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Gomez K, Santiago U, Nelson TS, Allen HN, Calderon-Rivera A, Hestehave S, Rodríguez Palma EJ, Zhou Y, Duran P, Loya-Lopez S, Zhu E, Kumar U, Shields R, Koseli E, McKiver B, Giuvelis D, Zuo W, Inyang KE, Dorame A, Chefdeville A, Ran D, Perez-Miller S, Lu Y, Liu X, Handoko, Arora PS, Patek M, Moutal A, Khanna M, Hu H, Laumet G, King T, Wang J, Damaj MI, Korczeniewska OA, Camacho CJ, Khanna R. A peptidomimetic modulator of the Ca V2.2 N-type calcium channel for chronic pain. Proc Natl Acad Sci U S A 2023; 120:e2305215120. [PMID: 37972067 PMCID: PMC10666126 DOI: 10.1073/pnas.2305215120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
Transmembrane Cav2.2 (N-type) voltage-gated calcium channels are genetically and pharmacologically validated, clinically relevant pain targets. Clinical block of Cav2.2 (e.g., with Prialt/Ziconotide) or indirect modulation [e.g., with gabapentinoids such as Gabapentin (GBP)] mitigates chronic pain but is encumbered by side effects and abuse liability. The cytosolic auxiliary subunit collapsin response mediator protein 2 (CRMP2) targets Cav2.2 to the sensory neuron membrane and regulates their function via an intrinsically disordered motif. A CRMP2-derived peptide (CBD3) uncouples the Cav2.2-CRMP2 interaction to inhibit calcium influx, transmitter release, and pain. We developed and applied a molecular dynamics approach to identify the A1R2 dipeptide in CBD3 as the anchoring Cav2.2 motif and designed pharmacophore models to screen 27 million compounds on the open-access server ZincPharmer. Of 200 curated hits, 77 compounds were assessed using depolarization-evoked calcium influx in rat dorsal root ganglion neurons. Nine small molecules were tested electrophysiologically, while one (CBD3063) was also evaluated biochemically and behaviorally. CBD3063 uncoupled Cav2.2 from CRMP2, reduced membrane Cav2.2 expression and Ca2+ currents, decreased neurotransmission, reduced fiber photometry-based calcium responses in response to mechanical stimulation, and reversed neuropathic and inflammatory pain across sexes in two different species without changes in sensory, sedative, depressive, and cognitive behaviors. CBD3063 is a selective, first-in-class, CRMP2-based peptidomimetic small molecule, which allosterically regulates Cav2.2 to achieve analgesia and pain relief without negative side effect profiles. In summary, CBD3063 could potentially be a more effective alternative to GBP for pain relief.
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Affiliation(s)
- Kimberly Gomez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Ulises Santiago
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA15261
| | - Tyler S. Nelson
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Heather N. Allen
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Aida Calderon-Rivera
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Sara Hestehave
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Erick J. Rodríguez Palma
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Yuan Zhou
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ85724
| | - Paz Duran
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Santiago Loya-Lopez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Elaine Zhu
- Department of Anesthesiology, Perioperative Care and Pain Medicine, New York University Grossman School of Medicine, New York, NY10016
- Interdisciplinary Pain Research Program, New York University Langone Health, New York, NY10016
| | - Upasana Kumar
- Department of Diagnostic Sciences, Center for Orofacial Pain and Temporomandibular Disorders, Rutgers School of Dental Medicine, Newark, NJ07101
| | - Rory Shields
- Rutgers School of Graduate Studies, Newark Health Science Campus, Newark, NJ07101
| | - Eda Koseli
- Department of Pharmacology and Toxicology and Translational Research Initiative for Pain and Neuropathy, Virginia Commonwealth University, Richmond, VA23298
| | - Bryan McKiver
- Department of Pharmacology and Toxicology and Translational Research Initiative for Pain and Neuropathy, Virginia Commonwealth University, Richmond, VA23298
| | - Denise Giuvelis
- Department of Biomedical Sciences, College of Osteopathic Medicine, Center for Excellence in the Neurosciences, University of New England, Biddeford, ME04005
| | - Wanhong Zuo
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ07103
| | | | - Angie Dorame
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ85724
| | - Aude Chefdeville
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ85724
| | - Dongzhi Ran
- Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing400016, China
| | - Samantha Perez-Miller
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Yi Lu
- Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing400016, China
| | - Xia Liu
- Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing400016, China
| | - Handoko
- Department of Chemistry, New York University, New York, NY10003
| | | | - Marcel Patek
- Bright Rock Path Limited Liability Company, Tucson, AZ85724
| | - Aubin Moutal
- Department of Pharmacology and Physiology, School of Medicine, St. Louis University, St. Louis, MO63104
| | - May Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Huijuan Hu
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ07103
| | - Geoffroy Laumet
- Department of Physiology, Michigan State University, East Lansing, MI48824
| | - Tamara King
- Department of Biomedical Sciences, College of Osteopathic Medicine, Center for Excellence in the Neurosciences, University of New England, Biddeford, ME04005
| | - Jing Wang
- Department of Anesthesiology, Perioperative Care and Pain Medicine, New York University Grossman School of Medicine, New York, NY10016
- Interdisciplinary Pain Research Program, New York University Langone Health, New York, NY10016
- Department of Neuroscience and Physiology and Neuroscience Institute, School of Medicine, New York University, New York, NY10010
| | - M. Imad Damaj
- Department of Pharmacology and Toxicology and Translational Research Initiative for Pain and Neuropathy, Virginia Commonwealth University, Richmond, VA23298
| | - Olga A. Korczeniewska
- Department of Diagnostic Sciences, Center for Orofacial Pain and Temporomandibular Disorders, Rutgers School of Dental Medicine, Newark, NJ07101
- Rutgers School of Graduate Studies, Newark Health Science Campus, Newark, NJ07101
| | - Carlos J. Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA15261
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
- Department of Neuroscience and Physiology and Neuroscience Institute, School of Medicine, New York University, New York, NY10010
- Chemical, and Biomolecular Engineering Department, Tandon School of Engineering, New York University, New York City, NY11201
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2
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Nazzaro A, Lu B, Sawyer N, Watkins AM, Arora PS. Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates. Angew Chem Int Ed Engl 2023; 62:e202303943. [PMID: 37170337 PMCID: PMC10592574 DOI: 10.1002/anie.202303943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
Mimics of protein secondary and tertiary structure offer rationally-designed inhibitors of biomolecular interactions. β-Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter-β-strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally-defined macrocyclic β-sheets without the requirement for natural or synthetic β-turns, thereby providing a minimal mimic of a protein β-sheet. To access turn-less antiparallel β-sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β-sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over-abundance of aromatic-aromatic, cation-π and ionic interactions in β-sheets. In correspondence with natural β-sheets, we find that minimal HBS mimics show robust β-sheet formation when specific amino acid residue pairings are incorporated. In isolated β-sheets, aromatic interactions endow superior conformational stability over ionic or cation-π interactions. Circular dichroism and NMR spectroscopies, along with high-resolution X-ray crystallography, support our design principles.
