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Giacon N, Lo Cascio E, Pennacchietti V, De Maio F, Santarelli G, Sibilia D, Tiberio F, Sanguinetti M, Lattanzi W, Toto A, Arcovito A. PDZ2-conjugated-PLGA nanoparticles are tiny heroes in the battle against SARS-CoV-2. Sci Rep 2024; 14:13059. [PMID: 38844490 PMCID: PMC11156922 DOI: 10.1038/s41598-024-63239-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has highlighted the urgent need for innovative antiviral strategies to fight viral infections. Although a substantial part of the overall effort has been directed at the Spike protein to create an effective global vaccination strategy, other proteins have also been examined and identified as possible therapeutic targets. Among them, although initially underestimated, there is the SARS-CoV-2 E-protein, which turned out to be a key factor in viral pathogenesis due to its role in virus budding, assembly and spreading. The C-terminus of E-protein contains a PDZ-binding motif (PBM) that plays a key role in SARS-CoV-2 virulence as it is recognized and bound by the PDZ2 domain of the human tight junction protein ZO-1. The binding between the PDZ2 domain of ZO-1 and the C-terminal portion of SARS-CoV-2 E-protein has been extensively characterized. Our results prompted us to develop a possible adjuvant therapeutic strategy aimed at slowing down or inhibiting virus-mediated pathogenesis. Such innovation consists in the design and synthesis of externally PDZ2-ZO1 functionalized PLGA-based nanoparticles to be used as intracellular decoy. Contrary to conventional strategies, this innovative approach aims to capitalize on the E protein-PDZ2 interaction to prevent virus assembly and replication. In fact, the conjugation of the PDZ2 domain to polymeric nanoparticles increases the affinity toward the E protein effectively creating a "molecular sponge" able to sequester E proteins within the intracellular environment of infected cells. Our in vitro studies on selected cellular models, show that these nanodevices significantly reduce SARS-CoV-2-mediated virulence, emphasizing the importance of exploiting viral-host interactions for therapeutic benefit.
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Affiliation(s)
- Noah Giacon
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Giulia Santarelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Diego Sibilia
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Federica Tiberio
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Wanda Lattanzi
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.
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2
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Bondarenko V, Chen Q, Tillman TS, Xu Y, Tang P. Unconventional PDZ Recognition Revealed in α7 nAChR-PICK1 Complexes. ACS Chem Neurosci 2024; 15:2070-2079. [PMID: 38691676 PMCID: PMC11099923 DOI: 10.1021/acschemneuro.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024] Open
Abstract
PDZ domains are modular domains that conventionally bind to C terminal or internal motifs of target proteins to control cellular functions through the regulation of protein complex assemblies. Almost all reported structures of PDZ-target protein complexes rely on fragments or peptides as target proteins. No intact target protein complexed with PDZ was structurally characterized. In this study, we used NMR spectroscopy and other biochemistry and biophysics tools to uncover insights into structural coupling between the PDZ domain of protein interacting with C-kinase 1 (PICK1) and α7 nicotinic acetylcholine receptors (α7 nAChR). Notably, the intracellular domains of both α7 nAChR and PICK1 PDZ exhibit a high degree of plasticity in their coupling. Specifically, the MA helix of α7 nAChR interacts with residues lining the canonical binding site of the PICK1 PDZ, while flexible loops also engage in protein-protein interactions. Both hydrophobic and electrostatic interactions mediate the coupling. Overall, the resulting structure of the α7 nAChR-PICK1 complex reveals an unconventional PDZ binding mode, significantly expanding the repertoire of functionally important PDZ interactions.
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Affiliation(s)
- Vasyl Bondarenko
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qiang Chen
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Tommy S. Tillman
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yan Xu
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmacology and Chemical Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Physics and Astronomy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmacology and Chemical Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Computational and Systems Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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3
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Ni C, Hong M. Oligomerization of drug transporters: Forms, functions, and mechanisms. Acta Pharm Sin B 2024; 14:1924-1938. [PMID: 38799641 PMCID: PMC11119549 DOI: 10.1016/j.apsb.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/07/2023] [Accepted: 01/05/2024] [Indexed: 05/29/2024] Open
Abstract
Drug transporters are essential players in the transmembrane transport of a wide variety of clinical drugs. The broad substrate spectra and versatile distribution pattern of these membrane proteins infer their pharmacological and clinical significance. With our accumulating knowledge on the three-dimensional structure of drug transporters, their oligomerization status has become a topic of intense study due to the possible functional roles carried out by such kind of post-translational modification (PTM). In-depth studies of oligomeric complexes formed among drug transporters as well as their interactions with other regulatory proteins can help us better understand the regulatory mechanisms of these membrane proteins, provide clues for the development of novel drugs, and improve the therapeutic efficacy. In this review, we describe different oligomerization forms as well as their structural basis of major drug transporters in the ATP-binding cassette and solute carrier superfamilies, summarize our current knowledge on the influence of oligomerization for protein expression level and transport function of these membrane proteins, and discuss the regulatory mechanisms of oligomerization. Finally, we highlight the challenges associated with the current oligomerization studies and propose some thoughts on the pharmaceutical application of this important drug transporter PTM.
