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Charles WZ, Faries CR, Street YT, Flowers LS, McNaughton B. Antibody‐Recruitment as a Therapeutic Strategy: A Brief History and Recent Advances. Chembiochem 2022; 23:e202200092. [DOI: 10.1002/cbic.202200092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/20/2022] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | | | - Brian McNaughton
- Delaware State University Delaware Institute for Science and Technology 1200 N Dupont Hwy 19901 Dover UNITED STATES
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2
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Ikeda T, Tennyson RL, Walker SN, Harris RS, McNaughton BR. Evolved Proteins Inhibit Entry of Enfuvirtide-Resistant HIV-1. ACS Infect Dis 2019; 5:634-640. [PMID: 30811933 DOI: 10.1021/acsinfecdis.8b00362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Drugs that block HIV-1 entry are relatively limited. Enfuvirtide is a 36-residue synthetic peptide that targets gp41 and blocks viral fusion. However, Enfuvirtide-resistant HIV has been reported, and this peptide drug requires daily injection. Previously, we have reported helix-grafted display proteins, consisting of HIV-1 gp41 C-peptide helix grafted onto Pleckstrin Homology domains. Some of these biologics inhibit HIV-1 entry with relatively modest and varied potency (IC50 = 190 nM to >1 μM). Here, we report that gp41 C-peptide helix-grafted Sac7d (Sac7d-Cpep) potently suppresses HIV-1 entry in a live virus assay (IC50 = 1.9-12.4 nM). Yeast display sequence optimization of solvent exposed helix residues led to new biologics with improved expression in E. coli (a common biosimilar expression host), with no appreciable change in entry inhibition. Evolved proteins inhibit the entry of a clinically relevant mutant of HIV-1 that is gp41 C-peptide sensitive and Enfuvirtide resistant. Fusion proteins designed for serum stability also potently suppress HIV-1 entry. Collectively, we report several evolved biologics that are functional against an Enfuvirtide-resistant strain and are designed for serum stability.
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Affiliation(s)
- Terumasa Ikeda
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 2231 6th Street S.E., Minneapolis, Minnesota 55455, United States
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States
| | - Rachel L. Tennyson
- Department of Chemistry, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523, United States
| | - Susanne N. Walker
- Department of Chemistry, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523, United States
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 2231 6th Street S.E., Minneapolis, Minnesota 55455, United States
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States
| | - Brian R. McNaughton
- Department of Chemistry, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523, United States
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3
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Fletcher JM, Horner KA, Bartlett GJ, Rhys GG, Wilson AJ, Woolfson DN. De novo coiled-coil peptides as scaffolds for disrupting protein-protein interactions. Chem Sci 2018; 9:7656-7665. [PMID: 30393526 PMCID: PMC6182421 DOI: 10.1039/c8sc02643b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/06/2018] [Indexed: 02/06/2023] Open
Abstract
Homo- and hetero-dimeric coiled coils as scaffolds for the presentation of α-helical protein-binding motifs.
Protein–protein interactions (PPIs) play pivotal roles in the majority of biological processes. Therefore, improved approaches to target and disrupt PPIs would provide tools for chemical biology and leads for therapeutic development. PPIs with α-helical components are appealing targets given that the secondary structure is well understood and can be mimicked or stabilised to render small-molecule and constrained-peptide-based inhibitors. Here we present a strategy to target α-helix-mediated PPIs that exploits de novo coiled-coil assemblies and test this using the MCL-1/NOXA-B PPI. First, computational alanine scanning is used to identify key α-helical residues from NOXA-B that contribute to the interface. Next, these residues are grafted onto the exposed surfaces of de novo designed homodimeric or heterodimeric coiled-coil peptides. The resulting synthetic peptides selectively inhibit a cognate MCL-1/BID complex in the mid-nM range. Furthermore, the heterodimeric system affords control as inhibition occurs only when both the grafted peptide and its designed partner are present. This establishes proof of concept for exploiting peptides stabilised in de novo coiled coils as inhibitors of PPIs. This dependence on supramolecular assembly introduces new possibilities for regulation and control.
