of the gp41 coiled coil groove. They were used to evaluate a sub-μM low molecular weight fusion inhibitor, resulting in the finding that the molecule bound specifically to the HP and attained its potency from a low off-rate.
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Affiliation(s)
- Miriam Gochin
- Department of Basic Science, Touro University-California, Vallejo, California, USA
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11
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Zhou G, Wu D, Snyder B, Ptak RG, Kaur H, Gochin M. Development of indole compounds as small molecule fusion inhibitors targeting HIV-1 glycoprotein-41. J Med Chem 2011; 54:7220-31. [PMID: 21928824 DOI: 10.1021/jm200791z] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nonpeptide inhibition of fusion remains an important goal in anti-HIV research, due to its potential for low cost prophylaxis or prevention of cell-cell transmission of the virus. We report here on a series of indole compounds that have been identified as fusion inhibitors of gp41 through a structure-based drug design approach. Experimental binding affinities of the compounds for the hydrophobic pocket were strongly correlated to fusion inhibitory data (R(2) = 0.91), and corresponding inhibition of viral replication confirmed the hydrophobic pocket as a valid target for low molecular weight fusion inhibitors. The most active compound bound to the hydrophobic pocket and inhibited cell-cell fusion and viral replication at submicromolar levels. A common binding mode for the inhibitors in this series was established by carrying out docking studies using structures of gp41 in the Protein Data Bank. The molecules were flexible enough to conform to the contours of the pocket, and the most active compound was able to adopt a structure mimicking the hydrophobic contacts of the D-peptide PIE7. The results enhance our understanding of indole compounds as inhibitors of gp41.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University-California, 1310 Club Drive, Mare Island, Vallejo, California 94592, United States.
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