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Affiliation(s)
- Chunxu Ni
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Mei Hong
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China
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4
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: A new OSPREY-based algorithm for designing de novo D-peptide inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579944. [PMID: 38405797 PMCID: PMC10888900 DOI: 10.1101/2024.02.12.579944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan, which enable exponential reductions in the size of the peptide sequence search space. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a new framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead therapeutic candidates. We provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors. Protein Eng Des Sel 2024; 37:gzae007. [PMID: 38757573 PMCID: PMC11099876 DOI: 10.1093/protein/gzae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead inhibitors. We also provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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Affiliation(s)
- Nathan Guerin
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
| | - Henry Childs
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
| | - Bruce R Donald
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
- Department of Mathematics, Duke University, 120 Science Drive, Durham, NC 27708, United States
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6
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Park S, Fan J, Chamakuri S, Palaniappan M, Sharma K, Qin X, Wang J, Tan Z, Judge A, Hu L, Sankaran B, Li F, Prasad BVV, Matzuk MM, Palzkill T. Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. J Med Chem 2024; 67:620-642. [PMID: 38117688 DOI: 10.1021/acs.jmedchem.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.
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Affiliation(s)
- Suhyeorn Park
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kiran Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Martin M Matzuk
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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Miura K, Suzuki Y, Ishida K, Arakawa M, Wu H, Fujioka Y, Emi A, Maeda K, Hamajima R, Nakano T, Tenno T, Hiroaki H, Morita E. Distinct motifs in the E protein are required for SARS-CoV-2 virus particle formation and lysosomal deacidification in host cells. J Virol 2023; 97:e0042623. [PMID: 37830820 PMCID: PMC10617393 DOI: 10.1128/jvi.00426-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has caused a global public health crisis. The E protein, a structural protein found in this virus particle, is also known to be a viroporin. As such, it forms oligomeric ion channels or pores in the host cell membrane. However, the relationship between these two functions is poorly understood. In this study, we showed that the roles of E protein in virus particle and viroporin formation are distinct. This study contributes to the development of drugs that inhibit SARS-CoV-2 virus particle formation. Additionally, we designed a highly sensitive and high-throughput virus-like particle detection system using the HiBiT tag, which is a useful tool for studying the release of SARS-CoV-2.
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Affiliation(s)
- Koya Miura
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Kotaro Ishida
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Masashi Arakawa
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Yoshihiko Fujioka
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Akino Emi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Koki Maeda
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Ryusei Hamajima
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Takeshi Tenno
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
- BeCellBar LLC, Nagoya, Aichi, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
- BeCellBar LLC, Nagoya, Aichi, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
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Giacon N, Lo Cascio E, Davidson DS, Polêto MD, Lemkul JA, Pennacchietti V, Pagano L, Zamparelli C, Toto A, Arcovito A. Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein. Comput Struct Biotechnol J 2023; 21:3259-3271. [PMID: 37293240 PMCID: PMC10210826 DOI: 10.1016/j.csbj.2023.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence of a PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ-containing proteins in the intracellular environment. One of the main binding partners of the SARS-CoV-2 E protein is the PDZ2 domain of ZO1, a protein with a crucial role in the formation of epithelial and endothelial tight junctions (TJs). In this work, through a combination of analytical ultracentrifugation analysis and equilibrium and kinetic folding experiments, we show that ZO1-PDZ2 domain is able to fold in a monomeric state, an alternative form to the dimeric conformation that is reported to be functional in the cell for TJs assembly. Importantly, surface plasmon resonance (SPR) data indicate that the PDZ2 monomer is fully functional and capable of binding the C-terminal portion of the E protein of SARS-CoV-2, with a measured affinity in the micromolar range. Moreover, we present a detailed computational analysis of the complex between the C-terminal portion of E protein with ZO1-PDZ2, both in its monomeric conformation (computed as a high confidence AlphaFold2 model) and dimeric conformation (obtained from the Protein Data Bank), by using both polarizable and nonpolarizable simulations. Together, our results indicate both the monomeric and dimeric states of PDZ2 to be functional partners of the E protein, with similar binding mechanisms, and provide mechanistic and structural information about a fundamental interaction required for the replication of SARS-CoV-2.