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Affiliation(s)
- Jordan M Fletcher
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Katherine A Horner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Gail J Bartlett
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Derek N Woolfson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; .,School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , UK.,BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol , BS8 1TQ , UK
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4
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Designing macrocyclic disulfide-rich peptides for biotechnological applications. Nat Chem Biol 2018; 14:417-427. [DOI: 10.1038/s41589-018-0039-y] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 12/18/2017] [Indexed: 12/21/2022]
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5
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Chapman AM, McNaughton BR. Scratching the Surface: Resurfacing Proteins to Endow New Properties and Function. Cell Chem Biol 2017; 23:543-553. [PMID: 27203375 DOI: 10.1016/j.chembiol.2016.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 12/22/2022]
Abstract
Protein engineering is an emerging discipline that dovetails modern molecular biology techniques with high-throughput screening, laboratory evolution technologies, and computational approaches to modify sequence, structure, and, in some cases, function and properties of proteins. The ultimate goal is to develop new proteins with improved or designer functions for use in biotechnology, medicine, and basic research. One way to engineer proteins is to change their solvent-exposed regions through focused or random "protein resurfacing." In this review we explain what protein resurfacing is, and discuss recent examples of how this strategy is used to generate proteins with altered or broadened recognition profiles, improved stability, solubility, and expression, cell-penetrating ability, and reduced immunogenicity. Additionally we comment on how these properties can be further improved using chemical resurfacing approaches. Protein resurfacing will likely play an increasingly important role as more biologics enter clinical use, and we present some arguments to support this view.
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Affiliation(s)
- Alex M Chapman
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian R McNaughton
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
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Tennyson RL, Walker SN, Ikeda T, Harris RS, McNaughton BR. Evaluation of sequence variability in HIV-1 gp41 C-peptide helix-grafted proteins. Bioorg Med Chem 2017; 26:1220-1224. [PMID: 28811070 DOI: 10.1016/j.bmc.2017.07.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 07/24/2017] [Accepted: 07/31/2017] [Indexed: 12/11/2022]
Abstract
Many therapeutically-relevant protein-protein interactions (PPIs) have been reported that feature a helix and helix-binding cleft at the interface. Given this, different approaches to disrupting such PPIs have been developed. While short peptides (<15 amino acids) typically do not fold into a stable helix, researchers have reported chemical approaches to constraining helix structure. However, these approaches rely on laborious, and often expensive, chemical synthesis and purification. Our premise is that protein-based solutions that stabilize a therapeutically-relevant helix offer a number of advantages. In contrast to chemically constrained helical peptides, or minimal/miniature proteins, which must be synthesized (at great expense and labor), a protein can be expressed in a cellular system (like all current protein therapeutics). If selected properly, the protein scaffold can stabilize the therapeutically-relevant helix. We recently reported a protein engineering strategy, which we call "helix-grafted display", and applied it to the challenge of suppressing HIV entry. We have reported helix-grafted display proteins that inhibit formation of an intramolecular PPI involving HIV gp41 C-peptide helix, and HIV gp41 N-peptide trimer, which contain C-peptide helix-binding clefts. Here, we used yeast display to screen a library of grafted C-peptide helices for N-peptide trimer recognition. Using 'hits' from yeast display library screening, we evaluated the effect helix mutations have on structure, expression, stability, function (target recognition), and suppression of HIV entry.
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Affiliation(s)
- Rachel L Tennyson
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Susanne N Walker
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Terumasa Ikeda
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
| | - Brian R McNaughton
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA; Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, USA.
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Tennyson RL, Walker SN, Ikeda T, Harris RS, Kennan AJ, McNaughton BR. Helix-Grafted Pleckstrin Homology Domains Suppress HIV-1 Infection of CD4-Positive Cells. Chembiochem 2016; 17:1945-1950. [PMID: 27441758 DOI: 10.1002/cbic.201600329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 12/26/2022]
Abstract
The size, functional group diversity and three-dimensional structure of proteins often allow these biomolecules to bind disease-relevant structures that challenge or evade small-molecule discovery. Additionally, folded proteins are often much more stable in biologically relevant environments compared to their peptide counterparts. We recently showed that helix-grafted display-extensive resurfacing and elongation of an existing solvent-exposed helix in a pleckstrin homology (PH) domain-led to a new protein that binds a surrogate of HIV-1 gp41, a validated target for inhibition of HIV-1 entry. Expanding on this work, we prepared a number of human-derived helix-grafted-display PH domains of varied helix length and measured properties relevant to therapeutic and basic research applications. In particular, we showed that some of these new reagents expressed well as recombinant proteins in Escherichia coli, were relatively stable in human serum, bound a mimic of pre-fusogenic HIV-1 gp41 in vitro and in complex biological environments, and significantly lowered the incidence of HIV-1 infection of CD4-positive cells.
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Affiliation(s)
- Rachel L Tennyson
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
| | - Susanne N Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Terumasa Ikeda
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Alan J Kennan
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Brian R McNaughton
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA. .,Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.
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