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Affiliation(s)
- Alex Nazzaro
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Brandon Lu
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | | | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
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3
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Kwok JG, Yuan Z, Arora PS. An Encodable Scaffold for Sequence-Specific Recognition of Duplex RNA. Angew Chem Int Ed Engl 2023; 62:e202308650. [PMID: 37548640 PMCID: PMC10528708 DOI: 10.1002/anie.202308650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/08/2023]
Abstract
RNA, unlike DNA, folds into a multitude of secondary and tertiary structures. This structural diversity has impeded the development of ligands that can sequence-specifically target this biomolecule. We sought to develop ligands for double-stranded RNA (dsRNA) segments, which are ubiquitous in RNA tertiary structure. The major groove of double-stranded DNA is sequence-specifically recognized by a range of dimeric helical transcription factors, including the basic leucine zippers (bZIP) and basic helix-loop-helix (bHLH) proteins; however, such simple structural motifs are not prevalent in RNA-binding proteins. We interrogated the high-resolution structures of DNA and RNA to identify requirements for a helix fork motif to occupy dsRNA major grooves akin to dsDNA. Our analysis suggested that the rigidity and angle of approach of dimeric helices in bZIP/bHLH motifs are not ideal for the binding of dsRNA major grooves. This investigation revealed that the replacement of the leucine zipper motifs in bHLH proteins with synthetic crosslinkers would allow recognition of dsRNA. We show that a model bHLH DNA-binding motif does not bind dsRNA but can be reengineered as an RNA ligand. Based on this hypothesis, we rationally designed a miniature synthetic crosslinked helix fork (CHF) as a generalizable proteomimetic scaffold for targeting dsRNA. We evaluated several CHF constructs against a set of RNA and DNA hairpins to probe the specificity of the designed construct. Our studies reveal a new class of proteomimetics as an encodable platform for sequence-specific recognition of dsRNA.
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Affiliation(s)
- Jonathan G. Kwok
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
| | - Zhi Yuan
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
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4
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Gomez K, Santiago U, Calderon-Rivera A, Duran P, Loya-Lopez S, Ran D, Perez-Miller S, Handoko H, Arora PS, Patek M, King TD, Hu H, Camacho CJ, Khanna R. A Selective Peptidomimetic Modulator Of Cav2.2 (N-Type) Voltage-Gated Calcium Channels For Chronic Pain. The Journal of Pain 2023. [DOI: 10.1016/j.jpain.2023.02.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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5
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Qi X, Jambu S, Ji Y, Belyk KM, Panigrahi NR, Arora PS, Strotman NA, Diao T. Late-Stage Modification of Oligopeptides by Nickel-Catalyzed Stereoselective Radical Addition to Dehydroalanine. Angew Chem Int Ed Engl 2022; 61:e202213315. [PMID: 36175367 PMCID: PMC9773866 DOI: 10.1002/anie.202213315] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Indexed: 12/24/2022]
Abstract
Radical addition to dehydroalanine (Dha) represents an appealing, modular strategy to access non-canonical peptide analogues for drug discovery. Prior studies on radical addition to the Dha residue of peptides and proteins have demonstrated outstanding functional group compatibility, but the lack of stereoselectivity has limited the synthetic utility of this approach. Herein, we address this challenge by employing chiral nickel catalysts to control the stereoselectivity of radical addition to Dha on oligopeptides. The conditions accommodate a variety of primary and secondary electrophiles to introduce polyethylene glycol, biotin, halo-tag, and hydrophobic and hydrophilic side chains to the peptide. The reaction features catalyst control to largely override substrate-based control of stereochemical outcome for modification of short peptides. We anticipate that the discovery of chiral nickel complexes that confer catalyst control will allow rapid, late-stage modification of peptides featuring nonnatural sidechains.
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Affiliation(s)
- Xiaoxu Qi
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Subramanian Jambu
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Yining Ji
- Department of Process Research and Development, Institution Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Kevin M Belyk
- Department of Process Research and Development, Institution Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Nihar R Panigrahi
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Neil A Strotman
- Department of Process Research and Development, Institution Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Tianning Diao
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
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6
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Merritt HI, Sawyer N, Watkins AM, Arora PS. Anchor Residues Govern Binding and Folding of an Intrinsically Disordered Domain. ACS Chem Biol 2022; 17:2723-2727. [PMID: 36153968 PMCID: PMC9773862 DOI: 10.1021/acschembio.2c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Minimal protein mimics have yielded novel classes of protein-protein interaction inhibitors; however, this success has not been extended to targeting intrinsically disordered proteins, which represent a significant proportion of important therapeutic targets. We sought to determine the requirements for binding an intrinsically disordered region (IDR) by its native binding partner as a prelude to developing minimal protein mimics that regulate IDR interactions. Our analysis reinforces the hypothesis that IDRs reside on a fulcrum between unfolded and folded states and that a handful of key binding residues on partner protein surfaces dictate their folding. Our studies also suggest that minimal mimics of protein surfaces may not offer specific ligands for IDRs and that it would be more judicious to target the globular protein partners of IDRs.
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Affiliation(s)
- Haley I Merritt
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nicholas Sawyer
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Andrew M Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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7
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Qi X, Jambu S, Ji Y, Belyk KM, Panigrahi NR, Arora PS, Strotman NA, Diao T. Late‐Stage Modification of Oligopeptides by Nickel‐Catalyzed Stereoselective Radical Addition to Dehydroalanine. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202213315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaoxu Qi
- New York University Chemistry UNITED STATES
| | | | - Yining Ji
- Merck & Co Inc Department of Process Research and Development UNITED STATES
| | - Kevin M. Belyk
- Merck & Co Inc Department of Process Research and Development UNITED STATES
| | | | | | - Neil A. Strotman
- Merck & Co Inc Department of Process Research and Development UNITED STATES
| | - Tianning Diao
- New York University Chemistry 100 Washington Square E.Silver Center, Room 705 10003 New york UNITED STATES
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8
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Affiliation(s)
- Handoko
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Nihar R. Panigrahi
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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9
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Modell AE, Marrone F, Panigrahi NR, Zhang Y, Arora PS. Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery. J Am Chem Soc 2022; 144:1198-1204. [PMID: 35029987 PMCID: PMC8959088 DOI: 10.1021/jacs.1c09666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Constrained peptides have proven to be a rich source of ligands for protein surfaces, but are often limited in their binding potency. Deployment of nonnatural side chains that access unoccupied crevices on the receptor surface offers a potential avenue to enhance binding affinity. We recently described a computational approach to create topographic maps of protein surfaces to guide the design of nonnatural side chains [J. Am. Chem. Soc. 2017, 139, 15560]. The computational method, AlphaSpace, was used to predict peptide ligands for the KIX domain of the p300/CBP coactivator. KIX has been the subject of numerous ligand discovery strategies, but potent inhibitors of its interaction with transcription factors remain difficult to access. Although the computational approach provided a significant enhancement in the binding affinity of the peptide, fine-tuning of nonnatural side chains required an experimental screening method. Here we implement a peptide-tethering strategy to screen fragments as nonnatural side chains on conformationally defined peptides. The combined computational-experimental approach offers a general framework for optimizing peptidomimetics as inhibitors of protein-protein interactions.