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Affiliation(s)
- Noah Giacon
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Darcy S. Davidson
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Marcelo D. Polêto
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Livia Pagano
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
- Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
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Pennacchietti V, Toto A. Different electrostatic forces drive the binding kinetics of SARS-CoV, SARS-CoV-2 and MERS-CoV Envelope proteins with the PDZ2 domain of ZO1. Sci Rep 2023; 13:7906. [PMID: 37193746 DOI: 10.1038/s41598-023-35079-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/12/2023] [Indexed: 05/18/2023] Open
Abstract
The Envelope protein (E) is a structural protein encoded by the genome of SARS-CoV, SARS-CoV-2 and MERS-CoV Coronaviruses. It is poorly present in the virus but highly expressed in the host cell, with prominent role in virus assembly and virulence. The E protein possesses a PDZ-binding motif (PBM) at its C terminus that allows it to interact with host PDZ domain containing proteins. ZO1 is a key protein in assembling the cytoplasmic plaque of epithelial and endothelial Tight Junctions (TJs) as well as in determining cell differentiation, proliferation and polarity. The PDZ2 domain of ZO1 is known to interact with the Coronaviruses Envelope proteins, however the molecular details of such interaction have not been established. In this paper we directly measured, through Fluorescence Resonance Energy Transfer and Stopped-Flow methodology, the binding kinetics of the PDZ2 domain of ZO1 with peptides mimicking the C-terminal portion of the Envelope protein from SARS-CoV, SARS-CoV-2 and MERS-CoV in different ionic strength conditions. Interestingly, the peptide mimicking the E protein from MERS-CoV display much higher microscopic association rate constant with PDZ2 compared to SARS-CoV and SARS-CoV-2 suggesting a stronger contribution of electrostatic forces in the early events of binding. A comparison of thermodynamic and kinetic data obtained at increasing ionic strengths put in evidence different contribution of electrostatics in the recognition and complex formation events for the three peptides. Our data are discussed under the light of available structural data of PDZ2 domain of ZO1 and of previous works about these protein systems.
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Affiliation(s)
- Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy.
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Zhao Y, Grigoryan G. Multiplex measurement of protein-peptide dissociation constants using dialysis and mass spectrometry. Protein Sci 2023; 32:e4607. [PMID: 36823715 PMCID: PMC10031237 DOI: 10.1002/pro.4607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
We propose a high-throughput method for quantitively measuring hundreds of protein-peptide binding affinities in parallel. In this assay a solution of protein is dialyzed into a buffer containing a pool of potential binding peptides, such that upon equilibration the relative abundance of a peptide species is mathematically related to that peptide's dissociation constant, Kd . We use isobaric multiplexed quantitative proteomics to simultaneously determine the relative abundance, and hence the Kd and its associated error, for an entire peptide library. We apply this technique, which we call PEDAL (Parallel Equilibrium Dialysis for Affinity Learning), to determine accurate Kd 's between a PDZ domain and hundreds of peptides, spanning an affinity range of multiple orders of magnitude in a single experiment. PEDAL is a convenient, fast, and low-cost method for measuring large numbers of protein-peptide affinities in parallel, providing a rare combination of true in-solution binding equilibria with the ability to multiplex. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yu Zhao
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire
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11
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Tang H, Wang L, Li S, Wei X, Lv M, Zhong F, Liu Y, Liu J, Fu B, Zhu Q, Wang D, Liu J, Ruan K, Gao J, Xu W. Inhibitors against Two PDZ Domains of MDA-9 Suppressed Migration of Breast Cancer Cells. Int J Mol Sci 2023; 24:ijms24043431. [PMID: 36834839 PMCID: PMC9964117 DOI: 10.3390/ijms24043431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Melanoma differentiation-associated gene 9 (MDA-9) is a small adaptor protein with tandem PDZ domains that promotes tumor progression and metastasis in various human cancers. However, it is difficult to develop drug-like small molecules with high affinity due to the narrow groove of the PDZ domains of MDA-9. Herein, we identified four novel hits targeting the PDZ1 and PDZ2 domains of MDA-9, namely PI1A, PI1B, PI2A, and PI2B, using a protein-observed nuclear magnetic resonance (NMR) fragment screening method. We also solved the crystal structure of the MDA-9 PDZ1 domain in complex with PI1B and characterized the binding poses of PDZ1-PI1A and PDZ2-PI2A, guided by transferred paramagnetic relaxation enhancement. The protein-ligand interaction modes were then cross-validated by the mutagenesis of the MDA-9 PDZ domains. Competitive fluorescence polarization experiments demonstrated that PI1A and PI2A blocked the binding of natural substrates to the PDZ1 and PDZ2 domains, respectively. Furthermore, these inhibitors exhibited low cellular toxicity, but suppressed the migration of MDA-MB-231 breast carcinoma cells, which recapitulated the phenotype of MDA-9 knockdown. Our work has paved the way for the development of potent inhibitors using structure-guided fragment ligation in the future.
