1
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Zhang W, Wang J, Shan C. The eEF1A protein in cancer: Clinical significance, oncogenic mechanisms, and targeted therapeutic strategies. Pharmacol Res 2024; 204:107195. [PMID: 38677532 DOI: 10.1016/j.phrs.2024.107195] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
Eukaryotic elongation factor 1A (eEF1A) is among the most abundant proteins in eukaryotic cells. Evolutionarily conserved across species, eEF1A is in charge of translation elongation for protein biosynthesis as well as a plethora of non-translational moonlighting functions for cellular homeostasis. In malignant cells, however, eEF1A becomes a pleiotropic driver of cancer progression via a broad diversity of pathways, which are not limited to hyperactive translational output. In the past decades, mounting studies have demonstrated the causal link between eEF1A and carcinogenesis, gaining deeper insights into its multifaceted mechanisms and corroborating its value as a prognostic marker in various cancers. On the other hand, an increasing number of natural and synthetic compounds were discovered as anticancer eEF1A-targeting inhibitors. Among them, plitidepsin was approved for the treatment of multiple myeloma whereas metarrestin was currently under clinical development. Despite significant achievements in these two interrelated fields, hitherto there lacks a systematic examination of the eEF1A protein in the context of cancer research. Therefore, the present work aims to delineate its clinical implications, molecular oncogenic mechanisms, and targeted therapeutic strategies as reflected in the ever expanding body of literature, so as to deepen mechanistic understanding of eEF1A-involved tumorigenesis and inspire the development of eEF1A-targeted chemotherapeutics and biologics.
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Affiliation(s)
- Weicheng Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China.
| | - Jiyan Wang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China
| | - Changliang Shan
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China.
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2
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Liu T, Liu J. Integration analysis of single-cell transcriptome reveals specific monocyte subsets associated with melanoma brain and leptomeningeal metastasis. Skin Res Technol 2024; 30:e13710. [PMID: 38616506 PMCID: PMC11016815 DOI: 10.1111/srt.13710] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Melanoma central nervous system (CNS) metastasis remains a leading cause of patient mortality, and the underlying pathological mechanism has not been fully elucidated, leading to a lack of effective therapeutic strategies. MATERIALS AND METHODS In this study, we conducted an integrated analysis of single-cell transcriptomic data related to melanoma brain metastasis (MBM) and leptomeningeal metastasis (LMM). We focused on differences of subset composition and molecular expression of monocytes in blood, primary tumor, brain metastases, and leptomeningeal metastases. RESULTS Significant differences were observed among monocytes in blood, primary tumor, and different CNS metastatic tissues, particularly in terms of subset differentiation and gene expression patterns. Subsequent analysis revealed the upregulation of cell proportions of six monocyte subsets in brain metastasis and leptomeningeal metastasis. Based on differential gene analysis, four of these subsets exhibited increased expression of factors promoting tumor migration and survival, including AREG+ monocytes (AREG, EREG, THBS1), FABP5+ monocytes (SPP1, CCL2, CTSL), and CXCL3+ monocytes (CXCL3, IL8, IL1B). The proportions of TPSB2+ monocytes (IL32, CCL5) were notably elevated in melanoma leptomeningeal metastasis tissues. Pathway analysis indicated the activation of signaling pathways such as NOD-like receptors, NFκB, and Toll-like receptors in these metastasis-related subsets. CONCLUSION Our findings elucidate that AREG+, FABP5+ and CXCL3+ monocytes are associated with brain metastasis and TPSB2+ monocytes are associated with leptomeningeal metastasis in melanoma, which may be contribute to the development of therapeutic strategies focusing on monocytes or cytokines for melanoma CNS metastasis.
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Affiliation(s)
- Tao Liu
- Department of General Surgerythe First People's Hospital of Shuangliu DistrictChengduChina
| | - Jian‐Ping Liu
- Department of General Surgerythe First People's Hospital of Shuangliu DistrictChengduChina
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3
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Zhang H, Cai J, Yu S, Sun B, Zhang W. Anticancer Small-Molecule Agents Targeting Eukaryotic Elongation Factor 1A: State of the Art. Int J Mol Sci 2023; 24:ijms24065184. [PMID: 36982256 PMCID: PMC10049629 DOI: 10.3390/ijms24065184] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Eukaryotic elongation factor 1A (eEF1A) canonically delivers amino acyl tRNA to the ribosomal A site during the elongation stage of protein biosynthesis. Yet paradoxically, the oncogenic nature of this instrumental protein has long been recognized. Consistently, eEF1A has proven to be targeted by a wide assortment of small molecules with excellent anticancer activity, among which plitidepsin has been granted approval for the treatment of multiple myeloma. Meanwhile, metarrestin is currently under clinical development for metastatic cancers. Bearing these exciting advances in mind, it would be desirable to present a systematic up-to-date account of the title topic, which, to the best of our knowledge, has thus far been unavailable in the literature. The present review summarizes recent advances in eEF1A-targeting anticancer agents, both naturally occurring and synthetically crafted, with regard to their discovery or design, target identification, structure–activity relationship, and mode of action. Their structural diversity and differential eEF1A-targeting mechanisms warrant continuing research in pursuit of curing eEF1A-driven malignancy.
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4
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Kochavi A, Lovecchio D, Faller WJ, Agami R. Proteome diversification by mRNA translation in cancer. Mol Cell 2023; 83:469-480. [PMID: 36521491 DOI: 10.1016/j.molcel.2022.11.014] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis and is well known to be altered by oncogenes to promote cancer development. This distorted mRNA translation is accompanied by the vulnerability of cancer to inhibitors of key mRNA translation components. Novel studies also suggest that these alternations could be utilized for immunotherapy. Ribosome heterogeneity and alternative responses to nutrient shortages, which aid cancer growth and spread, are proposed to elicit aberrant protein production but may also result in previously unidentified therapeutic targets, such as the presentation of cancer-specific peptides at the surface of cancer cells (neoepitopes). This review will assess the driving forces in tRNA and ribosome function that underlie proteome diversification due to alterations in mRNA translation in cancer cells.