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Affiliation(s)
- Ashley E. Modell
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Frank Marrone
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nihar R. Panigrahi
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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10
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Blosser SL, Sawyer N, Maksimovic I, Ghosh B, Arora PS. Covalent and Noncovalent Targeting of the Tcf4/β-Catenin Strand Interface with β-Hairpin Mimics. ACS Chem Biol 2021; 16:1518-1525. [PMID: 34286954 DOI: 10.1021/acschembio.1c00389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
β-Strands are a fundamental component of protein structure, and these extended peptide regions serve as binding epitopes for numerous protein-protein complexes. However, synthetic mimics that capture the conformation of these epitopes and inhibit selected protein-protein interactions are rare. Here we describe covalent and noncovalent β-hairpin mimics of an extended strand region mediating the Tcf4/β-catenin interaction. Our efforts afford a rationally designed lead for an underexplored region of β-catenin, which has been the subject of numerous ligand discovery campaigns.
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Affiliation(s)
- Sarah L. Blosser
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Igor Maksimovic
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Brahma Ghosh
- Discovery Chemistry, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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11
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Torner JM, Yang Y, Rooklin D, Zhang Y, Arora PS. Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics. ACS Chem Biol 2021; 16:1179-1183. [PMID: 34228913 DOI: 10.1021/acschembio.1c00418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Minimal mimics of protein conformations provide rationally designed ligands to modulate protein function. The advantage of minimal mimics is that they can be chemically synthesized and coaxed to be proteolytically resistant; a key disadvantage is that minimization of the protein binding epitope may be associated with loss of affinity and specificity. Several approaches to overcome this challenge may be envisioned, including deployment of covalent warheads and use of nonnatural residues to improve contacts with the binding surface. Herein, we describe our computational and experimental efforts to enhance the minimal protein mimics with fragments that can contact undiscovered binding pockets on Mdm2 and MdmX-two well-studied protein partners of p53.
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Affiliation(s)
- Justin M. Torner
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yuwei Yang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - David Rooklin
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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12
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Abstract
The coiled coil is a common protein tertiary structure intimately involved in mediating protein recognition and function. Due to their structural simplicity, coiled coils have served as attractive scaffolds for the development of functional biomaterials. Herein we describe the design of conformationally-defined coiled coil photoswitches as potential environmentally-sensitive biomaterials.
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Affiliation(s)
- Justin M Torner
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA.
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13
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Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Alan Harris R, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Le MD, Manu S, Rabarivola CJ, Zaramody A, Andriaholinirina N, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KK, Rogers J, Marques‐Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. Am J Primatol 2021; 83:e23255. [PMID: 33792947 PMCID: PMC8250314 DOI: 10.1002/ajp.23255] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022]
Abstract
The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
- Department of Medical GeneticsUniversity of CalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryAlbertaCanada
| | - Joseph D. Orkin
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Mareike C. Janiak
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Alejandro Valenzuela
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Lukas Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Frank Marrone
- Department of ChemistryNew York UniversityNew YorkUSA
| | - Hasinala Ramangason
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
| | - Julie E. Horvath
- Genomics & Microbiology Research LaboratoryNorth Carolina Museum of Natural SciencesRaleighNorth CarolinaUSA
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth CarolinaUSA
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth CarolinaUSA
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate CenterLeibniz Institute for Primate ResearchGöettingenGermany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland and School of GeosciencesUniversity of EdinburghEdinburghUK
| | - Chiea Chuen Khor
- Genome Institute of SingaporeAgency for Science, Technology and ResearchSingapore
- Singapore Eye Research InstituteSingapore National Eye CentreSingapore
| | - Weng Khong Lim
- SingHealth Duke‐NUS Institute of Precision MedicineSingapore Health ServicesSingapore
- SingHealth Duke‐NUS Genomic Medicine CentreSingapore Health ServicesSingapore
- Cancer and Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingapore
| | - Jessica G. H. Lee
- Department of Conservation, Research and Veterinary ServicesWildlife Reserves SingaporeSingapore
| | - Patrick Tan
- Genome Institute of SingaporeAgency for Science, Technology and ResearchSingapore
- SingHealth Duke‐NUS Institute of Precision MedicineSingapore Health ServicesSingapore
- Cancer and Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingapore
| | - Govindhaswamy Umapathy
- CSIR‐Laboratory for the Conservation of Endangered SpeciesCentre for Cellular and Molecular BiologyHyderabadIndia
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Esther Lizano
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Tilo Nadler
- Cuc Phuong CommuneNho Quan DistrictNinh Binh ProvinceVietnam
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate CenterLeibniz Institute for Primate ResearchGoettingenGermany
- Leibniz Science Campus Primate CognitionGoettingenGermany
- Department of Primate CognitionGeorg‐August‐University, GoettingenGermany
| | - Minh D. Le
- Department of Environmental Ecology, University of Science and Central Institute for Natural Resources and Environmental StudiesVietnam National UniversityHanoiVietnam
| | - Sivakumara Manu
- CSIR‐Laboratory for the Conservation of Endangered SpeciesCentre for Cellular and Molecular BiologyHyderabadIndia
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Steig E. Johnson
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
| | - Erich D. Jarvis
- The Vertebrate Genomes LabThe Rockefeller UniversityNew YorkNew YorkUSA
- Laboratory of Neurogenetics of LanguageThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Olivier Fedrigo
- The Vertebrate Genomes LabThe Rockefeller UniversityNew YorkNew YorkUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Kunming Natural History Museum of Zoology, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- China National GenebankBGI‐ShenzhenShenzhenChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Tomas Marques‐Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Arcadi Navarro
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - David Juan
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | | | - James P. Higham
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA
- New York Consortium in Evolutionary PrimatologyNew YorkNew YorkUSA
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14
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Abstract
The design of a stimuli-responsive peptide whose conformation is controlled by wavelength-specific light and metal coordination is described. The peptide adopts a defined tertiary structure and its conformation can be modulated between an α-helical coiled coil and β-sheet. The peptide is designed with a hydrophobic interface to induce coiled coil formation and is based on a recently described strategy to obtain switchable helix dimers. Herein, we endowed the helix dimer with 8-hydroxyquinoline (HQ) groups to achieve metal coordination and shift to a β-sheet structure. It was found that the conformational shift only occurs upon introduction of Zn2+ ; other metal ions (Cu2+ , Fe3+ , Co2+ , Mg2 , and Ni2+ ) do not offer switching likely due to non-specific metal-peptide coordination. A control peptide lacking the metal-coordinating residues does not show conformational switching with Zn2+ supporting the role of this metal in stabilizing the β-sheet conformation in a defined manner.
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Affiliation(s)
- Pritam Ghosh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa, 3200008, Israel
| | - Justin Torner
- Department of Chemistry, New York University, New York, New York, 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York, 10003, United States
| | - Galia Maayan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa, 3200008, Israel
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15
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Abstract
Examination of complexes of proteins with biomolecular ligands reveals that proteins tend to interact with partners via folded sub-domains, in which the backbone possesses secondary structure. α-Helices comprising the largest class of protein secondary structures, play fundamental roles in a multitude of highly specific protein-protein and protein-nucleic acid interactions. We have demonstrated a unique strategy for stabilization of the α-helical conformation that involves replacement of one of the main chain i and i+4 hydrogen bonds in the target α-helix with a covalent bond. We termed this synthetic strategy a hydrogen bond surrogate (HBS) approach. Two salient features of this approach are: (1) the internal placement of the crosslink allows development of helices such that none of the solvent-exposed surfaces are blocked by the constraining element, i.e., all side chains of the constrained helices remain available for molecular recognition. (2) This approach can be deployed to constrain very short peptides (<10 amino acid residues) into highly stable α-helices. This chapter presents the biophysical basis for the development of the hydrogen bond surrogate approach, as well as methods for the synthesis and conformational analysis of the artificial helices.
