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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 DOI: 10.1016/j.jmb.2024.168650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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He L, Zhou G, Sofiyev V, Garcia E, Nguyen N, Li KH, Gochin M. Targeting a Conserved Lysine in the Hydrophobic Pocket of HIV-1 gp41 Improves Small Molecule Antiviral Activity. Viruses 2022; 14:v14122703. [PMID: 36560708 PMCID: PMC9784957 DOI: 10.3390/v14122703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Human Immunodeficiency virus (HIV-1) fusion is mediated by glycoprotein-41, a protein that has not been widely exploited as a drug target. Small molecules directed at the gp41 ectodomain have proved to be poorly drug-like, having moderate efficacy, high hydrophobicity and/or high molecular weight. We recently investigated conversion of a fairly potent hydrophobic inhibitor into a covalent binder, by modifying it to react with a lysine residue on the protein. We demonstrated a 10-fold improvement in antiviral efficacy. Here, we continue this study, utilizing instead molecules with better inherent drug-like properties. Molecules possessing low to no antiviral activity as equilibrium binders were converted into µM inhibitors upon addition of an electrophilic warhead in the form of a sulfotetrafluorophenyl (STP) activated ester. We confirmed specificity for gp41 and for entry. The small size of the inhibitors described here offers an opportunity to expand their reach into neighboring pockets while retaining drug-likeness. STP esterification of equilibrium binders is a promising avenue to explore for inhibiting HIV-1 entry. Many gp41 targeting molecules studied over the years possess carboxylic acid groups which can be easily converted into the corresponding STP ester. It may be worth the effort to evaluate a library of such inhibitors as a way forward to small molecule inhibition of fusion of HIV and possibly other enveloped viruses.
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Affiliation(s)
- Li He
- Department of Basic Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Guangyan Zhou
- Department of Basic Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Vladimir Sofiyev
- Department of Basic Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Eddie Garcia
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Newton Nguyen
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Kathy H. Li
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
| | - Miriam Gochin
- Department of Basic Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
- Correspondence: ; Tel.: +1-707-638-5463
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Zhou G, He L, Li KH, Pedroso CCS, Gochin M. A targeted covalent small molecule inhibitor of HIV-1 fusion. Chem Commun (Camb) 2021; 57:4528-4531. [PMID: 33956029 DOI: 10.1039/d1cc01013a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a low molecular weight covalent inhibitor targeting a conserved lysine residue within the hydrophobic pocket of HIV-1 glycoprotein-41. The inhibitor bound selectively to the hydrophobic pocket and exhibited an order of magnitude enhancement of anti-fusion activity against HIV-1 compared to its non-covalent counterpart. The findings represent a significant advance in the quest to obtain non-peptide fusion inhibitors.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA.
| | - Li He
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA.
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
| | - Cássio C S Pedroso
- Lawrence Berkeley National Laboratory, The Molecular Foundry, 1 Cyclotron Road, 67R5114, Berkeley, CA 94720, USA
| | - Miriam Gochin
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA. and Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
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Zhou G, Chu S, Kohli A, Szoka FC, Gochin M. Biophysical studies of HIV-1 glycoprotein-41 interactions with peptides and small molecules - Effect of lipids and detergents. Biochim Biophys Acta Gen Subj 2020; 1864:129724. [PMID: 32889078 DOI: 10.1016/j.bbagen.2020.129724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND The hydrophobic pocket (HP) of HIV-1 glycoprotein-41 ectodomain is defined by two chains of the N-heptad repeat trimer, within the protein-protein interface that mediates 6HB formation. It is a potential target for inhibitors of viral fusion, but its hydrophobic nature and proximity to membrane in situ has precluded ready analysis of inhibitor interactions. METHODS We evaluated the sensitivity of 19F NMR and fluorescence for detecting peptide and small molecule binding to the HP and explored the effect of non-denaturing detergent or phospholipid as cosolvents and potential mimics of the membrane environment surrounding gp41. RESULTS Chemical shifts of aromatic fluorines were found to be sensitive to changes in the hydrogen bonding network that occurred when inhibitors transitioned from solvent into the HP or into ordered detergent micelles. Fluorescence intensities and emission maxima of autofluorescent compounds responded to changes in the local environment. CONCLUSIONS Gp41 - ligand binding occurred under all conditions, but was diminished in the presence of detergents. NMR and fluorescence studies revealed that dodecylphosphocholine (DPC) was a poor substitute for membrane in this system, while liposomes could mimic the membrane surroundings. GENERAL SIGNIFICANCE Our findings suggest that development of high potency small molecule binders to the HP may be frustrated by competition between binding to the HP and binding to the bilayer membrane.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America
| | - Shidong Chu
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America
| | - Aditya Kohli
- Department of Bioengineering and Therapeutic Sciences, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America
| | - Francis C Szoka
- Department of Bioengineering and Therapeutic Sciences, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America; Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America
| | - Miriam Gochin
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America; Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America.
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Chu S, Zhou G, Gochin M. Evaluation of ligand-based NMR screening methods to characterize small molecule binding to HIV-1 glycoprotein-41. Org Biomol Chem 2017; 15:5210-5219. [PMID: 28590477 PMCID: PMC5530879 DOI: 10.1039/c7ob00954b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule inhibitors of glycoprotein-41 (gp41) are able to prevent HIV infection by binding to a hydrophobic pocket (HP) contained within the gp41 ectodomain, and preventing progression of fusion. There is little structural information on gp41-ligand complexes, owing to hydrophobicity of the ligands, occlusion of the HP in folded gp41 ectodomain, and failure to form crystals of complexes. Here we used an engineered gp41 ectodomain protein containing an exposed HP and a small molecule designed to bind with weak affinity to the HP. We evaluated NMR methods, including WaterLOGSY, Saturation Transfer Difference spectroscopy (STD-NMR) and 1H relaxation rate difference spectroscopy with and without target irradiation (DIRECTION) for their ability to probe complex formation and structure. WaterLOGSY was the most sensitive technique for monitoring formation of the complex. STD-NMR and DIRECTION experiments gave similar pharmacophore mapping profiles, although the low dynamic range of the DIRECTION experiment limited its discrimination and sensitivity. A unique binding pose was identified from the STD data and provided clues for future optimization. Advantages and disadvantages of the techniques are discussed. This is the first example of the use of STD for structural analysis of a gp41-small molecule complex.
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Affiliation(s)
- Shidong Chu
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, USA.
| | - Guangyan Zhou
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, USA.
| | - Miriam Gochin
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, USA. and Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94143, USA
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