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Affiliation(s)
- Adva Kochavi
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Domenica Lovecchio
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.
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5
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Oltion K, Carelli JD, Yang T, See SK, Wang HY, Kampmann M, Taunton J. An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes. Cell 2023; 186:346-362.e17. [PMID: 36638793 PMCID: PMC9994462 DOI: 10.1016/j.cell.2022.12.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 03/21/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 01/14/2023]
Abstract
Ribosomes frequently stall during mRNA translation, resulting in the context-dependent activation of quality control pathways to maintain proteostasis. However, surveillance mechanisms that specifically respond to stalled ribosomes with an occluded A site have not been identified. We discovered that the elongation factor-1α (eEF1A) inhibitor, ternatin-4, triggers the ubiquitination and degradation of eEF1A on stalled ribosomes. Using a chemical genetic approach, we unveiled a signaling network comprising two E3 ligases, RNF14 and RNF25, which are required for eEF1A degradation. Quantitative proteomics revealed the RNF14 and RNF25-dependent ubiquitination of eEF1A and a discrete set of ribosomal proteins. The ribosome collision sensor GCN1 plays an essential role by engaging RNF14, which directly ubiquitinates eEF1A. The site-specific, RNF25-dependent ubiquitination of the ribosomal protein RPS27A/eS31 provides a second essential signaling input. Our findings illuminate a ubiquitin signaling network that monitors the ribosomal A site and promotes the degradation of stalled translation factors, including eEF1A and the termination factor eRF1.
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Affiliation(s)
- Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan D Carelli
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tangpo Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stephanie K See
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hao-Yuan Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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6
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Wang HY, Yang H, Holm M, Tom H, Oltion K, Al-Khdhairawi AAQ, Weber JFF, Blanchard SC, Ruggero D, Taunton J. Synthesis and single-molecule imaging reveal stereospecific enhancement of binding kinetics by the antitumour eEF1A antagonist SR-A3. Nat Chem 2022; 14:1443-1450. [PMID: 36123449 PMCID: PMC10018702 DOI: 10.1038/s41557-022-01039-3] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 08/08/2022] [Indexed: 01/04/2023]
Abstract
Ternatin-family cyclic peptides inhibit protein synthesis by targeting the eukaryotic elongation factor-1α. A potentially related cytotoxic natural product ('A3') was isolated from Aspergillus, but only 4 of its 11 stereocentres could be assigned. Here, we synthesized SR-A3 and SS-A3-two out of 128 possible A3 epimers-and discovered that synthetic SR-A3 is indistinguishable from naturally derived A3. Relative to SS-A3, SR-A3 exhibits an enhanced residence time and rebinding kinetics, as revealed by single-molecule fluorescence imaging of elongation reactions catalysed by eukaryotic elongation factor-1α in vitro. An increased residence time-stereospecifically conferred by the unique β-hydroxyl in SR-A3-was also observed in cells. Consistent with its prolonged duration of action, thrice-weekly dosing with SR-A3 led to a reduced tumour burden and increased survival in an aggressive Myc-driven mouse lymphoma model. Our results demonstrate the potential of SR-A3 as a cancer therapeutic and exemplify an evolutionary mechanism for enhancing cyclic peptide binding kinetics via stereospecific side-chain hydroxylation.
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Affiliation(s)
- Hao-Yuan Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Haojun Yang
- Department of Urology, University of California, San Francisco, CA, USA
| | - Mikael Holm
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Harrison Tom
- Department of Urology, University of California, San Francisco, CA, USA
| | - Keely Oltion
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | - Jean-Frédéric F Weber
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA (UiTM) Selangor Branch, Bandar Puncak Alam, Malaysia
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Davide Ruggero
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
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7
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Yang X, Wu W, Li H, Zhang M, Chu Z, Wang X, Sun P. Natural occurrence, bioactivity, and biosynthesis of triene-ansamycins. Eur J Med Chem 2022; 244:114815. [DOI: 10.1016/j.ejmech.2022.114815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022]
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8
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Juette MF, Carelli JD, Rundlet EJ, Brown A, Shao S, Ferguson A, Wasserman MR, Holm M, Taunton J, Blanchard SC. Didemnin B and ternatin-4 differentially inhibit conformational changes in eEF1A required for aminoacyl-tRNA accommodation into mammalian ribosomes. eLife 2022; 11:e81608. [PMID: 36264623 PMCID: PMC9584604 DOI: 10.7554/elife.81608] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/03/2022] [Indexed: 12/11/2022] Open
Abstract
Rapid and accurate mRNA translation requires efficient codon-dependent delivery of the correct aminoacyl-tRNA (aa-tRNA) to the ribosomal A site. In mammals, this fidelity-determining reaction is facilitated by the GTPase elongation factor-1 alpha (eEF1A), which escorts aa-tRNA as an eEF1A(GTP)-aa-tRNA ternary complex into the ribosome. The structurally unrelated cyclic peptides didemnin B and ternatin-4 bind to the eEF1A(GTP)-aa-tRNA ternary complex and inhibit translation but have different effects on protein synthesis in vitro and in vivo. Here, we employ single-molecule fluorescence imaging and cryogenic electron microscopy to determine how these natural products inhibit translational elongation on mammalian ribosomes. By binding to a common site on eEF1A, didemnin B and ternatin-4 trap eEF1A in an intermediate state of aa-tRNA selection, preventing eEF1A release and aa-tRNA accommodation on the ribosome. We also show that didemnin B and ternatin-4 exhibit distinct effects on the dynamics of aa-tRNA selection that inform on observed disparities in their inhibition efficacies and physiological impacts. These integrated findings underscore the value of dynamics measurements in assessing the mechanism of small-molecule inhibition and highlight potential of single-molecule methods to reveal how distinct natural products differentially impact the human translation mechanism.