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Affiliation(s)
- Ganesh S Jedhe
- Department of Chemistry, New York University, New York, NY, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, United States.
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16
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Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Harris RA, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KKH, Rogers J, Marques-Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. bioRxiv 2021:2021.02.03.429540. [PMID: 33564767 PMCID: PMC7872355 DOI: 10.1101/2021.02.03.429540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and Archaeology, University of Calgary, Canada
- Department of Medical Genetics, University of Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Joseph D. Orkin
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford, United Kingdom
| | - Alejandro Valenzuela
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Lukas Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Frank Marrone
- Department of Chemistry, New York University, United States
| | | | - Julie E. Horvath
- Genomics & Microbiology Research Laboratory, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göettingen, Germany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland and School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore Health Services, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jessica G. H. Lee
- Department of Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Govindhaswamy Umapathy
- CSIR-Laboratory for the Conservation of Endangered Species, Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Esther Lizano
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz Science Campus Primate Cognition, Goettingen, Germany
- Department of Primate Cognition, Georg-August-University, Goettingen, Germany
| | - Steig E. Johnson
- Department of Anthropology and Archaeology, University of Calgary, Canada
| | - Erich D. Jarvis
- The Vertebrate Genomes Lab, The Rockefeller University, New York, United States
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Olivier Fedrigo
- The Vertebrate Genomes Lab, The Rockefeller University, New York, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Tomas Marques-Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - David Juan
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | | | - James P. Higham
- Department of Anthropology, New York University, United States
- New York Consortium in Evolutionary Primatology, New York, United States
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17
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Abstract
The emergence of SARS-CoV-2 has caused over a million human deaths and massive global disruption. The viral infection may also represent a threat to our closest living relatives, nonhuman primates. The contact surface of the host cell receptor, ACE2, displays amino acid residues that are critical for virus recognition, and variations at these critical residues modulate infection susceptibility. Infection studies have shown that some primate species develop COVID-19-like symptoms; however, the susceptibility of most primates is unknown. Here, we show that all apes and African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at critical contact residues, and protein modeling predicts that these differences should greatly reduce SARS-CoV-2 binding affinity. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, and some lemurs, are likely to be highly susceptible to SARS-CoV-2. Urgent actions have been undertaken to limit the exposure of great apes to humans, and similar efforts may be necessary for many other primate species. Amanda Melin et al. compare variation in 29 primate species at 12 amino acid residue sites coded by the ACE2 gene and show that apes and African and Asian monkeys exhibit the same set of twelve key amino acid residues as human ACE2. These results suggest that these primates are likely to be susceptible to SARS-CoV-2, whereas ACE2 gene sequences and protein-protein interaction models suggest reduced susceptibility for platyrrhines, tarsiers, lorisoids, and some lemurs.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada. .,Department of Medical Genetics, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Dr, NW, Calgary, AB, T2N 4N1, Canada.
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Dr, NW, Calgary, AB, T2N 4N1, Canada
| | - Frank Marrone
- Department of Chemistry, New York University, 100 Washington Square East, 10th Floor, New York, NY, 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, 10th Floor, New York, NY, 10003, USA
| | - James P Higham
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY, 10003, USA. .,New York Consortium in Evolutionary Primatology, New York, NY, USA.
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18
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Arora PS, Raines RT. Daniel S. Kemp (1936-2020): A Pioneer of Bioorganic Chemistry. ACS Chem Biol 2020; 15:2620-2622. [PMID: 33059455 DOI: 10.1021/acschembio.0c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paramjit S Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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19
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Yoo DY, Barros SA, Brown GC, Rabot C, Bar-Sagi D, Arora PS. Macropinocytosis as a Key Determinant of Peptidomimetic Uptake in Cancer Cells. J Am Chem Soc 2020; 142:14461-14471. [PMID: 32786217 DOI: 10.1021/jacs.0c02109] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptides and peptidomimetics represent the middle space between small molecules and large proteins-they retain the relatively small size and synthetic accessibility of small molecules while providing high binding specificity for biomolecular partners typically observed with proteins. During the course of our efforts to target intracellular protein-protein interactions in cancer, we observed that the cellular uptake of peptides is critically determined by the cell line-specifically, we noted that peptides show better uptake in cancer cells with enhanced macropinocytic indices. Here, we describe the results of our analysis of cellular penetration by different classes of conformationally stabilized peptides. We tested the uptake of linear peptides, peptide macrocycles, stabilized helices, β-hairpin peptides, and cross-linked helix dimers in 11 different cell lines. Efficient uptake of these conformationally defined constructs directly correlated with the macropinocytic activity of each cell line: high uptake of compounds was observed in cells with mutations in certain signaling pathways. Significantly, the study shows that constrained peptides follow the same uptake mechanism as proteins in macropinocytic cells, but unlike proteins, peptide mimics can be readily designed to resist denaturation and proteolytic degradation. Our findings expand the current understanding of cellular uptake in cancer cells by designed peptidomimetics and suggest that cancer cells with certain mutations are suitable mediums for the study of biological pathways with peptide leads.
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Affiliation(s)
- Daniel Y Yoo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Stephanie A Barros
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Gordon C Brown
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Christian Rabot
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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20
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Abstract
The emergence of the novel coronavirus SARS-CoV-2, which in humans is highly infectious and leads to the potentially fatal disease COVID-19, has caused hundreds of thousands of deaths and huge global disruption. The viral infection may also represent an existential threat to our closest living relatives, the nonhuman primates, many of which are endangered and often reduced to small populations. The virus engages the host cell receptor, angiotensin-converting enzyme-2 (ACE2), through the receptor binding domain (RBD) on the spike protein. The contact surface of ACE2 displays amino acid residues that are critical for virus recognition, and variations at these critical residues are likely to modulate infection susceptibility across species. While infection studies are emerging and have shown that some primates, such as rhesus macaques and vervet monkeys, develop COVID-19-like symptoms when exposed to the virus, the susceptibility of many other nonhuman primates is unknown. Here, we show that all apes, including chimpanzees, bonobos, gorillas, and orangutans, and all African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at significant contact residues, and protein modeling predicts that these differences should greatly reduce the binding affinity of the ACE2 for the virus, hence moderating their susceptibility for infection. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, as well as some lemurs are all likely to be highly susceptible to SARS-CoV-2, representing a critical threat to their survival. Urgent actions have been undertaken to limit the exposure of Great Apes to humans, and similar efforts may be necessary for many other primate species.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, CA
- Department of Medical Genetics, University of Calgary, CA
- Alberta Children's Hospital Research Institute, University of Calgary, CA
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, CA
- Alberta Children's Hospital Research Institute, University of Calgary, CA
| | | | | | - James P Higham
- Department of Anthropology, New York University, US
- New York Consortium in Evolutionary Primatology, New York, US
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21
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Affiliation(s)
- Handoko
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Zacharia Benslimane
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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22
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Abstract
Protein-protein interactions (PPIs) play a critical role in fundamental biological processes. Competitive inhibition of these interfaces requires compounds that can access discontinuous binding epitopes along a large, shallow binding surface area. Conformationally defined protein surface mimics present a viable route to target these interactions. However, the development of minimal protein mimics that engage intracellular targets with high affinity remains a major challenge because mimicry of a portion of the binding interface is often associated with the loss of critical binding interactions. Covalent targeting provides an attractive approach to overcome the loss of noncovalent contacts but have the inherent risk of dominating noncovalent contacts and increasing the likelihood of nonselective binding. Here, we report the iterative design of a proteolytically stable α3β chimeric helix mimic that covalently targets oncogenic Ras G12C as a model system. We explored several electrophiles to optimize preferential alkylation with the desired C12 on Ras. The designed lead peptide modulates nucleotide exchange, inhibits activation of the Ras-mediated signaling cascade, and is selectively toxic toward mutant Ras G12C cancer cells. The relatively high frequency of acquired cysteines as missense mutations in cancer and other diseases suggests that covalent peptides may offer an untapped therapeutic approach for targeting aberrant protein interactions.
