1
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Shao S, Zhang N, Specht GP, You S, Song L, Fu Q, Huang D, You H, Shu J, Domissy A, Li S, Nguyen-Tran V, Joseph SB, Chatterjee AK, Chen JJ, Schultz PG, Bollong MJ. Pharmacological expansion of type 2 alveolar epithelial cells promotes regenerative lower airway repair. Proc Natl Acad Sci U S A 2024; 121:e2400077121. [PMID: 38598345 PMCID: PMC11032444 DOI: 10.1073/pnas.2400077121] [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: 01/03/2024] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
Type 2 alveolar epithelial cells (AEC2s) are stem cells in the adult lung that contribute to lower airway repair. Agents that promote the selective expansion of these cells might stimulate regeneration of the compromised alveolar epithelium, an etiology-defining event in several pulmonary diseases. From a high-content imaging screen of the drug repurposing library ReFRAME, we identified that dipeptidyl peptidase 4 (DPP4) inhibitors, widely used type 2 diabetes medications, selectively expand AEC2s and are broadly efficacious in several mouse models of lung damage. Mechanism of action studies revealed that the protease DPP4, in addition to processing incretin hormones, degrades IGF-1 and IL-6, essential regulators of AEC2 expansion whose levels are increased in the luminal compartment of the lung in response to drug treatment. To selectively target DPP4 in the lung with sufficient drug exposure, we developed NZ-97, a locally delivered, lung persistent DPP4 inhibitor that broadly promotes efficacy in mouse lung damage models with minimal peripheral exposure and good tolerability. This work reveals DPP4 as a central regulator of AEC2 expansion and affords a promising therapeutic approach to broadly stimulate regenerative repair in pulmonary disease.
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Affiliation(s)
- Sida Shao
- Calibr, a Division of Scripps Research, La Jolla, CA92037
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA92037
| | - Nan Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA92037
| | - Gregory P. Specht
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA92037
| | - Shaochen You
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA92037
| | - Lirui Song
- Calibr, a Division of Scripps Research, La Jolla, CA92037
| | - Qiangwei Fu
- Calibr, a Division of Scripps Research, La Jolla, CA92037
| | - David Huang
- Calibr, a Division of Scripps Research, La Jolla, CA92037
| | - Hengyao You
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA92037
| | - Jian Shu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA02129
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - Alain Domissy
- DNA Array Core, The Scripps Research Institute, La Jolla, CA92037
| | - Shuangwei Li
- Calibr, a Division of Scripps Research, La Jolla, CA92037
| | | | - Sean B. Joseph
- Calibr, a Division of Scripps Research, La Jolla, CA92037
| | | | | | - Peter G. Schultz
- Calibr, a Division of Scripps Research, La Jolla, CA92037
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA92037
| | - Michael J. Bollong
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA92037
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2
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Dayan Elshan NGR, Wolff KC, Riva L, Woods AK, Grabovyi G, Wilson K, Pedroarena J, Ghorai S, Nazarian A, Weiss F, Liu Y, Mazumdar W, Song L, Okwor N, Malvin J, Bakowski MA, Beutler N, Kirkpatrick MG, Gebara-Lamb A, Huang E, Nguyen-Tran VTB, Chi V, Li S, Rogers TF, McNamara CW, Gupta AK, Rahimi A, Chen JJ, Joseph SB, Schultz PG, Chatterjee AK. Discovery of CMX990: A Potent SARS-CoV-2 3CL Protease Inhibitor Bearing a Novel Warhead. J Med Chem 2024; 67:2369-2378. [PMID: 38335279 PMCID: PMC10895651 DOI: 10.1021/acs.jmedchem.3c01938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
There remains a need to develop novel SARS-CoV-2 therapeutic options that improve upon existing therapies by an increased robustness of response, fewer safety liabilities, and global-ready accessibility. Functionally critical viral main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target due to its homology within the coronaviral family, and lack thereof toward human proteases. In this disclosure, we outline the advent of a novel SARS-CoV-2 3CLpro inhibitor, CMX990, bearing an unprecedented trifluoromethoxymethyl ketone warhead. Compared with the marketed drug nirmatrelvir (combination with ritonavir = Paxlovid), CMX990 has distinctly differentiated potency (∼5× more potent in primary cells) and human in vitro clearance (>4× better microsomal clearance and >10× better hepatocyte clearance), with good in vitro-to-in vivo correlation. Based on its compelling preclinical profile and projected once or twice a day dosing supporting unboosted oral therapy in humans, CMX990 advanced to a Phase 1 clinical trial as an oral drug candidate for SARS-CoV-2.