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Affiliation(s)
- Manuel F Juette
- Department of Physiology and Biophysics, Weill Cornell MedicineNew YorkUnited States
| | - Jordan D Carelli
- Chemistry and Chemical Biology Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Emily J Rundlet
- Department of Physiology and Biophysics, Weill Cornell MedicineNew YorkUnited States
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell MedicineNew YorkUnited States
| | - Alan Brown
- MRC-LMB, Francis Crick AvenueCambridgeUnited Kingdom
| | - Sichen Shao
- MRC-LMB, Francis Crick AvenueCambridgeUnited Kingdom
| | - Angelica Ferguson
- Department of Physiology and Biophysics, Weill Cornell MedicineNew YorkUnited States
| | - Michael R Wasserman
- Department of Physiology and Biophysics, Weill Cornell MedicineNew YorkUnited States
| | - Mikael Holm
- Department of Physiology and Biophysics, Weill Cornell MedicineNew YorkUnited States
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Jack Taunton
- Chemistry and Chemical Biology Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell MedicineNew YorkUnited States
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
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9
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Martín-Acosta P, Meng Q, Klimek J, Reddy AP, David L, Petrie SK, Li BX, Xiao X. A clickable photoaffinity probe of betulinic acid identifies tropomyosin as a target. Acta Pharm Sin B 2022; 12:2406-2416. [PMID: 35646545 PMCID: PMC9136574 DOI: 10.1016/j.apsb.2021.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022] Open
Abstract
Target identification of bioactive compounds is important for understanding their mechanisms of action and provides critical insights into their therapeutic utility. While it remains a challenge, unbiased chemoproteomics strategy using clickable photoaffinity probes is a useful and validated approach for target identification. One major limitation of this approach is the efficient synthesis of appropriately substituted clickable photoaffinity probes. Herein, we describe an efficient and consistent method to prepare such probes. We further employed this method to prepare a highly stereo-congested probe based on naturally occurring triterpenoid betulinic acid. With this photoaffinity probe, we identified tropomyosin as a novel target for betulinic acid that can account for the unique biological phenotype on cellular cytoskeleton induced by betulinic acid.
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Affiliation(s)
- Pedro Martín-Acosta
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Qianli Meng
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - John Klimek
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ashok P. Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Larry David
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stefanie Kaech Petrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Bingbing X. Li
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xiangshu Xiao
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
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10
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Kovalski JR, Kuzuoglu‐Ozturk D, Ruggero D. Protein synthesis control in cancer: selectivity and therapeutic targeting. EMBO J 2022; 41:e109823. [PMID: 35315941 PMCID: PMC9016353 DOI: 10.15252/embj.2021109823] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 09/27/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
Translational control of mRNAs is a point of convergence for many oncogenic signals through which cancer cells tune protein expression in tumorigenesis. Cancer cells rely on translational control to appropriately adapt to limited resources while maintaining cell growth and survival, which creates a selective therapeutic window compared to non-transformed cells. In this review, we first discuss how cancer cells modulate the translational machinery to rapidly and selectively synthesize proteins in response to internal oncogenic demands and external factors in the tumor microenvironment. We highlight the clinical potential of compounds that target different translation factors as anti-cancer therapies. Next, we detail how RNA sequence and structural elements interface with the translational machinery and RNA-binding proteins to coordinate the translation of specific pro-survival and pro-growth programs. Finally, we provide an overview of the current and emerging technologies that can be used to illuminate the mechanisms of selective translational control in cancer cells as well as within the microenvironment.
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Affiliation(s)
- Joanna R Kovalski
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Duygu Kuzuoglu‐Ozturk
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
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11
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Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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12
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Kittakoop P, Darshana D, Sangsuwan R, Mahidol C. Alkaloids and Alkaloid-Like Compounds are Potential Scaffolds of Antiviral Agents against SARS-CoV-2 (COVID-19) Virus. HETEROCYCLES 2022. [DOI: 10.3987/rev-22-sr(r)3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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El Hassab M, Hemeda L, Elsayed Z, Al-Rashood S, Amin M, Abdel-Azizf H, Eldehna W. Computational prediction of the potential target of SARS-CoV-2 inhibitor plitidepsin via molecular docking, dynamic simulations and MM-PBSA calculations. Chem Biodivers 2021; 19:e202100719. [PMID: 34813168 PMCID: PMC9011487 DOI: 10.1002/cbdv.202100719] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/22/2021] [Indexed: 11/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication depends on the interaction between the viral proteins and the human translation machinery. The cytotoxic peptide plitidepsin was found to inhibit CoV-2 up to 90% at a concentration of 0.88 nM. In vitro studies suggest that this activity may be attributed to the inhibition of the eukaryotic translation elongation factor 1A (eEF1A). However, recent reports raised the potential for other cellular targets which plitidepsin may use to exert its potent antiviral activity. The lack of data about these potential targets represents a major limitation for its structural optimization. This work describes the use of a molecular modeling approach to rationalize the in vitro antiviral activity of plitidepsin and to identify potential cellular targets. The developed protocol involves an initial molecular docking step followed by molecular dynamics and binding free energy calculations. The results reveal the potential for plitidepsin to bind to the active site of the key enzyme SARS-CoV-2 RdRp. The results also highlight the importance of van der Waals interactions for proper binding with the enzyme. We believe that the results presented in this study could provide the grounds for the optimization of plitidepsin analogues as SARS-CoV-2 inhibitors.