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Affiliation(s)
- Daniel Y. Yoo
- Department of Chemistry, New York University, New York, 10003, U.S.A
| | - Andrew D. Hauser
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, U.S.A
| | - Stephen T. Joy
- Department of Chemistry, New York University, New York, 10003, U.S.A
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, U.S.A
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, 10003, U.S.A
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23
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Sadek J, Wuo MG, Rooklin D, Hauenstein A, Hong SH, Gautam A, Wu H, Zhang Y, Cesarman E, Arora PS. Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat Commun 2020; 11:1786. [PMID: 32286300 PMCID: PMC7156456 DOI: 10.1038/s41467-020-15576-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 03/12/2020] [Indexed: 01/07/2023] Open
Abstract
Protein-protein interactions featuring intricate binding epitopes remain challenging targets for synthetic inhibitors. Interactions of NEMO, a scaffolding protein central to NF-κB signaling, exemplify this challenge. Various regulators are known to interact with different coiled coil regions of NEMO, but the topological complexity of this protein has limited inhibitor design. We undertook a comprehensive effort to block the interaction between vFLIP, a Kaposi’s sarcoma herpesviral oncoprotein, and NEMO using small molecule screening and rational design. Our efforts reveal that a tertiary protein structure mimic of NEMO is necessary for potent inhibition. The rationally designed mimic engages vFLIP directly causing complex disruption, protein degradation and suppression of NF-κB signaling in primary effusion lymphoma (PEL). NEMO mimic treatment induces cell death and delays tumor growth in a PEL xenograft model. Our studies with this inhibitor reveal the critical nexus of signaling complex stability in the regulation of NF-κB by a viral oncoprotein. NF-κB signalling involves the scaffold protein NEMO, which can be bound by the oncoprotein vFLIP to promote cell survival and oncogenic transformation. Here the authors rationally engineer a tertiary protein mimic of NEMO to disrupt the vFLIP-NEMO interaction to induce cell death.
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Affiliation(s)
- Jouliana Sadek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Michael G Wuo
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - David Rooklin
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Arthur Hauenstein
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Seong Ho Hong
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Archana Gautam
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, 10003, USA.,NYU-ECNU Center for Computational Chemistry, New York University-Shanghai, 200122, Shanghai, China
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, 10003, USA.
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24
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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25
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Abstract
Amide bonds are ubiquitous in peptides, proteins, pharmaceuticals, and polymers. The formation of amide bonds is a straightforward process: amide bonds can be synthesized with relative ease because of the availability of efficient coupling agents. However, there is a substantive need for methods that do not require excess reagents. A catalyst that condenses amino acids could have an important impact by reducing the significant waste generated during peptide synthesis. We describe the rational design of a biomimetic catalyst that can efficiently couple amino acids featuring standard protecting groups. The catalyst design combines lessons learned from enzymes, peptide biosynthesis, and organocatalysts. Under optimized conditions, 5 mol % catalyst efficiently couples Fmoc amino acids without notable racemization. Importantly, we demonstrate that the catalyst is functional for the synthesis of oligopeptides on solid phase. This result is significant because it illustrates the potential of the catalyst to function on a substrate with a multitude of amide bonds, which may be expected to inhibit a hydrogen-bonding catalyst.
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Affiliation(s)
- Handoko
- Department of Chemistry New York University , New York , New York 10003 , United States
| | - Sakilam Satishkumar
- Department of Chemistry New York University , New York , New York 10003 , United States
| | - Nihar R Panigrahi
- Department of Chemistry New York University , New York , New York 10003 , United States
| | - Paramjit S Arora
- Department of Chemistry New York University , New York , New York 10003 , United States
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26
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Abstract
Helical secondary and tertiary motifs are commonly observed as binding epitopes in natural and engineered protein scaffolds. While several strategies have been described to constrain α-helices or reproduce their binding attributes in synthetic mimics, general strategies to mimic tertiary helical motifs remain in their infancy. We recently described a synthetic strategy to develop helical dimers ( J. Am. Chem. Soc. 2015, 137, 11618-11621). We found that replacement of an interhelical salt bridge with a covalent bond can stabilize antiparallel motifs in short sequences. Here we show that the approach can be generalized to obtain antiparallel and parallel dimers as well as trimer motifs. Helical stabilization requires judiciously designed cross-linkers as well as optimal interhelical hydrophobic packing. We anticipate that these mimics would afford new classes of modulators of biological function.
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Affiliation(s)
- Michael G Wuo
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Seong Ho Hong
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Arunima Singh
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Paramjit S Arora
- Department of Chemistry , New York University , New York , New York 10003 , United States
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27
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Abstract
Peptide secondary and tertiary structure motifs frequently serve as inspiration for the development of protein-protein interaction (PPI) inhibitors. While a wide variety of strategies have been used to stabilize or imitate α-helices, similar strategies for β-sheet stabilization are more limited. Synthetic scaffolds that stabilize reverse turns and cross-strand interactions have provided important insights into β-sheet stability and folding. However, these templates occupy regions of the β-sheet that might impact the β-sheet's ability to bind at a PPI interface. Here, we present the hydrogen bond surrogate (HBS) approach for stabilization of β-hairpin peptides. The HBS linkage replaces a cross-strand hydrogen bond with a covalent linkage, conferring significant conformational and proteolytic resistance. Importantly, this approach introduces the stabilizing linkage in the buried β-sheet interior, retains all side chains for further functionalization, and allows efficient solid-phase macrocyclization. We anticipate that HBS stabilization of PPI β-sheets will enhance the development of β-sheet PPI inhibitors and expand the repertoire of druggable PPIs.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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28
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Wuo MG, Arora PS. Engineered protein scaffolds as leads for synthetic inhibitors of protein-protein interactions. Curr Opin Chem Biol 2018; 44:16-22. [PMID: 29803113 DOI: 10.1016/j.cbpa.2018.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/09/2018] [Indexed: 11/18/2022]
Abstract
Rationally designed protein-protein interaction inhibitors mimic interfacial binding epitopes, specifically residues that contribute significantly to binding. However, direct mimicry often does not lead to high affinity ligands because the natural complexes themselves are functionally transient and of low affinity. The mimics typically need to be optimized for potency. Engineered proteins displaying conformationally-defined epitopes may serve as attractive alternatives to natural protein partners as they can be strictly screened for tight binding. The advantage of focused screens with conformationally-defined protein scaffolds is that conservation of the geometry of the natural binding epitopes may preserve binding site specificity while allowing direct mimicry by various synthetic secondary structure scaffolds. Here we review different classes of engineered proteins for their binding epitope geometry and as leads for synthetic secondary and tertiary structure mimics.