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Affiliation(s)
- N G R Dayan Elshan
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Karen C Wolff
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laura Riva
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ashley K Woods
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gennadii Grabovyi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Katy Wilson
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - James Pedroarena
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sourav Ghorai
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Armen Nazarian
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Frank Weiss
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yuyin Liu
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Wrickban Mazumdar
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lirui Song
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Neechi Okwor
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jacqueline Malvin
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Malina A Bakowski
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, 10466 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Melanie G Kirkpatrick
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Amal Gebara-Lamb
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Edward Huang
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vân T B Nguyen-Tran
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Victor Chi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shuangwei Li
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, 10466 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Case W McNamara
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anil Kumar Gupta
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alireza Rahimi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jian Jeffrey Chen
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sean B Joseph
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Arnab K Chatterjee
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
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3
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Grzelak EM, Elshan NGRD, Shao S, Bulos ML, Joseph SB, Chatterjee AK, Chen JJ, Nguyên-Trân V, Schultz PG, Bollong MJ. Pharmacological YAP activation promotes regenerative repair of cutaneous wounds. Proc Natl Acad Sci U S A 2023; 120:e2305085120. [PMID: 37399395 PMCID: PMC10334740 DOI: 10.1073/pnas.2305085120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/02/2023] [Accepted: 05/26/2023] [Indexed: 07/05/2023] Open
Abstract
Chronic cutaneous wounds remain a persistent unmet medical need that decreases life expectancy and quality of life. Here, we report that topical application of PY-60, a small-molecule activator of the transcriptional coactivator Yes-associated protein (YAP), promotes regenerative repair of cutaneous wounds in pig and human models. Pharmacological YAP activation enacts a reversible pro-proliferative transcriptional program in keratinocytes and dermal cells that results in accelerated re-epithelization and regranulation of the wound bed. These results demonstrate that transient topical administration of a YAP activating agent may represent a generalizable therapeutic approach to treating cutaneous wounds.
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Affiliation(s)
- Edyta M. Grzelak
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | | | - Sida Shao
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Maya L. Bulos
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Sean B. Joseph
- Calibr, A Division of Scripps Research, San Diego, CA92037
| | | | | | | | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
- Calibr, A Division of Scripps Research, San Diego, CA92037
| | - Michael J. Bollong
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
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4
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Ko Y, Hong M, Lee S, Kumar M, Ibrahim L, Nutsch K, Stanton C, Sondermann P, Sandoval B, Bulos ML, Iaconelli J, Chatterjee AK, Wiseman RL, Schultz PG, Bollong MJ. S-lactoyl modification of KEAP1 by a reactive glycolytic metabolite activates NRF2 signaling. Proc Natl Acad Sci U S A 2023; 120:e2300763120. [PMID: 37155889 PMCID: PMC10193962 DOI: 10.1073/pnas.2300763120] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 01/13/2023] [Accepted: 04/05/2023] [Indexed: 05/10/2023] Open
Abstract
KEAP1 (Kelch-like ECH-associated protein), a cytoplasmic repressor of the oxidative stress responsive transcription factor Nuclear factor erythroid 2-related factor 2 (NRF2), senses the presence of electrophilic agents by modification of its sensor cysteine residues. In addition to xenobiotics, several reactive metabolites have been shown to covalently modify key cysteines on KEAP1, although the full repertoire of these molecules and their respective modifications remain undefined. Here, we report the discovery of sAKZ692, a small molecule identified by high-throughput screening that stimulates NRF2 transcriptional activity in cells by inhibiting the glycolytic enzyme pyruvate kinase. sAKZ692 treatment promotes the buildup of glyceraldehyde 3-phosphate, a metabolite which leads to S-lactate modification of cysteine sensor residues of KEAP1, resulting in NRF2-dependent transcription. This work identifies a posttranslational modification of cysteine derived from a reactive central carbon metabolite and helps further define the complex relationship between metabolism and the oxidative stress-sensing machinery of the cell.
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Affiliation(s)
- Yeonjin Ko
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Mannkyu Hong
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Seungbeom Lee
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Manoj Kumar
- Calibr, A Division of Scripps Research, San Diego, CA92037
| | - Lara Ibrahim
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
- Department of Molecular Medicine, The Scripps Research Institute, San Diego, CA92037
| | - Kayla Nutsch
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Caroline Stanton
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
- Department of Molecular Medicine, The Scripps Research Institute, San Diego, CA92037
| | - Phillip Sondermann
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Braddock Sandoval
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Maya L. Bulos
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | - Jonathan Iaconelli
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
| | | | - R. Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, San Diego, CA92037
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
- Calibr, A Division of Scripps Research, San Diego, CA92037
| | - Michael J. Bollong
- Department of Chemistry, The Scripps Research Institute, San Diego, CA92037
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5
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Martínez-Peña F, Pearson AD, Tang EL, Kuburich NA, Mani SA, Schultz PG, Bollong MJ, Lairson LL. Synthesis and biological evaluation of novel FiVe1 derivatives as potent and selective agents for the treatment of mesenchymal cancers. Eur J Med Chem 2022; 242:114638. [PMID: 36001933 PMCID: PMC10377566 DOI: 10.1016/j.ejmech.2022.114638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/29/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Epithelial-mesenchymal transition (EMT) endows stem cell-like properties to cancer cells. Targeting this process represents a potential therapeutic approach to overcome cancer metastasis and chemotherapy resistance. FiVe1 was identified from an EMT-based synthetic lethality screen and was found to inhibit the stem cell-like properties and proliferation of not only cancer cells undergoing EMT, but also more broadly in mesenchymal cancers that include therapeutically intractable soft tissue sarcomas. FiVe1 functions by directly binding to the type III intermediate filament protein vimentin (VIM) in a mode that induces hyperphosphorylation of Ser56, which results in selective disruption of mitosis and induced multinucleation in transformed VIM-expressing mesenchymal cancer cell types. Cell-based potency (IC50 = 1.6 μM, HT-1080 fibrosarcoma), poor solubility (<1 μM) and low oral bioavailability limits the direct application of FiVe1 as an in vivo probe or therapeutic agent. To overcome these drawbacks, we performed structure-activity relationship (SAR) studies and synthesized a set of 35 new compounds, consisting of diverse modifications of the FiVe1 scaffold. Among these compounds, 4e showed a marked improvement in potency (IC50 = 44 nM, 35-fold improvement, HT-1080) and cell type selectivity (19-fold improvement), when compared to FiVe1. Improvements in the potency of 4e, in terms of overall cytotoxicity, directly correlate with VIM Ser56 phosphorylation status and the oral bioavailability and pharmacokinetic profiles of 4e in mouse are superior to FiVe1. Successful optimization also resulted in potent and selective derivatives 11a, 11j and 11k, which exhibited superior pharmacological profiles, in terms of metabolic stability and aqueous solubility. Collectively, these optimization efforts have resulted in the development of promising FiVe1 analogs with potential applications in the treatment of mesenchymal cancers, as well as in the study of VIM-related biology.