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Affiliation(s)
- Mahmoud El Hassab
- King Salman International University, Medicinal chemistry, Ras sudr, Egypt, 35566, Ras sudr, EGYPT
| | - Loah Hemeda
- Beni Suef University Faculty of Pharmacy, medicinal chemistry, Beni-Suef, Beni-Suef, EGYPT
| | - Zainab Elsayed
- Kafrelsheikh University, Pharmaceutical chemistry, Kafrelsheikh, Kafrelsheikh, EGYPT
| | - Sara Al-Rashood
- King Saud University College of Pharmacy, pharmaceutical chemistry, Riyad, Riyad, SAUDI ARABIA
| | - Mohammed Amin
- South Metropolitan Health Service, south metropolitan health service, Murdoch, Murdoch, AUSTRALIA
| | - Hatem Abdel-Azizf
- National Research Center Inc, Applied organic chemistry, Dokki, Dokki, EGYPT
| | - Wagdy Eldehna
- Kafrelsheikh University, pharmaceutical chemistry, Faculty of pharmacy, Kafrelsheikh University, 33516, Kafrelsheikh, EGYPT
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14
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Rashwan AK, Karim N, Xu Y, Xie J, Cui H, Mozafari MR, Chen W. Potential micro-/nano-encapsulation systems for improving stability and bioavailability of anthocyanins: An updated review. Crit Rev Food Sci Nutr 2021:1-24. [PMID: 34661483 DOI: 10.1080/10408398.2021.1987858] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Anthocyanins (ACNs) are notable hydrophilic compounds that belong to the flavonoid family, which are available in plants. They have excellent antioxidants, anti-obesity, anti-diabetic, anti-inflammatory, anticancer activity, and so on. Furthermore, ACNs can be used as a natural dye in the food industry (food colorant). On the other hand, the stability of ACNs can be affected by processing and storage conditions, for example, pH, temperature, light, oxygen, enzymes, and so on. These factors further reduce the bioavailability (BA) and biological efficacy of ACNs, as well as limit ACNs application in both food and pharmaceutics field. The stability and BA of ACNs can be improved via loading them in encapsulation systems including nanoemulsions, liposomes, niosomes, biopolymer-based nanoparticles, nanogel, complex coacervates, and tocosomes. Among all systems, biopolymer-based nanoparticles, nanohydrogels, and complex coacervates are comparatively suitable for improving the stability and BA of ACNs. These three systems have excellent functional properties such as high encapsulation efficiency and well-stable against unfavorable conditions. Furthermore, these carrier systems can be used for coating of other encapsulation systems (such as liposome). Additionally, tocosomes are a new system that can be used for encapsulating ACNs. ACNs-loaded encapsulation systems can improve the stability and BA of ACNs. However, further studies regarding stability, BA, and in vivo work of ACNs-loaded micro/nano-encapsulation systems could shed a light to evaluate the therapeutic efficacy including physicochemical stability, target mechanisms, cellular internalization, and release kinetics.
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Affiliation(s)
- Ahmed K Rashwan
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China.,Department of Food and Dairy Sciences, Faculty of Agriculture, South Valley University, Qena, Egypt
| | - Naymul Karim
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Yang Xu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Jiahong Xie
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Haoxin Cui
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - M R Mozafari
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), 8054 Monash University LPO, Clayton, Victoria, Australia
| | - Wei Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
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15
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Abstract
Covering: 2000 to 2020 The translation of mRNA into proteins is a precisely regulated, complex process that can be divided into three main stages, i.e. initiation, elongation, termination, and recycling. This contribution is intended to highlight how natural products interfere with the elongation phase of eukaryotic protein biosynthesis. Cycloheximide, isolated from Streptomyces griseus, has long been the prototype inhibitor of eukaryotic translation elongation. In the last three decades, a variety of natural products from different origins were discovered to also address the elongation step in different manners, including interference with the elongation factors eEF1 and eEF2 as well as binding to A-, P- or E-sites of the ribosome itself. Recent advances in the crystallization of the ribosomal machinery together with natural product inhibitors allowed characterizing similarities as well as differences in their mode of action. Since aberrations in protein synthesis are commonly observed in tumors, and malfunction or overexpression of translation factors can cause cellular transformation, the protein synthesis machinery has been realized as an attractive target for anticancer drugs. The therapeutic use of the first natural products that reached market approval, plitidepsin (Aplidin®) and homoharringtonine (Synribo®), will be introduced. In addition, we will highlight two other potential indications for translation elongation inhibitors, i.e. viral infections and genetic disorders caused by premature termination of translation.
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Affiliation(s)
- Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany. and Center of Biomolecular Drug Research (BMWZ), Leibniz University, 30159 Hannover, Germany and German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
| | - Florenz Sasse
- Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.
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16
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Klein VG, Bray WM, Wang HY, Edmondson Q, Schwochert J, Ono S, Naylor MR, Turmon AC, Faris JH, Okada O, Taunton J, Lokey RS. Identifying the Cellular Target of Cordyheptapeptide A and Synthetic Derivatives. ACS Chem Biol 2021; 16:1354-1364. [PMID: 34251165 DOI: 10.1021/acschembio.1c00094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cordyheptapeptide A is a lipophilic cyclic peptide from the prized Cordyceps fungal genus that shows potent cytotoxicity in multiple cancer cell lines. To better understand the bioactivity and physicochemical properties of cordyheptapeptide A with the ultimate goal of identifying its cellular target, we developed a solid-phase synthesis of this multiply N-methylated cyclic heptapeptide which enabled rapid access to both side chain- and backbone-modified derivatives. Removal of one of the backbone amide N-methyl (N-Me) groups maintained bioactivity, while membrane permeability was also preserved due to the formation of a new intramolecular hydrogen bond in a low dielectric solvent. Based on its cytotoxicity profile in the NCI-60 cell line panel, as well as its phenotype in a microscopy-based cytological assay, we hypothesized that cordyheptapeptide was acting on cells as a protein synthesis inhibitor. Further studies revealed the molecular target of cordyheptapeptide A to be the eukaryotic translation elongation factor 1A (eEF1A), a target shared by other lipophilic cyclic peptide natural products. This work offers a strategy to study and improve cyclic peptide natural products while highlighting the ability of these lipophilic compounds to effectively inhibit intracellular disease targets.