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Affiliation(s)
- Michael G Wuo
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA.
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29
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30
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Watkins AM, Craven TW, Renfrew PD, Arora PS, Bonneau R. Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers. Structure 2017; 25:1771-1780.e3. [PMID: 29033287 PMCID: PMC5845441 DOI: 10.1016/j.str.2017.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 06/21/2017] [Accepted: 09/14/2017] [Indexed: 01/28/2023]
Abstract
β-Amino acids offer attractive opportunities to develop biologically active peptidomimetics, either employed alone or in conjunction with natural α-amino acids. Owing to their potential for unique conformational preferences that deviate considerably from α-peptide geometries, β-amino acids greatly expand the possible chemistries and physical properties available to polyamide foldamers. Complete in silico support for designing new molecules incorporating non-natural amino acids typically requires representing their side-chain conformations as sets of discrete rotamers for model refinement and sequence optimization. Such rotamer libraries are key components of several state-of-the-art design frameworks. Here we report the development, incorporation in to the Rosetta macromolecular modeling suite, and validation of rotamer libraries for β3-amino acids.
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Affiliation(s)
- Andrew M Watkins
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Timothy W Craven
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10009, USA; Institute for Protein Design, University of Washington, Seattle, WA 98102, USA
| | - P Douglas Renfrew
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10009, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Richard Bonneau
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10009, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, NY 10009, USA.
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31
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Affiliation(s)
- Huabin Wu
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Handoko
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Monika Raj
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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32
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Abstract
The use of peptidomimetic scaffolds to target protein-protein interfaces is a promising strategy for inhibitor design. The strategy relies on mimicry of protein motifs that exhibit a concentration of native hot spot residues. To address this constraint, we present a pocket-centric computational design strategy guided by AlphaSpace to identify high-quality pockets near the peptidomimetic motif that are both targetable and unoccupied. Alpha-clusters serve as a spatial representation of pocket space and are used to guide the selection of natural and non-natural amino acid mutations to design inhibitors that optimize pocket occupation across the interface. We tested the strategy against a challenging protein-protein interaction target, KIX/MLL, by optimizing a single helical motif within MLL to compete against the full-length wild-type MLL sequence. Molecular dynamics simulation and experimental fluorescence polarization assays are used to verify the efficacy of the optimized peptide sequence.
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Affiliation(s)
- David Rooklin
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ashley E Modell
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Haotian Li
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Viktoriya Berdan
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University , New York, New York 10003, United States.,NYU-ECNU Center for Computational Chemistry, New York University-Shanghai , Shanghai 200122, China
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33
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Abstract
Protein-protein interactions (PPIs) are ubiquitous in biological systems and often misregulated in disease. As such, specific PPI modulators are desirable to unravel complex PPI pathways and expand the number of druggable targets available for therapeutic intervention. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets. This Account describes our systematic approach using secondary and tertiary protein domain mimics (PDMs) to specifically modulate PPIs. Our strategy focuses on mimicry of regular secondary and tertiary structure elements from one of the PPI partners to inspire rational PDM design. We have compiled three databases (HIPPDB, SIPPDB, and DIPPDB) of secondary and tertiary structures at PPI interfaces to guide our designs and better understand the energetics of PPI secondary and tertiary structures. Our efforts have focused on three of the most common secondary and tertiary structures: α-helices, β-strands, and helix dimers (e.g., coiled coils). To mimic α-helices, we designed the hydrogen bond surrogate (HBS) as an isosteric PDM and the oligooxopiperazine helix mimetic (OHM) as a topographical PDM. The nucleus of the HBS approach is a peptide macrocycle in which the N-terminal i, i + 4 main-chain hydrogen bond is replaced with a covalent carbon-carbon bond. In mimicking a main-chain hydrogen bond, the HBS approach stabilizes the α-helical conformation while leaving all helical faces available for functionalization to tune binding affinity and specificity. The OHM approach, in contrast, envisions a tetrapeptide to mimic one face of a two-turn helix. We anticipated that placement of ethylene bridges between adjacent amides constrains the tetrapeptide backbone to mimic the i, i + 4, and i + 7 side chains on one face of an α-helix. For β-strands, we developed triazolamers, a topographical PDM where the peptide bonds are replaced by triazoles. The triazoles simultaneously stabilize the extended, zigzag conformation of β-strands and transform an otherwise ideal protease substrate into a stable molecule by replacement of the peptide bonds. We turned to a salt bridge surrogate (SBS) approach as a means for stabilizing very short helix dimers. As with the HBS approach, the SBS strategy replaces a noncovalent interaction with a covalent bond. Specifically, we used a bis-triazole linkage that mimics a salt bridge interaction to drive helix association and folding. Using this approach, we were able to stabilize helix dimers that are less than half of the length required to form a coiled coil from two independent strands. In addition to demonstrating the stabilization of desired structures, we have also shown that our designed PDMs specifically modulate target PPIs in vitro and in vivo. Examples of PPIs successfully targeted include HIF1α/p300, p53/MDM2, Bcl-xL/Bak, Ras/Sos, and HIV gp41. The PPI databases and designed PDMs created in these studies will aid development of a versatile set of molecules to probe complex PPI functions and, potentially, PPI-based therapeutics.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Andrew M. Watkins
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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34
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Ghosal K, Colby JM, Das D, Joy ST, Arora PS, Krantz BA. Dynamic Phenylalanine Clamp Interactions Define Single-Channel Polypeptide Translocation through the Anthrax Toxin Protective Antigen Channel. J Mol Biol 2017; 429:900-910. [PMID: 28192089 DOI: 10.1016/j.jmb.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/03/2017] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
Abstract
Anthrax toxin is an intracellularly acting toxin where sufficient detail is known about the structure of its channel, allowing for molecular investigations of translocation. The toxin is composed of three proteins, protective antigen (PA), lethal factor (LF), and edema factor (EF). The toxin's translocon, PA, translocates the large enzymes, LF and EF, across the endosomal membrane into the host cell's cytosol. Polypeptide clamps located throughout the PA channel catalyze the translocation of LF and EF. Here, we show that the central peptide clamp, the ϕ clamp, is a dynamic site that governs the overall peptide translocation pathway. Single-channel translocations of a 10-residue, guest-host peptide revealed that there were four states when peptide interacted with the channel. Two of the states had intermediate conductances of 10% and 50% of full conductance. With aromatic guest-host peptides, the 50% conducting intermediate oscillated with the fully blocked state. A Trp guest-host peptide was studied by manipulating its stereochemistry and prenucleating helix formation with a covalent linkage in the place of a hydrogen bond or hydrogen-bond surrogate (HBS). The Trp peptide synthesized with ʟ-amino acids translocated more efficiently than peptides synthesized with D- or alternating D,ʟ-amino acids. HBS stapled Trp peptide exhibited signs of steric hindrance and difficulty translocating. However, when mutant ϕ clamp (F427A) channels were tested, the HBS peptide translocated normally. Overall, peptide translocation is defined by dynamic interactions between the peptide and ϕ clamp. These dynamics require conformational flexibility, such that the peptide productively forms both extended-chain and helical states during translocation.