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6
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Wilburn KM, Montague CR, Qin B, Woods AK, Love MS, McNamara CW, Schultz PG, Southard TL, Huang L, Petrassi HM, VanderVen BC. Pharmacological and genetic activation of cAMP synthesis disrupts cholesterol utilization in Mycobacterium tuberculosis. PLoS Pathog 2022; 18:e1009862. [PMID: 35134095 PMCID: PMC8856561 DOI: 10.1371/journal.ppat.1009862] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/18/2022] [Accepted: 01/18/2022] [Indexed: 01/27/2023] Open
Abstract
There is a growing appreciation for the idea that bacterial utilization of host-derived lipids, including cholesterol, supports Mycobacterium tuberculosis (Mtb) pathogenesis. This has generated interest in identifying novel antibiotics that can disrupt cholesterol utilization by Mtb in vivo. Here we identify a novel small molecule agonist (V-59) of the Mtb adenylyl cyclase Rv1625c, which stimulates 3', 5'-cyclic adenosine monophosphate (cAMP) synthesis and inhibits cholesterol utilization by Mtb. Similarly, using a complementary genetic approach that induces bacterial cAMP synthesis independent of Rv1625c, we demonstrate that inducing cAMP synthesis is sufficient to inhibit cholesterol utilization in Mtb. Although the physiological roles of individual adenylyl cyclase enzymes in Mtb are largely unknown, here we demonstrate that the transmembrane region of Rv1625c is required during cholesterol metabolism. Finally, the pharmacokinetic properties of Rv1625c agonists have been optimized, producing an orally-available Rv1625c agonist that impairs Mtb pathogenesis in infected mice. Collectively, this work demonstrates a role for Rv1625c and cAMP signaling in controlling cholesterol metabolism in Mtb and establishes that cAMP signaling can be pharmacologically manipulated for the development of new antibiotic strategies.
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Affiliation(s)
- Kaley M. Wilburn
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - Christine R. Montague
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - Bo Qin
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Ashley K. Woods
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Melissa S. Love
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Case W. McNamara
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Peter G. Schultz
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Teresa L. Southard
- Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Lu Huang
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - H. Michael Petrassi
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Brian C. VanderVen
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
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7
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Abstract
The maturation of chemical synthesis during the 20th century has elevated the discipline from a largely empirical into a rational science. This ability to purposefully craft matter at the molecular level has put chemists in a privileged position to contribute to progress in neighboring natural sciences. Recently, we have witnessed another major advance in the field in which chemists use chemical and biological "synthetic" methods together to alter the structures and properties of biological macromolecules in ways heretofore unimagined. This interdisciplinary approach to synthesis has even allowed us to expand upon the defining characteristics of living organisms at the molecular level. In this perspective, we present a case study for the successful addition of new chemistries to the fundamental processes of the central dogma of molecular biology, exemplified by the expansion of the genetic code.
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Affiliation(s)
- Christian S. Diercks
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - David A. Dik
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - Peter G. Schultz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Lead contact
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8
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Lee SC, Ma JSY, Kim MS, Laborda E, Choi SH, Hampton EN, Yun H, Nunez V, Muldong MT, Wu CN, Ma W, Kulidjian AA, Kane CJ, Klyushnichenko V, Woods AK, Joseph SB, Petrassi M, Wisler J, Li J, Jamieson CAM, Schultz PG, Kim CH, Young TS. A PSMA-targeted bispecific antibody for prostate cancer driven by a small-molecule targeting ligand. Sci Adv 2021; 7:7/33/eabi8193. [PMID: 34380625 PMCID: PMC8357232 DOI: 10.1126/sciadv.abi8193] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Despite the development of next-generation antiandrogens, metastatic castration-resistant prostate cancer (mCRPC) remains incurable. Here, we describe a unique semisynthetic bispecific antibody that uses site-specific unnatural amino acid conjugation to combine the potency of a T cell-recruiting anti-CD3 antibody with the specificity of an imaging ligand (DUPA) for prostate-specific membrane antigen. This format enabled optimization of structure and function to produce a candidate (CCW702) with specific, potent in vitro cytotoxicity and improved stability compared with a bispecific single-chain variable fragment format. In vivo, CCW702 eliminated C4-2 xenografts with as few as three weekly subcutaneous doses and prevented growth of PCSD1 patient-derived xenograft tumors in mice. In cynomolgus monkeys, CCW702 was well tolerated up to 34.1 mg/kg per dose, with near-complete subcutaneous bioavailability and a PK profile supporting testing of a weekly dosing regimen in patients. CCW702 is being evaluated in a first in-human clinical trial for men with mCRPC who had progressed on prior therapies (NCT04077021).