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Affiliation(s)
- Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Walter M. Bray
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Hao-Yuan Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, 94158, United States
| | - Quinn Edmondson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Satoshi Ono
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kanagawa 227-0033, Japan
| | - Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Alexandra C. Turmon
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Justin H. Faris
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Okimasa Okada
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kanagawa 227-0033, Japan
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, 94158, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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17
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Madhavan M, AlOmair LA, Ks D, Mustafa S. Exploring peptide studies related to SARS-CoV to accelerate the development of novel therapeutic and prophylactic solutions against COVID-19. J Infect Public Health 2021; 14:1106-19. [PMID: 34280732 DOI: 10.1016/j.jiph.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/18/2021] [Accepted: 06/27/2021] [Indexed: 01/18/2023] Open
Abstract
Recent advances in peptide research revolutionized therapeutic discoveries for various infectious diseases. In view of the ongoing threat of the COVID-19 pandemic, there is an urgent need to develop potential therapeutic options. Intense and accomplishing research is being carried out to develop broad-spectrum vaccines and treatment options for corona viruses, due to the risk of recurrent infection by the existing strains or pandemic outbreaks by new mutant strains. Developing a novel medicine is costly and time consuming, which increases the value of repurposing existing therapies. Since, SARS-CoV-2 shares significant genomic homology with SARS-CoV, we have summarized various peptides identified against SARS-CoV using in silico and molecular studies and also the peptides effective against SARS-CoV-2. Dissecting the molecular mechanisms underlying viral infection could yield fundamental insights in the discovery of new antiviral agents, targeting viral proteins or host factors. We postulate that these peptides can serve as effective components for therapeutic options against SARS-CoV-2, supporting clinical scientists globally in selectively identifying and testing the therapeutic and prophylactic agents for COVID-19 treatment. In addition, we also summarized the latest updates on peptide therapeutics against SARS-CoV-2.
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18
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Abstract
Eukaryotic ribosome and cap-dependent translation are attractive targets in the antitumor, antiviral, anti-inflammatory, and antiparasitic therapies. Currently, a broad array of small-molecule drugs is known that specifically inhibit protein synthesis in eukaryotic cells. Many of them are well-studied ribosome-targeting antibiotics that block translocation, the peptidyl transferase center or the polypeptide exit tunnel, modulate the binding of translation machinery components to the ribosome, and induce miscoding, premature termination or stop codon readthrough. Such inhibitors are widely used as anticancer, anthelmintic and antifungal agents in medicine, as well as fungicides in agriculture. Chemicals that affect the accuracy of stop codon recognition are promising drugs for the nonsense suppression therapy of hereditary diseases and restoration of tumor suppressor function in cancer cells. Other compounds inhibit aminoacyl-tRNA synthetases, translation factors, and components of translation-associated signaling pathways, including mTOR kinase. Some of them have antidepressant, immunosuppressive and geroprotective properties. Translation inhibitors are also used in research for gene expression analysis by ribosome profiling, as well as in cell culture techniques. In this article, we review well-studied and less known inhibitors of eukaryotic protein synthesis (with the exception of mitochondrial and plastid translation) classified by their targets and briefly describe the action mechanisms of these compounds. We also present a continuously updated database (http://eupsic.belozersky.msu.ru/) that currently contains information on 370 inhibitors of eukaryotic protein synthesis.
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Affiliation(s)
- S E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - D O Vladimirov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - K A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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19
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De P, Chakraborty I, Karna B, Mazumder N. Brief review on repurposed drugs and vaccines for possible treatment of COVID-19. Eur J Pharmacol 2021; 898:173977. [PMID: 33639193 DOI: 10.1016/j.ejphar.2021.173977] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/06/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the pandemic coronavirus disease 2019 (Covid-19) has claimed more than a million lives. Various in silico, in vitro, and in vivo studies are being conducted to understand the effect of SARS-CoV-2 on the cellular metabolism of humans and the various drugs and drug-targets that may be used. In this review, we discuss protein-protein interactions (PPIs) between viral and human proteins as well as viral targets like proteases. We try to understand the molecular mechanism of various repurposed antiviral drugs against SARS-CoV-2, their combination therapies, drug dosage regimens, and their adverse effects along with possible alternatives like non-toxic antiviral phytochemicals. Ultimately, randomized controlled trials are needed to identify which of these compounds has the required balance of efficacy and safety. We also focus on the recent advancements in diagnostic methods and vaccine candidates developed around the world to fight against Covid-19.