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Affiliation(s)
- Heng Tang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Lei Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Shuju Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiaoli Wei
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Mengqi Lv
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Fumei Zhong
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yaqian Liu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bangguo Fu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qizhi Zhu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Dan Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiajia Liu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Ke Ruan
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jia Gao
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Correspondence: (J.G.); (W.X.)
| | - Weiping Xu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Correspondence: (J.G.); (W.X.)
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12
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Stewart BZ, Caria S, Humbert PO, Kvansakul M. Structural analysis of human papillomavirus E6 interactions with Scribble PDZ domains. FEBS J 2023. [PMID: 36609831 DOI: 10.1111/febs.16718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/16/2022] [Accepted: 01/05/2022] [Indexed: 01/08/2023]
Abstract
The cell polarity regulator Scribble has been shown to be a critical regulator of the establishment and development of tissue architecture, and its dysregulation promotes or suppresses tumour development in a context-dependent manner. Scribble activity is subverted by numerous viruses. This includes human papillomaviruses (HPVs), who target Scribble via the E6 protein. Binding of E6 from high-risk HPV strains to Scribble via a C-terminal PDZ-binding motif leads to Scribble degradation in vivo. However, the precise molecular basis for Scribble-E6 interactions remains to be defined. We now show that Scribble PDZ1 and PDZ3 are the major interactors of HPV E6 from multiple high-risk strains, with each E6 protein displaying a unique interaction profile. We then determined crystal structures of Scribble PDZ1 and PDZ3 domains in complex with the PDZ-binding motif (PBM) motifs of E6 from HPV strains 16, 18 and 66. Our findings reveal distinct interaction patterns for each E6 PBM motif from a given HPV strain, suggesting that a complex molecular interplay exists that underpins the overt Scribble-HPV E6 interaction and controls E6 carcinogenic potential.
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Affiliation(s)
- Bryce Z Stewart
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Sofia Caria
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Patrick O Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.,Department of Biochemistry & Pharmacology, University of Melbourne, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, VIC, 3010, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
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13
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HPV-18E6 Inhibits Interactions between TANC2 and SNX27 in a PBM-Dependent Manner and Promotes Increased Cell Proliferation. J Virol 2022; 96:e0136522. [PMID: 36326272 PMCID: PMC9683006 DOI: 10.1128/jvi.01365-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
While a great deal is known about the role of the E6 PDZ binding motif (PBM) in modulating the cellular proteins involved in regulating cell polarity, much less is known about the consequences of E6's interactions with SNX27 and the endocytic sorting machinery. We reasoned that a potential consequence of such interactions could be to affect the fate of multiple SNX27 endosomal partners, such as transmembrane proteins or soluble accessory proteins.
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14
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Brusa I, Sondo E, Falchi F, Pedemonte N, Roberti M, Cavalli A. Proteostasis Regulators in Cystic Fibrosis: Current Development and Future Perspectives. J Med Chem 2022; 65:5212-5243. [PMID: 35377645 PMCID: PMC9014417 DOI: 10.1021/acs.jmedchem.1c01897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In cystic fibrosis (CF), the deletion of phenylalanine 508 (F508del) in the CF transmembrane conductance regulator (CFTR) leads to misfolding and premature degradation of the mutant protein. These defects can be targeted with pharmacological agents named potentiators and correctors. During the past years, several efforts have been devoted to develop and approve new effective molecules. However, their clinical use remains limited, as they fail to fully restore F508del-CFTR biological function. Indeed, the search for CFTR correctors with different and additive mechanisms has recently increased. Among them, drugs that modulate the CFTR proteostasis environment are particularly attractive to enhance therapy effectiveness further. This Perspective focuses on reviewing the recent progress in discovering CFTR proteostasis regulators, mainly describing the design, chemical structure, and structure-activity relationships. The opportunities, challenges, and future directions in this emerging and promising field of research are discussed, as well.
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Affiliation(s)
- Irene Brusa
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Elvira Sondo
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | | | | | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
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