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Affiliation(s)
- Sung Chang Lee
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jennifer S Y Ma
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Min Soo Kim
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eduardo Laborda
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sei-Hyun Choi
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eric N Hampton
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hwayoung Yun
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vanessa Nunez
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michelle T Muldong
- Department of Urology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christina N Wu
- Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wenxue Ma
- Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna A Kulidjian
- Department of Orthopedic Surgery, Scripps MD Anderson Cancer Center, La Jolla, CA 92093, USA
| | - Christopher J Kane
- Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vadim Klyushnichenko
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ashley K Woods
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean B Joseph
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mike Petrassi
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John Wisler
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jing Li
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christina A M Jamieson
- Department of Urology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peter G Schultz
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chan Hyuk Kim
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Travis S Young
- Department of Biology, Calibr, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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9
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Bakowski MA, Beutler N, Wolff KC, Kirkpatrick MG, Chen E, Nguyen TTH, Riva L, Shaabani N, Parren M, Ricketts J, Gupta AK, Pan K, Kuo P, Fuller M, Garcia E, Teijaro JR, Yang L, Sahoo D, Chi V, Huang E, Vargas N, Roberts AJ, Das S, Ghosh P, Woods AK, Joseph SB, Hull MV, Schultz PG, Burton DR, Chatterjee AK, McNamara CW, Rogers TF. Drug repurposing screens identify chemical entities for the development of COVID-19 interventions. Nat Commun 2021; 12:3309. [PMID: 34083527 PMCID: PMC8175350 DOI: 10.1038/s41467-021-23328-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [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: 03/04/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022] Open
Abstract
The ongoing pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates strategies to identify prophylactic and therapeutic drug candidates for rapid clinical deployment. Here, we describe a screening pipeline for the discovery of efficacious SARS-CoV-2 inhibitors. We screen a best-in-class drug repurposing library, ReFRAME, against two high-throughput, high-content imaging infection assays: one using HeLa cells expressing SARS-CoV-2 receptor ACE2 and the other using lung epithelial Calu-3 cells. From nearly 12,000 compounds, we identify 49 (in HeLa-ACE2) and 41 (in Calu-3) compounds capable of selectively inhibiting SARS-CoV-2 replication. Notably, most screen hits are cell-line specific, likely due to different virus entry mechanisms or host cell-specific sensitivities to modulators. Among these promising hits, the antivirals nelfinavir and the parent of prodrug MK-4482 possess desirable in vitro activity, pharmacokinetic and human safety profiles, and both reduce SARS-CoV-2 replication in an orthogonal human differentiated primary cell model. Furthermore, MK-4482 effectively blocks SARS-CoV-2 infection in a hamster model. Overall, we identify direct-acting antivirals as the most promising compounds for drug repurposing, additional compounds that may have value in combination therapies, and tool compounds for identification of viral host cell targets.
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Affiliation(s)
- Malina A Bakowski
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA.
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karen C Wolff
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | | | - Emily Chen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Tu-Trinh H Nguyen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Riva
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - James Ricketts
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anil K Gupta
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Kastin Pan
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Peiting Kuo
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - MacKenzie Fuller
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linlin Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debashis Sahoo
- Department of Computer Science and Engineering, Jacobs School of Engineering, UC San Diego, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego, La Jolla, CA, USA
| | - Victor Chi
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Edward Huang
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Natalia Vargas
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Amanda J Roberts
- Animal Models Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Soumita Das
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
- Department of Pathology, UC San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
- Department of Medicine, UC San Diego, La Jolla, CA, USA
| | - Ashley K Woods
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Sean B Joseph
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Mitchell V Hull
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Peter G Schultz
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Case W McNamara
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- UC San Diego Division of Infectious Diseases and Global Public Health, UC San Diego School of Medicine, La Jolla, CA, USA.