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20
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Abstract
PURPOSE The coronavirus outbreak emerged as a severe pandemic, claiming more than 0.8 million lives across the world and raised a major global health concern. We survey the history and mechanism of coronaviruses, and the structural characteristics of the spike protein and its key residues responsible for human transmissions. METHODS We have carried out a systematic review to summarize the origin, transmission and etiology of COVID-19. The structural analysis of the spike protein and its disordered residues explains the mechanism of the viral transmission. A meta-data analysis of the therapeutic compounds targeting the SARS-CoV-2 is also included. RESULTS Coronaviruses can cross the species barrier and infect humans with unexpected consequences for public health. The transmission rate of SARS-CoV-2 infection is higher compared to that of the closely related SARS-CoV infections. In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. The key residues of the spike protein have stronger binding affinity with ACE2. These can be probable reasons for the higher transmission rate of SARS-CoV-2. In addition, we have also discussed the therapeutic compounds and the vaccines to target SARS-CoV-2, which can help researchers to develop effective drugs/vaccines for COVID-19. The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Ambuj Srivastava
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
- School of Computing, Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
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21
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White KM, Rosales R, Yildiz S, Kehrer T, Miorin L, Moreno E, Jangra S, Uccellini MB, Rathnasinghe R, Coughlan L, Martinez-Romero C, Batra J, Rojc A, Bouhaddou M, Fabius JM, Obernier K, Dejosez M, Guillén MJ, Losada A, Avilés P, Schotsaert M, Zwaka T, Vignuzzi M, Shokat KM, Krogan NJ, García-Sastre A. Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. Science 2021; 371:926-931. [PMID: 33495306 PMCID: PMC7963220 DOI: 10.1126/science.abf4058] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [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: 10/28/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins interact with the eukaryotic translation machinery, and inhibitors of translation have potent antiviral effects. We found that the drug plitidepsin (aplidin), which has limited clinical approval, possesses antiviral activity (90% inhibitory concentration = 0.88 nM) that is more potent than remdesivir against SARS-CoV-2 in vitro by a factor of 27.5, with limited toxicity in cell culture. Through the use of a drug-resistant mutant, we show that the antiviral activity of plitidepsin against SARS-CoV-2 is mediated through inhibition of the known target eEF1A (eukaryotic translation elongation factor 1A). We demonstrate the in vivo efficacy of plitidepsin treatment in two mouse models of SARS-CoV-2 infection with a reduction of viral replication in the lungs by two orders of magnitude using prophylactic treatment. Our results indicate that plitidepsin is a promising therapeutic candidate for COVID-19.
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Affiliation(s)
- Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa B Uccellini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology and Immunology and Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carles Martinez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Marion Dejosez
- Huffington Foundation Center for Cell-Based Research in Parkinson's Disease, Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - María José Guillén
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Alejandro Losada
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Pablo Avilés
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Zwaka
- Huffington Foundation Center for Cell-Based Research in Parkinson's Disease, Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Kevan M Shokat
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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22
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Abstract
Inhibiting eukaryotic protein translation with small molecules is emerging as a powerful therapeutic strategy. The advantage of targeting cellular translational machinery is that it is required for the highly proliferative state of many neoplastic cells, replication of certain viruses, and ultimately the expression of a wide variety of protein targets. Although, this approach has been exploited to develop clinical agents, such as homoharringtonine (HHT, 1), used to treat chronic myeloid leukemia (CML), inhibiting components of the translational machinery is often associated with cytotoxic phenotypes. However, recent studies have demonstrated that certain small molecules can inhibit the translation of specific subsets of proteins, leading to lower cytotoxicity, and opening-up therapeutic opportunities for translation inhibitors to be deployed in indications beyond oncology and infectious disease. This review summarizes efforts to develop inhibitors of the eukaryotic translational machinery as therapeutic agents and highlights emerging opportunities for translation inhibitors in the future.
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Affiliation(s)
- Angela Fan
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Phillip P Sharp
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
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23
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Huang T, Sun L, Kang D, Poongavanam V, Liu X, Zhan P, Menéndez-Arias L. Search, Identification, and Design of Effective Antiviral Drugs Against Pandemic Human Coronaviruses. Adv Exp Med Biol 2021; 1322:219-260. [PMID: 34258743 DOI: 10.1007/978-981-16-0267-2_9] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Recent coronavirus outbreaks of SARS-CoV-1 (2002-2003), MERS-CoV (since 2012), and SARS-CoV-2 (since the end of 2019) are examples of how viruses can damage health care and generate havoc all over the world. Coronavirus can spread quickly from person to person causing high morbidity and mortality. Unfortunately, the antiviral armamentarium is insufficient to fight these infections. In this chapter, we provide a detailed summary of the current situation in the development of drugs directed against pandemic human coronaviruses. Apart from the recently licensed remdesivir, other antiviral agents discussed in this review include molecules targeting viral components (e.g., RNA polymerase inhibitors, entry inhibitors, or protease inhibitors), compounds interfering with virus-host interactions, and drugs identified in large screening assays, effective against coronavirus replication, but with an uncertain mechanism of action.
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Affiliation(s)
- Tianguang Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | | | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid, Madrid, Spain.
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24
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Zhou H, Guan Y, Feng M, Fu Y, Tachibana H, Cheng X. Evaluation on Elongation Factor 1 Alpha of Entamoeba histolytica Interaction with the Intermediate Subunit of the Gal/GalNAc Lectin and Actin in Phagocytosis. Pathogens 2020; 9:E702. [PMID: 32867020 DOI: 10.3390/pathogens9090702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 11/17/2022] Open
Abstract
Entamoeba histolytica is the causative agent of amoebiasis. This disease results in 40,000 to 100,000 deaths annually. The pathogenic molecules involved in the invasion of trophozoites had been constantly being clarified. This study explored the role of elongation factor 1 alpha (EF1a) in E. histolytica pathogenicity. Biolayer interferometry binding and pull-down assays suggest that EF1a and intermediate subunit of lectin (Igl) binding are specific. Submembranous distribution of EF1a closely aligns with the localization of Igl, which appear in abundance on membranes of trophozoites. Messenger RNA (mRNA) expression of EF1a is positively correlated with trends in Igl levels after co-incubation with Chinese hamster ovary (CHO) cells in vitro, suggesting a regulatory linkage between these proteins. Erythrophagocytosis assays also imply a role for EF1a in phagocytosis. Finally, EF1a and actin are collocated in trophozoites. These results indicated elongation factor 1a is associated with E. histolytica phagocytosis, and the relationships between EF1a, Igl, and actin are worth further study to better understand the pathogenic process.
