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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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Tubiana J, Adriana-Lifshits L, Nissan M, Gabay M, Sher I, Sova M, Wolfson HJ, Gal M. Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions. PLoS Comput Biol 2023; 19:e1010874. [PMID: 36730443 PMCID: PMC9928118 DOI: 10.1371/journal.pcbi.1010874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/14/2023] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Design of peptide binders is an attractive strategy for targeting "undruggable" protein-protein interfaces. Current design protocols rely on the extraction of an initial sequence from one known protein interactor of the target protein, followed by in-silico or in-vitro mutagenesis-based optimization of its binding affinity. Wet lab protocols can explore only a minor portion of the vast sequence space and cannot efficiently screen for other desirable properties such as high specificity and low toxicity, while in-silico design requires intensive computational resources and often relies on simplified binding models. Yet, for a multivalent protein target, dozens to hundreds of natural protein partners already exist in the cellular environment. Here, we describe a peptide design protocol that harnesses this diversity via a machine learning generative model. After identifying putative natural binding fragments by literature and homology search, a compositional Restricted Boltzmann Machine is trained and sampled to yield hundreds of diverse candidate peptides. The latter are further filtered via flexible molecular docking and an in-vitro microchip-based binding assay. We validate and test our protocol on calcineurin, a calcium-dependent protein phosphatase involved in various cellular pathways in health and disease. In a single screening round, we identified multiple 16-length peptides with up to six mutations from their closest natural sequence that successfully interfere with the binding of calcineurin to its substrates. In summary, integrating protein interaction and sequence databases, generative modeling, molecular docking and interaction assays enables the discovery of novel protein-protein interaction modulators.
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Affiliation(s)
- Jérôme Tubiana
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Lucia Adriana-Lifshits
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michael Nissan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Matan Gabay
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Inbal Sher
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marina Sova
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haim J. Wolfson
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Maayan Gal
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Cytoskeletal regulation of a transcription factor by DNA mimicry via coiled-coil interactions. Nat Cell Biol 2022; 24:1088-1098. [PMID: 35725768 PMCID: PMC10016618 DOI: 10.1038/s41556-022-00935-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/06/2022] [Indexed: 02/07/2023]
Abstract
A long-established strategy for transcription regulation is the tethering of transcription factors to cellular membranes. By contrast, the principal effectors of Hedgehog signalling, the GLI transcription factors, are regulated by microtubules in the primary cilium and the cytoplasm. How GLI is tethered to microtubules remains unclear. Here, we uncover DNA mimicry by the ciliary kinesin KIF7 as a mechanism for the recruitment of GLI to microtubules, wherein the coiled-coil dimerization domain of KIF7, characterized by its striking shape, size and charge similarity to DNA, forms a complex with the DNA-binding zinc fingers in GLI, thus revealing a mode of tethering a DNA-binding protein to the cytoskeleton. GLI increases KIF7 microtubule affinity and consequently modulates the localization of both proteins to microtubules and the cilium tip. Thus, the kinesin-microtubule system is not a passive GLI tether but a regulatable platform tuned by the kinesin-transcription factor interaction. We retooled this coiled-coil-based GLI-KIF7 interaction to inhibit the nuclear and cilium localization of GLI. This strategy can potentially be exploited to downregulate erroneously activated GLI in human cancers.
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Foight GW, Wang Z, Wei CT, Jr Greisen P, Warner KM, Cunningham-Bryant D, Park K, Brunette TJ, Sheffler W, Baker D, Maly DJ. Multi-input chemical control of protein dimerization for programming graded cellular responses. Nat Biotechnol 2019; 37:1209-1216. [PMID: 31501561 PMCID: PMC6776690 DOI: 10.1038/s41587-019-0242-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/25/2019] [Indexed: 12/11/2022]
Abstract
Chemical and optogenetic methods for post-translationally controlling protein function have enabled modulation and engineering of cellular functions. However, most of these methods only confer single-input, single-output control. To increase the diversity of post-translational behaviors that can be programmed, we built a system based on a single protein receiver that can integrate multiple drug inputs, including approved therapeutics. Our system translates drug inputs into diverse outputs using a suite of engineered reader proteins to provide variable dimerization states of the receiver protein. We show that our single receiver protein architecture can be used to program a variety of cellular responses, including graded and proportional dual-output control of transcription and mammalian cell signaling. We apply our tools to titrate the competing activities of the Rac and Rho GTPases to control cell morphology. Our versatile tool set will enable researchers to post-translationally program mammalian cellular processes and to engineer cell therapies.
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Affiliation(s)
- Glenna Wink Foight
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Zhizhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Cindy T Wei
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Per Jr Greisen
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Global Research, Novo Nordisk A/S, Måløv, Denmark
| | - Katrina M Warner
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | | | - Keunwan Park
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Systems Biotechnology Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - T J Brunette
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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Jenson JM, Ryan JA, Grant RA, Letai A, Keating AE. Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1. eLife 2017; 6:e25541. [PMID: 28594323 PMCID: PMC5464773 DOI: 10.7554/elife.25541] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/16/2017] [Indexed: 01/07/2023] Open
Abstract
Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs. High-resolution crystal structures show that designed peptide FS2 binds Bfl-1 in a shifted geometry, relative to PUMA and other binding partners, due to a set of epistatic mutations. FS2 modified with an electrophile reacts with a cysteine near the peptide-binding groove to augment specificity. Designed Bfl-1 binders provide reagents for cellular profiling and leads for developing enhanced and cell-permeable peptide or small-molecule inhibitors.
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Affiliation(s)
- Justin M Jenson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Jeremy A Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States,Department of Biology, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States,
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