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10
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Shalhout SZ, Yang PY, Grzelak EM, Nutsch K, Shao S, Zambaldo C, Iaconelli J, Ibrahim L, Stanton C, Chadwick SR, Chen E, DeRan M, Li S, Hull M, Wu X, Chatterjee AK, Shen W, Camargo FD, Schultz PG, Bollong MJ. YAP-dependent proliferation by a small molecule targeting annexin A2. Nat Chem Biol 2021; 17:767-775. [PMID: 33723431 DOI: 10.1038/s41589-021-00755-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/27/2021] [Indexed: 12/21/2022]
Abstract
The transcriptional coactivator Yes-associated protein 1 (YAP) orchestrates a proproliferative transcriptional program that controls the fate of somatic stem cells and the regenerative responses of certain tissues. As such, agents that activate YAP may hold therapeutic potential in disease states exacerbated by insufficient proliferative repair. Here we report the discovery of a small molecule, termed PY-60, which robustly activates YAP transcriptional activity in vitro and promotes YAP-dependent expansion of epidermal keratinocytes in mouse following topical drug administration. Chemical proteomics revealed the relevant target of PY-60 to be annexin A2 (ANXA2), a protein that directly associates with YAP at the cell membrane in response to increased cell density. PY-60 treatment liberates ANXA2 from the membrane, ultimately promoting a phosphatase-bound, nonphosphorylated and transcriptionally active form of YAP. This work reveals ANXA2 as a previously undescribed, druggable component of the Hippo pathway and suggests a mechanistic rationale to promote regenerative repair in disease.
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Affiliation(s)
- Sophia Z Shalhout
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Boston, MA, USA
| | - Peng-Yu Yang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.,Calibr, a division of Scripps Research, La Jolla, CA, USA
| | - Edyta M Grzelak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Kayla Nutsch
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Sida Shao
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Claudio Zambaldo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan Iaconelli
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Lara Ibrahim
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Caroline Stanton
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Stormi R Chadwick
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Chen
- Calibr, a division of Scripps Research, La Jolla, CA, USA
| | - Michael DeRan
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Sijia Li
- Calibr, a division of Scripps Research, La Jolla, CA, USA
| | - Mitchell Hull
- Calibr, a division of Scripps Research, La Jolla, CA, USA
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | | | - Weijun Shen
- Calibr, a division of Scripps Research, La Jolla, CA, USA.
| | - Fernando D Camargo
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Boston, MA, USA.
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,Calibr, a division of Scripps Research, La Jolla, CA, USA.
| | - Michael J Bollong
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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11
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Jo J, Ibrahim L, Iaconelli J, Kwak J, Kumar M, Jung Y, Lairson LL, Chatterjee AK, Schultz PG, Bollong MJ, Yun H. Discovery and SAR studies of 3-amino-4-(phenylsulfonyl)tetrahydrothiophene 1,1-dioxides as non-electrophilic antioxidant response element (ARE) activators. Bioorg Chem 2021; 108:104614. [PMID: 33508678 DOI: 10.1016/j.bioorg.2020.104614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/13/2020] [Accepted: 12/28/2020] [Indexed: 12/20/2022]
Abstract
The transcription factor NRF2 controls resistance to oxidative insult and is thus a key therapeutic target for treating a number of disease states associated with oxidative stress and aging. We previously reported CBR-470-1, a bis-sulfone which activates NRF2 by increasing the levels of methylglyoxal, a metabolite that covalently modifies NRF2 repressor KEAP1. Here, we report the design, synthesis, and structure activity relationship of a series of bis-sulfones derived from this unexplored chemical template. We identify analogs with sub-micromolar potencies, 7f and 7g, as well as establish that efficacious NRF2 activation can be achieved by non-toxic analogs 7c, 7e, and 9, a key limitation with CBR-470-1. Further efforts to identify non-covalent NRF2 activators of this kind will likely provide new insight into revealing the role of central metabolism in cellular signaling.
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Affiliation(s)
- Jeyun Jo
- College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
| | - Lara Ibrahim
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines, La Jolla, CA 92037, United States
| | - Jonathan Iaconelli
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines, La Jolla, CA 92037, United States
| | - Jinsook Kwak
- College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
| | - Manoj Kumar
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, CA 92037, United States
| | - Yunjin Jung
- College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
| | - Luke L Lairson
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines, La Jolla, CA 92037, United States
| | - Arnab K Chatterjee
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, CA 92037, United States
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines, La Jolla, CA 92037, United States; California Institute for Biomedical Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, CA 92037, United States
| | - Michael J Bollong
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines, La Jolla, CA 92037, United States.
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea; Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines, La Jolla, CA 92037, United States.
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12
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Li JC, Nasertorabi F, Xuan W, Han GW, Stevens RC, Schultz PG. A Single Reactive Noncanonical Amino Acid is Able to Dramatically Stabilize Protein Structure. ACS Chem Biol 2020; 15:2842. [PMID: 33006884 DOI: 10.1021/acschembio.0c00196] [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] [Indexed: 11/29/2022]
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13
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Schultz PG. Special issue preface. Bioorg Med Chem 2020; 28:115814. [PMID: 33137620 DOI: 10.1016/j.bmc.2020.115814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Peter G Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, United States.