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Affiliation(s)
- Koyel Ghosal
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, 650 W, Baltimore Street, Baltimore, MD 21201, USA
| | - Jennifer M Colby
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Debasis Das
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, 650 W, Baltimore Street, Baltimore, MD 21201, USA
| | - Stephen T Joy
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Bryan A Krantz
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, 650 W, Baltimore Street, Baltimore, MD 21201, USA.
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35
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36
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Abstract
We describe a modular approach to identify and inhibit protein-protein interactions (PPIs) that are mediated by protein secondary and tertiary structures with rationally designed peptidomimetics. Our analysis begins with entries of high-resolution complexes in the Protein Data Bank and utilizes conformational sampling, scoring, and design capabilities of advanced biomolecular modeling software to develop peptidomimetics.
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Affiliation(s)
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 29 Washington Place, Brown Bldg., Room 360, New York, NY, USA.
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37
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Abstract
Substitution of a main chain i → i + 4 hydrogen bond with a covalent bond can nucleate and stabilize the α-helical conformation in peptides. Herein we describe the potential of different alkene isosteres to mimic intramolecular hydrogen bonds and stabilize α-helices in diverse peptide sequences.
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Affiliation(s)
- Stephen T Joy
- Department of Chemistry, New York University, New York, NY 10003, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA.
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38
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Abstract
Protein secondary structures serve as geometrically constrained scaffolds for the display of key interacting residues at protein interfaces. Given the critical role of secondary structures in protein folding and the dependence of folding propensities on backbone dihedrals, secondary structure is expected to influence the identity of residues that are important for complex formation. Counter to this expectation, we find that a narrow set of residues dominates the binding energy in protein-protein complexes independent of backbone conformation. This finding suggests that the binding epitope may instead be substantially influenced by the side-chain conformations adopted. We analyzed side-chain conformational preferences in residues that contribute significantly to binding. This analysis suggests that preferred rotamers contribute directly to specificity in protein complex formation and provides guidelines for peptidomimetic inhibitor design.
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Affiliation(s)
| | - Richard Bonneau
- Center for Computational Biology, Simons Foundation , New York, New York 10010, United States
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39
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Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
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40
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Abstract
![]()
The
modulation of protein–protein interactions (PPIs) by
means of creating or stabilizing secondary structure conformations
is a rapidly growing area of research. Recent success in the inhibition
of difficult PPIs by secondary structure mimetics also points to potential
limitations, because often, specific cases require tertiary structure
mimetics. To streamline protein structure-based inhibitor design,
we have previously described the examination of protein complexes
in the Protein Data Bank where α-helices or β-strands
form critical contacts. Here, we examined coiled coils and helix bundles
that mediate complex formation to create a platform for the discovery
of potential tertiary structure mimetics. Though there has been extensive
analysis of coiled coil motifs, the interactions between pre-formed
coiled coils and globular proteins have not been systematically analyzed.
This article identifies critical features of these helical interfaces
with respect to coiled coil and other helical PPIs. We expect the
analysis to prove useful for the rational design of modulators of
this fundamental class of protein assemblies.
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Affiliation(s)
- Andrew M Watkins
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Michael G Wuo
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University , New York, New York 10003, United States
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41
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Abstract
Coiled coils are a major motif in proteins and orchestrate multimerization of various complexes important for biological processes. Inhibition of coiled coil-mediated interactions has significant biomedical potential. However, general approaches that afford short peptides with defined coiled coil conformation remain elusive. We evaluated several strategies to stabilize minimal helical bundles, with the dimer motif as the initial focus. A stable dimeric scaffold was realized in a synthetic sequence by replacing an interhelical ionic bond with a covalent bond. Application of this strategy to a more challenging native protein-protein interaction (PPI) suggested that an additional constraint, a disulfide bond at the internal a/d' position along with a linker at the e/e' position, is required for enhanced conformational stability. We anticipate the coiled coil stabilization methodology described herein to yield new classes of modulators for PPIs.
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Affiliation(s)
- Michael G Wuo
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Andrew B Mahon
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University , New York, New York 10003, United States
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42
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Abstract
![]()
Inhibition
of protein–protein interactions (PPIs) is emerging
as a promising therapeutic strategy despite the difficulty in targeting
such interfaces with drug-like small molecules. PPIs generally feature
large and flat binding surfaces as compared to typical drug targets.
These features pose a challenge for structural characterization of
the surface using geometry-based pocket-detection methods. An attractive
mapping strategy—that builds on the principles of fragment-based
drug discovery (FBDD)—is to detect the fragment-centric modularity
at the protein surface and then characterize the large PPI interface
as a set of localized, fragment-targetable interaction regions. Here,
we introduce AlphaSpace, a computational analysis tool designed for
fragment-centric topographical mapping (FCTM) of PPI interfaces. Our
approach uses the alpha sphere construct, a geometric feature of a
protein’s Voronoi diagram, to map out concave interaction space
at the protein surface. We introduce two new features—alpha-atom
and alpha-space—and the concept of the alpha-atom/alpha-space
pair to rank pockets for fragment-targetability and to facilitate
the evaluation of pocket/fragment complementarity. The resulting high-resolution
interfacial map of targetable pocket space can be used to guide the
rational design and optimization of small molecule or biomimetic PPI
inhibitors.
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Affiliation(s)
- David Rooklin
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Cheng Wang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Joseph Katigbak
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University , New York, New York 10003, United States.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
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43
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Abstract
Chemoselective reactions for amide bond formation have transformed the ability to access synthetic proteins and other bioconjugates through ligation of fragments. In these ligations, amide bond formation is accelerated by transient enforcement of an intramolecular reaction between the carboxyl and the amine termini of two fragments. Building on this principle, we introduce an aldehyde capture ligation that parlays the high chemoselective reactivity of aldehydes and amines to enforce amide bond formation between amino acid residues and peptides that are difficult to ligate by existing technologies.
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Affiliation(s)
- Monika Raj
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Huabin Wu
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Sarah L Blosser
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Marc A Vittoria
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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44
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Nickerson S, Joy ST, Arora PS, Bar-Sagi D. Abstract B46: Stabilized helices targeting the RAS-SOS interaction as inhibitors of RAS-dependent cancer cell growth. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.rasonc14-b46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Accumulating evidence supports an essential role for wild-type RAS isoforms in oncogenic RAS-driven tumorigenesis. Recently, we demonstrated that allosteric stimulation of SOS by oncogenic RAS facilitates cross-activation of wild-type RAS and is required for malignancy. To inhibit SOS-mediated activation of RAS we generated stabilized peptide α-helices derived from the catalytic helix of SOS using the hydrogen bond surrogate approach (HBSSOS). Treatment of RAS-mutant cancer cells with HBSSOS inhibits cell proliferation and induces a G2/M phase checkpoint arrest. Importantly, HBSSOS is taken up into cells by macropinocytosis, an endocytic mechanism that is elevated in RAS-mutant cancer cells, and the levels of macropinocytosis for a given cell line correlate inversely with the half maximum effective concentration (EC50) of HBSSOS, indicating preferential uptake of HBSSOS by RAS-mutant cells. Our results identify macropinocytic uptake of stabilized helices as a potential strategy for inhibiting RAS-dependent cancer cell growth.