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020; 583:459-468. [PMID: 32353859 PMCID: PMC7431030 DOI: 10.1038/s41586-020-2286-9] [Citation(s) in RCA: 2872] [Impact Index Per Article: 718.0] [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: 03/23/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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26
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020. [PMID: 32353859 DOI: 10.1038/s41586‐020‐2286‐9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.,Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,J. David Gladstone Institutes, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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27
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv 2020:2020.03.22.002386. [PMID: 32511329 PMCID: PMC7239059 DOI: 10.1101/2020.03.22.002386] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [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: 02/06/2023]
Abstract
An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption 1,2 . There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Kala B Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Rakesh Ramachandran
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco
| | | | - Yizhu Lin
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,Biophysics Graduate Program, University of California, San Francisco
| | - Markus Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Raphael Trenker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Devin Cavero
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joe Hiatt
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Theo Roth
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ujjwal Rathore
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Björn Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Kris M White
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa Miorin
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - David Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Biochemistry & Biophysics and Quantitative Biosciences Institute UCSF 600 16th St San Francisco, CA 94143
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98103
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Adolfo García-Sastre
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Psychiatry, San Francisco, CA, 94158, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Christophe d'Enfert
- Direction Scientifique, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Matt Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Stephen Floor
- Department of Cell and Tissue Biology, University of California, San Francisco.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - John Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kevan Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
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28
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Abstract
As a convergent mechanism downstream of most oncogenic signals, control of mRNA translation has emerged as a key driver in establishing and tuning gene expression at specific steps in cancer development. Translation control is the most energetically expensive molecular process in the cell that needs to be modulated upon adaption to limited cellular resources, such as cellular stress. It thereby serves as the Achilles’ heel for cancer cells, particularly in response to changes in the microenvironment as well as to nutrient and metabolic shifts characteristic of cancer cell growth and metastasis. In this review, we discuss emerging discoveries that reveal how cancer cells modulate the translation machinery to adapt to oncogenic stress, the mechanisms that guide mRNA translation specificity in cancer, and how this selective mode of gene regulation provides advantages for cancer progression. We also provide an overview of promising preclinical and clinical efforts aimed at targeting the unique vulnerabilities of cancer cells that rely on the remodeling of mRNA translation for their infinite growth and survival.
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Affiliation(s)
- Yichen Xu
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94157, USA
| | - Davide Ruggero
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94157, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
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29
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Choi JS, Joo SH. Recent Trends in Cyclic Peptides as Therapeutic Agents and Biochemical Tools. Biomol Ther (Seoul) 2020; 28:18-24. [PMID: 31597413 PMCID: PMC6939695 DOI: 10.4062/biomolther.2019.082] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/26/2022] Open
Abstract
Notable progress has been made in the therapeutic and research applications of cyclic peptides since our previous review. New drugs based on cyclic peptides are entering the market, such as plecanatide, a cyclic peptide approved by the United States Food and Drug Administration in 2017 for the treatment of chronic idiopathic constipation. In this review, we discuss recent developments in stapled peptides, prepared with the use of chemical linkers, and bicyclic/tricyclic peptides with more than two rings. These have widespread applications for clinical and research purposes: imaging, diagnostics, improvement of oral absorption, enzyme inhibition, development of receptor agonist/antagonist, and the modulation of protein-protein interaction or protein-RNA interaction. Many cyclic peptides are expected to emerge as therapeutics and biochemical tools.
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Affiliation(s)
- Joon-Seok Choi
- College of Pharmacy, Daegu Catholic University, Gyeongsan 38430, Republic of Korea
| | - Sang Hoon Joo
- College of Pharmacy, Daegu Catholic University, Gyeongsan 38430, Republic of Korea
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30
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Zhang M, Sunaba T, Sun Y, Sasaki K, Isoda H, Kigoshi H, Kita M. Anti-inflammatory marine cyclic peptide stylissatin A and its derivatives inhibit differentiation of murine preadipocytes. Chem Commun (Camb) 2019; 55:5471-5474. [PMID: 31012472 DOI: 10.1039/c9cc02517k] [Citation(s) in RCA: 10] [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: 01/22/2023]
Abstract
Stylissatin A, an anti-inflammatory cyclic heptapeptide, and its derivatives potently inhibited the differentiation of preadipocytes and reduced triglyceride accumulation in mature adipocytes, with little cytotoxicity. Our studies might contribute to the development of leads for new anti-inflammatory and anti-obesity agents.
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Affiliation(s)
- Menghua Zhang
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
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31
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Tian Y, Ding Y, Xu X, Bai Y, Tang Y, Hao X, Zhang W, Chen Y. Total synthesis and biological evaluation of nannocystin analogues modified at the polyketide phenyl moiety. Tetrahedron Lett 2018; 59:3206-9. [DOI: 10.1016/j.tetlet.2018.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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32
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Abstract
In this review, we highlight the current understanding of translation elongation and recoding in eukaryotes. In addition to providing an overview of the process, recent advances in our understanding of the role of the factor eIF5A in both translation elongation and termination are discussed. We also highlight mechanisms of translation recoding with a focus on ribosomal frameshifting during elongation. We see that the balance between the basic steps in elongation and the less common recoding events is determined by the kinetics of the different processes as well as by specific sequence determinants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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33
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Choudhry P, Galligan D, Wiita AP. Seeking Convergence and Cure with New Myeloma Therapies. Trends Cancer 2018; 4:567-582. [PMID: 30064664 DOI: 10.1016/j.trecan.2018.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 02/01/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 02/06/2023]
Abstract
For over a decade, the mainstay of multiple myeloma therapy has been small molecules that directly attack malignant plasma cell biology. However, potent immunotherapies have recently emerged, transforming the myeloma therapeutic landscape. Here we first review new promising strategies to target plasma cells through protein homeostasis and epigenetic modulators. We then discuss emerging immunotherapy strategies that are leading to dramatic results in patients. Finally, we focus on recent preclinical data suggesting that enforcing cell-surface antigen expression through small molecules may enhance immunotherapy efficacy and avoid resistance. We argue that these emerging observations point the way toward potential convergence between drug classes. With recent rapid progress we may finally be on the verge of the 'C' word: a cure for myeloma.