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14
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Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Pache L, Burgstaller-Muehlbacher S, De Jesus PD, Teriete P, Hull MV, Chang MW, Chan JFW, Cao J, Poon VKM, Herbert KM, Cheng K, Nguyen TTH, Rubanov A, Pu Y, Nguyen C, Choi A, Rathnasinghe R, Schotsaert M, Miorin L, Dejosez M, Zwaka TP, Sit KY, Martinez-Sobrido L, Liu WC, White KM, Chapman ME, Lendy EK, Glynne RJ, Albrecht R, Ruppin E, Mesecar AD, Johnson JR, Benner C, Sun R, Schultz PG, Su AI, García-Sastre A, Chatterjee AK, Yuen KY, Chanda SK. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature 2020; 586:113-119. [PMID: 32707573 PMCID: PMC7603405 DOI: 10.1038/s41586-020-2577-1] [Citation(s) in RCA: 559] [Impact Index Per Article: 139.8] [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: 04/20/2020] [Accepted: 07/17/2020] [Indexed: 02/08/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 has triggered an ongoing global pandemic of the severe pneumonia-like disease coronavirus disease 2019 (COVID-19)1. The development of a vaccine is likely to take at least 12-18 months, and the typical timeline for approval of a new antiviral therapeutic agent can exceed 10 years. Thus, repurposing of known drugs could substantially accelerate the deployment of new therapies for COVID-19. Here we profiled a library of drugs encompassing approximately 12,000 clinical-stage or Food and Drug Administration (FDA)-approved small molecules to identify candidate therapeutic drugs for COVID-19. We report the identification of 100 molecules that inhibit viral replication of SARS-CoV-2, including 21 drugs that exhibit dose-response relationships. Of these, thirteen were found to harbour effective concentrations commensurate with probable achievable therapeutic doses in patients, including the PIKfyve kinase inhibitor apilimod2-4 and the cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825 and ONO 5334. Notably, MDL-28170, ONO 5334 and apilimod were found to antagonize viral replication in human pneumocyte-like cells derived from induced pluripotent stem cells, and apilimod also demonstrated antiviral efficacy in a primary human lung explant model. Since most of the molecules identified in this study have already advanced into the clinic, their known pharmacological and human safety profiles will enable accelerated preclinical and clinical evaluation of these drugs for the treatment of COVID-19.
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Affiliation(s)
- Laura Riva
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Laura Martin-Sancho
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Naoko Matsunaga
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lars Pache
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sebastian Burgstaller-Muehlbacher
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Paul D De Jesus
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Peter Teriete
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Max W Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Jianli Cao
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Vincent Kwok-Man Poon
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Kristina M Herbert
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
- Biological Sciences Graduate Program, University of Maryland, College Park, MD, USA
| | | | - Andrey Rubanov
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Yuan Pu
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Courtney Nguyen
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Angela Choi
- 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
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Raveen Rathnasinghe
- 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
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael Schotsaert
- 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
| | - 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
| | - Marion Dejosez
- Huffington Foundation Center for Cell-based Research in Parkinson's Disease, Department for Cell, Regenerative and Developmental Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas P Zwaka
- Huffington Foundation Center for Cell-based Research in Parkinson's Disease, Department for Cell, Regenerative and Developmental Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ko-Yung Sit
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | | | - Wen-Chun Liu
- 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
| | - 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
| | - Mackenzie E Chapman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Emma K Lendy
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Randy Albrecht
- 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
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | | | - Andrew I Su
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - 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
| | | | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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15
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Chin EN, Yu C, Vartabedian VF, Jia Y, Kumar M, Gamo AM, Vernier W, Ali SH, Kissai M, Lazar DC, Nguyen N, Pereira LE, Benish B, Woods AK, Joseph SB, Chu A, Johnson KA, Sander PN, Martínez-Peña F, Hampton EN, Young TS, Wolan DW, Chatterjee AK, Schultz PG, Petrassi HM, Teijaro JR, Lairson LL. Antitumor activity of a systemic STING-activating non-nucleotide cGAMP mimetic. Science 2020; 369:993-999. [PMID: 32820126 DOI: 10.1126/science.abb4255] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022]
Abstract
Stimulator of interferon genes (STING) links innate immunity to biological processes ranging from antitumor immunity to microbiome homeostasis. Mechanistic understanding of the anticancer potential for STING receptor activation is currently limited by metabolic instability of the natural cyclic dinucleotide (CDN) ligands. From a pathway-targeted cell-based screen, we identified a non-nucleotide, small-molecule STING agonist, termed SR-717, that demonstrates broad interspecies and interallelic specificity. A 1.8-angstrom cocrystal structure revealed that SR-717 functions as a direct cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) mimetic that induces the same "closed" conformation of STING. SR-717 displayed antitumor activity; promoted the activation of CD8+ T, natural killer, and dendritic cells in relevant tissues; and facilitated antigen cross-priming. SR-717 also induced the expression of clinically relevant targets, including programmed cell death 1 ligand 1 (PD-L1), in a STING-dependent manner.