Citation Format: Seth Nickerson, Stephen T. Joy, Paramjit S. Arora, Dafna Bar-Sagi. Stabilized helices targeting the RAS-SOS interaction as inhibitors of RAS-dependent cancer cell growth. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr B46. doi: 10.1158/1557-3125.RASONC14-B46
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45
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Abstract
The development of inhibitors for protein-protein interactions frequently involves the mimicry of secondary structure motifs. While helical protein-protein interactions have been heavily targeted, a similar level of success for the inhibition of β-strand and β-sheet rich interfaces has been elusive. We describe an assessment of the full range of β-strand interfaces whose high-resolution structures are available in the Protein Data Bank. This analysis identifies complexes where a β-stand or β-sheet contributes significantly to binding. The results highlight the molecular recognition complexity in strand-mediated interactions relative to helical interfaces and offer guidelines for the construction of β-strand and β-sheet mimics as ligands for protein receptors. The online data set will potentially serve as an entry-point to new classes of protein-protein interaction inhibitors.
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Affiliation(s)
- Andrew M. Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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46
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Udomprasert A, Bongiovanni MN, Sha R, Sherman WB, Wang T, Arora PS, Canary JW, Gras SL, Seeman NC. Amyloid fibrils nucleated and organized by DNA origami constructions. Nat Nanotechnol 2014; 9:537-41. [PMID: 24880222 PMCID: PMC4082467 DOI: 10.1038/nnano.2014.102] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/23/2014] [Indexed: 05/24/2023]
Abstract
Amyloid fibrils are ordered, insoluble protein aggregates that are associated with neurodegenerative conditions such as Alzheimer's disease. The fibrils have a common rod-like core structure, formed from an elongated stack of β-strands, and have a rigidity similar to that of silk (Young's modulus of 0.2-14 GPa). They also exhibit high thermal and chemical stability and can be assembled in vitro from short synthetic non-disease-related peptides. As a result, they are of significant interest in the development of self-assembled materials for bionanotechnology applications. Synthetic DNA molecules have previously been used to form intricate structures and organize other materials such as metal nanoparticles and could in principle be used to nucleate and organize amyloid fibrils. Here, we show that DNA origami nanotubes can sheathe amyloid fibrils formed within them. The fibrils are built by modifying the synthetic peptide fragment corresponding to residues 105-115 of the amyloidogenic protein transthyretin and a DNA origami construct is used to form 20-helix DNA nanotubes with sufficient space for the fibrils inside. Once formed, the fibril-filled nanotubes can be organized onto predefined two-dimensional platforms via DNA-DNA hybridization interactions.
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Affiliation(s)
| | - Marie N. Bongiovanni
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - William B. Sherman
- Bard High School Early College - Queens, 30-20 Thomson Ave., Queens, NY 11101, USA
| | - Tong Wang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sally L. Gras
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
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47
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Abstract
The α-helix is a prevalent secondary structure in proteins and is critical in mediating protein-protein interactions (PPIs). Peptide mimetics that adopt stable helices have become powerful tools for the modulation of PPIs in vitro and in vivo. Hydrogen-bond surrogate (HBS) α-helices utilize a covalent bond in place of an N-terminal i to i+4 hydrogen bond and have been used to target and disrupt PPIs that become dysregulated in disease states. These compounds have improved conformational stability and cellular uptake as compared to their linear peptide counterparts. The protocol presented here describes current methodology for the synthesis of HBS α-helical mimetics. The solid-phase synthesis of HBS helices involves solid-phase peptide synthesis with three key steps involving incorporation of N-allyl functionality within the backbone of the peptide, coupling of a secondary amine, and a ring-closing metathesis step.
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Affiliation(s)
- Stephen E Miller
- Department of Chemistry, New York University, New York, New York
| | - Paul F Thomson
- Department of Chemistry, New York University, New York, New York
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York
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48
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Lao BB, Drew K, Guarracino DA, Brewer TF, Heindel DW, Bonneau R, Arora PS. Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions. J Am Chem Soc 2014; 136:7877-88. [PMID: 24972345 PMCID: PMC4353027 DOI: 10.1021/ja502310r] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
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Protein–protein
interactions encompass large surface areas, but
often a handful of key residues dominate the binding energy landscape.
Rationally designed small molecule scaffolds that reproduce the relative
positioning and disposition of important binding residues, termed
“hotspot residues”, have been shown to successfully
inhibit specific protein complexes. Although this strategy has led
to development of novel synthetic inhibitors of protein complexes,
often direct mimicry of natural amino acid residues does not lead
to potent inhibitors. Experimental screening of focused compound libraries
is used to further optimize inhibitors but the number of possible
designs that can be efficiently synthesized and experimentally tested
in academic settings is limited. We have applied the principles of
computational protein design to optimization of nonpeptidic helix
mimics as ligands for protein complexes. We describe the development
of computational tools to design helix mimetics from canonical and
noncanonical residue libraries and their application to two therapeutically
important protein–protein interactions: p53-MDM2 and p300-HIF1α.
The overall study provides a streamlined approach for discovering
potent peptidomimetic inhibitors of protein–protein interactions.
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Affiliation(s)
- Brooke Bullock Lao
- Department of Chemistry and ‡Departments of Biology and Computer Science, New York University , New York, New York 10003, United States
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49
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Abstract
Rat sarcoma (RAS) proteins are signaling nodes that transduce extracellular cues into precise alterations in cellular physiology by engaging effector pathways. RAS signaling thus regulates diverse cell processes including proliferation, migration, differentiation, and survival. Owing to this central role in governing mitogenic signals, RAS pathway components are often dysregulated in human diseases. Targeted therapy of RAS pathways has generally not been successful, largely because of the robust biochemistry of the targets and their multifaceted network of molecular regulators. The rate-limiting step of RAS activation is Son of Sevenless (SOS)-mediated nucleotide exchange involving a single evolutionarily conserved catalytic helix from SOS. Structure function data of this mechanism provided a strong platform to design an SOS-derived, helically constrained peptide mimic as an inhibitor of the RAS-SOS interaction. In this chapter, we review RAS-SOS signaling dynamics and present evidence supporting the novel paradigm of inhibiting their interaction as a therapeutic strategy. We then describe a method of generating helically constrained peptide mimics of protein surfaces, which we have employed to inhibit the RAS-SOS active site interaction. The biochemical and functional properties of this SOS mimic support the premise that inhibition of RAS-nucleotide exchange can effectively block RAS activation and downstream signaling.
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Affiliation(s)
- Seth Nickerson
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - Stephen T Joy
- Department of Chemistry, New York University, New York, USA
| | | | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA.
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50
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Arora PS, Canary JW. Organic Chemistry: Principles in Context. A Story Telling Historical Approach, by Mark M. Green. ISBN: 0615702716. Chirality 2013. [DOI: 10.1002/chir.22167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - James W. Canary
- Department of Chemistry; New York University; New York; New York
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