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Affiliation(s)
- Priya Choudhry
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; These authors contributed equally
| | - Derek Galligan
- Department of Medicine, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; These authors contributed equally
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
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34
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Gentile DR, Rathinaswamy MK, Jenkins ML, Moss SM, Siempelkamp BD, Renslo AR, Burke JE, Shokat KM. Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States. Cell Chem Biol 2017; 24:1455-1466.e14. [PMID: 29033317 PMCID: PMC5915340 DOI: 10.1016/j.chembiol.2017.08.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [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: 04/02/2017] [Revised: 07/31/2017] [Accepted: 08/30/2017] [Indexed: 12/31/2022]
Abstract
Covalent inhibitors of K-Ras(G12C) have been reported that exclusively recognize the GDP state. Here, we utilize disulfide tethering of a non-natural cysteine (K-Ras(M72C)) to identify a new switch-II pocket (S-IIP) binding ligand (2C07) that engages the active GTP state. Co-crystal structures of 2C07 bound to H-Ras(M72C) reveal binding in a cryptic groove we term S-IIG. In the GppNHp state, 2C07 binding to a modified S-IIP pushes switch I away from the nucleotide, breaking the network of polar contacts essential for adopting the canonical GTP state. Biochemical studies show that 2C07 alters nucleotide preference and inhibits SOS binding and catalyzed nucleotide exchange. 2C07 was converted to irreversible covalent analogs, which target both nucleotide states, inhibit PI3K activation in vitro, and function as occupancy probes to detect reversible engagement in competition assays. Targeting both nucleotide states opens the possibility of inhibiting oncogenic mutants of Ras, which exist predominantly in the GTP state in cells.
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Affiliation(s)
- Daniel R Gentile
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Steven M Moss
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Braden D Siempelkamp
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Adam R Renslo
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada.
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA.
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35
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Sánchez-murcia PA, Cortés-cabrera Á, Gago F. Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B. J Comput Aided Mol Des 2017; 31:915-28. [DOI: 10.1007/s10822-017-0066-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 01/24/2023]
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36
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Osuna BA, Howard CJ, Kc S, Frost A, Weinberg DE. In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing. eLife 2017; 6. [PMID: 28718767 PMCID: PMC5562442 DOI: 10.7554/elife.27949] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/11/2017] [Indexed: 12/25/2022] Open
Abstract
Ribosomes can stall during translation due to defects in the mRNA template or translation machinery, leading to the production of incomplete proteins. The Ribosome-associated Quality control Complex (RQC) engages stalled ribosomes and targets nascent polypeptides for proteasomal degradation. However, how each RQC component contributes to this process remains unclear. Here we demonstrate that key RQC activities-Ltn1p-dependent ubiquitination and Rqc2p-mediated Carboxy-terminal Alanine and Threonine (CAT) tail elongation-can be recapitulated in vitro with a yeast cell-free system. Using this approach, we determined that CAT tailing is mechanistically distinct from canonical translation, that Ltn1p-mediated ubiquitination depends on the poorly characterized RQC component Rqc1p, and that the process of CAT tailing enables robust ubiquitination of the nascent polypeptide. These findings establish a novel system to study the RQC and provide a framework for understanding how RQC factors coordinate their activities to facilitate clearance of incompletely synthesized proteins.
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Affiliation(s)
- Beatriz A Osuna
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Conor J Howard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, San Francisco, United States.,Chan Zuckerberg Biohub, San Francisco, United States
| | - Subheksha Kc
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, San Francisco, United States.,Chan Zuckerberg Biohub, San Francisco, United States.,Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - David E Weinberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Sandler Faculty Fellows Program, University of California, San Francisco, San Francisco, United States
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37
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Shao S, Murray J, Brown A, Taunton J, Ramakrishnan V, Hegde RS. Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Cell 2017; 167:1229-1240.e15. [PMID: 27863242 PMCID: PMC5119991 DOI: 10.1016/j.cell.2016.10.046] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/03/2016] [Accepted: 10/25/2016] [Indexed: 11/30/2022]
Abstract
In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the mammalian ribosome engaged with decoding factor⋅GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA⋅eEF1A), termination (eRF1⋅eRF3), and ribosome rescue (Pelota⋅Hbs1l). Comparative analyses reveal that each decoding factor exploits the plasticity of the ribosomal decoding center to differentially remodel ribosomal proteins and rRNA. This leads to varying degrees of large-scale ribosome movements and implies distinct mechanisms for communicating information from the decoding center to each GTPase. Additional structural snapshots of the translation termination pathway reveal the conformational changes that choreograph the accommodation of decoding factors into the peptidyl transferase center. Our results provide a structural framework for how different states of the mammalian ribosome are selectively recognized by the appropriate decoding factor⋅GTPase complex to ensure translational fidelity.
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Affiliation(s)
- Sichen Shao
- MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jason Murray
- MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alan Brown
- MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
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38
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Affiliation(s)
- Linping Liao
- Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Jingjing Zhou
- Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Zhengshuang Xu
- Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Tao Ye
- Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
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39
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Affiliation(s)
- Linping Liao
- Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Jingjing Zhou
- Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Zhengshuang Xu
- Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Tao Ye
- Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
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