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Affiliation(s)
- Emily N Chin
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chenguang Yu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Vincent F Vartabedian
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ying Jia
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Manoj Kumar
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ana M Gamo
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - William Vernier
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sabrina H Ali
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mildred Kissai
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Daniel C Lazar
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nhan Nguyen
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Laura E Pereira
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Brent Benish
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ashley K Woods
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sean B Joseph
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Alan Chu
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kristen A Johnson
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Philipp N Sander
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Francisco Martínez-Peña
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eric N Hampton
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Travis S Young
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dennis W Wolan
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Arnab K Chatterjee
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Michael Petrassi
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - John R Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Luke L Lairson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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16
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Lear S, Pflimlin E, Zhou Z, Huang D, Weng S, Nguyen-Tran V, Joseph SB, Roller S, Peterson S, Li J, Tremblay M, Schultz PG, Shen W. Engineering of a Potent, Long-Acting NPY2R Agonist for Combination with a GLP-1R Agonist as a Multi-Hormonal Treatment for Obesity. J Med Chem 2020; 63:9660-9671. [PMID: 32844654 DOI: 10.1021/acs.jmedchem.0c00740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bariatric surgery results in increased intestinal secretion of hormones GLP-1 and anorexigenic PYY, which is believed to contribute to the clinical efficacy associated with the procedure. This observation raises the question whether combination treatment with gut hormone analogs might recapitulate the efficacy and mitigate the significant risks associated with surgery. Despite PYY demonstrating excellent efficacy and safety profiles with regard to food intake reduction, weight loss, and glucose control in preclinical animal models, PYY-based therapeutic development remains challenging given a low serum stability and half-life for the native peptide. Here, combined peptide stapling and PEG-fatty acid conjugation affords potent PYY analogs with >14 h rat half-lives, which are expected to translate into a human half-life suitable for once-weekly dosing. Excellent efficacy in glucose control, food intake reduction, and weight loss for lead candidate 22 in combination with our previously reported long-acting GLP-1 analog is demonstrated in a diet-induced obesity mouse model.
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Affiliation(s)
- Sam Lear
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Elsa Pflimlin
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Zhihong Zhou
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - David Huang
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Sharon Weng
- Intarcia Therapeutics, Inc., Research Triangle Park, 6 Davis Drive, Durham, North Carolina 27709, United States
| | - Van Nguyen-Tran
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Sean B Joseph
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Shane Roller
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Scott Peterson
- Intarcia Therapeutics, Inc., Research Triangle Park, 6 Davis Drive, Durham, North Carolina 27709, United States
| | - Jing Li
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Matthew Tremblay
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Peter G Schultz
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Weijun Shen
- The Scripps Research Institute, d/b/a Calibr, a division of Scripps Research, 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
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17
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Abstract
The cell wall is an elaborate framework of peptidoglycan that serves to protect the bacterium against osmotic challenge. This exoskeleton is composed of repeating saccharides covalently cross-linked by peptide stems. The general structure of the cell wall is widely conserved across diverse Gram-negative bacteria. To begin to explore the biological consequence of introducing non-canonical cross-links into the cell wall of Escherichia coli, we generated a bacterium where up to 31% of the cell-wall cross-links are formed by a non-enzymatic reaction between a sulfonyl fluoride and an amino group. Bacteria with these non-canonical cell-wall cross-links achieve a high optical density in culture, divide and elongate successfully, and display no loss of outer membrane integrity. This work represents a first step in the design of bacteria with non-canonical "synthetic" cell walls.
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Affiliation(s)
- David A Dik
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nan Zhang
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jason S Chen
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bill Webb
- Center for Metabolomics and Mass Spectrometry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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18
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Zambaldo C, Vinogradova EV, Qi X, Iaconelli J, Suciu RM, Koh M, Senkane K, Chadwick SR, Sanchez BB, Chen JS, Chatterjee AK, Liu P, Schultz PG, Cravatt BF, Bollong MJ. 2-Sulfonylpyridines as Tunable, Cysteine-Reactive Electrophiles. J Am Chem Soc 2020; 142:8972-8979. [PMID: 32302104 DOI: 10.1021/jacs.0c02721] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The emerging use of covalent ligands as chemical probes and drugs would benefit from an expanded repertoire of cysteine-reactive electrophiles for efficient and diverse targeting of the proteome. Here we use the endogenous electrophile sensor of mammalian cells, the KEAP1-NRF2 pathway, to discover cysteine-reactive electrophilic fragments from a reporter-based screen for NRF2 activation. This strategy identified a series of 2-sulfonylpyridines that selectively react with biological thiols via nucleophilic aromatic substitution (SNAr). By tuning the electrophilicity and appended recognition elements, we demonstrate the potential of the 2-sulfonylpyridine reactive group with the discovery of a selective covalent modifier of adenosine deaminase (ADA). Targeting a cysteine distal to the active site, this molecule attenuates the enzymatic activity of ADA and inhibits proliferation of lymphocytic cells. This study introduces a modular and tunable SNAr-based reactive group for targeting reactive cysteines in the human proteome and illustrates the pharmacological utility of this electrophilic series.
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Affiliation(s)
- Claudio Zambaldo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ekaterina V Vinogradova
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xiaotian Qi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jonathan Iaconelli
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Minseob Koh
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kristine Senkane
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Stormi R Chadwick
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Brittany B Sanchez
- Automated Synthesis Facility, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jason S Chen
- Automated Synthesis Facility, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Arnab K Chatterjee
- California Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michael J Bollong
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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19
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Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Burgstaller-Muehlbacher S, Pache L, De Jesus PP, Hull MV, Chang M, Chan JFW, Cao J, Poon VKM, Herbert K, Nguyen TT, Pu Y, Nguyen C, Rubanov A, Martinez-Sobrido L, Liu WC, Miorin L, White KM, Johnson JR, Benner C, Sun R, Schultz PG, Su A, Garcia-Sastre A, Chatterjee AK, Yuen KY, Chanda SK. A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals. bioRxiv 2020:2020.04.16.044016. [PMID: 32511357 PMCID: PMC7263415 DOI: 10.1101/2020.04.16.044016] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The emergence of novel SARS coronavirus 2 (SARS-CoV-2) in 2019 has triggered an ongoing global pandemic of severe pneumonia-like disease designated as coronavirus disease 2019 (COVID-19). To date, more than 2.1 million confirmed cases and 139,500 deaths have been reported worldwide, and there are currently no medical countermeasures available to prevent or treat the disease. As the development of a vaccine could require at least 12-18 months, and the typical timeline from hit finding to drug registration of an antiviral is >10 years, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we profiled a library of known drugs encompassing approximately 12,000 clinical-stage or FDA-approved small molecules. Here, we report the identification of 30 known drugs that inhibit viral replication. Of these, six were characterized for cellular dose-activity relationships, and showed effective concentrations likely to be commensurate with therapeutic doses in patients. These include the PIKfyve kinase inhibitor Apilimod, cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825, and ONO 5334, and the CCR1 antagonist MLN-3897. Since many of these molecules have advanced into the clinic, the known pharmacological and human safety profiles of these compounds will accelerate their preclinical and clinical evaluation for COVID-19 treatment.
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20
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Yang PY, Zou H, Amso Z, Lee C, Huang D, Woods AK, Nguyen-Tran VTB, Schultz PG, Shen W. New Generation Oxyntomodulin Peptides with Improved Pharmacokinetic Profiles Exhibit Weight Reducing and Anti-Steatotic Properties in Mice. Bioconjug Chem 2020; 31:1167-1176. [DOI: 10.1021/acs.bioconjchem.0c00093] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Peng-Yu Yang
- Calibr at The Scripps Research Institute, La Jolla, California 92037, United States
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Huafei Zou
- Calibr at The Scripps Research Institute, La Jolla, California 92037, United States
| | - Zaid Amso
- Calibr at The Scripps Research Institute, La Jolla, California 92037, United States
| | - Candy Lee
- Calibr at The Scripps Research Institute, La Jolla, California 92037, United States
| | - David Huang
- Calibr at The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ashley K. Woods
- Calibr at The Scripps Research Institute, La Jolla, California 92037, United States
| | | | - Peter G. Schultz
- Calibr at The Scripps Research Institute, La Jolla, California 92037, United States
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Weijun Shen
- Calibr at The Scripps Research Institute, La Jolla, California 92037, United States
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21
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Iaconelli J, Ibrahim L, Chen E, Hull M, Schultz PG, Bollong MJ. Small-Molecule Stimulators of NRF1 Transcriptional Activity. Chembiochem 2019; 21:1816-1819. [PMID: 31596542 DOI: 10.1002/cbic.201900487] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 08/06/2019] [Revised: 09/25/2019] [Indexed: 01/09/2023]
Abstract
The transcription factor nuclear factor erythroid 2-related factor 1 (NRF1) maintains proteostasis and promotes cellular resilience by stimulating the transcription of proteasomal subunits and a host of protective enzymes. Although NRF1 activation would likely be beneficial in a number of disease states, information regarding its ligandability and upstream regulation are lacking. Herein we report a high-throughput chemical screen that identified selective stimulators of NRF1-driven transcription, including unannotated inhibitors of the ubiquitin proteasome system (UPS) as well as two non-UPS-targeted compounds that synergistically activate NRF1 in the context of submaximal UPS inhibition. This work introduces a suite of tool molecules to study the NRF1 transcriptional response and to uncover the druggable components governing NRF1 activity in cells.
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Affiliation(s)
- Jonathan Iaconelli
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Lara Ibrahim
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Emily Chen
- California Institute for Biomedical Research (Calibr), La Jolla, CA, 92037, USA
| | - Mitchell Hull
- California Institute for Biomedical Research (Calibr), La Jolla, CA, 92037, USA
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael J Bollong
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
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22
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Ardestani A, Li S, Annamalai K, Lupse B, Geravandi S, Dobrowolski A, Yu S, Zhu S, Baguley TD, Surakattula M, Oetjen J, Hauberg-Lotte L, Herranz R, Awal S, Altenhofen D, Nguyen-Tran V, Joseph S, Schultz PG, Chatterjee AK, Rogers N, Tremblay MS, Shen W, Maedler K. Neratinib protects pancreatic beta cells in diabetes. Nat Commun 2019; 10:5015. [PMID: 31676778 PMCID: PMC6825211 DOI: 10.1038/s41467-019-12880-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023] Open
Abstract
The loss of functional insulin-producing β-cells is a hallmark of diabetes. Mammalian sterile 20-like kinase 1 (MST1) is a key regulator of pancreatic β-cell death and dysfunction; its deficiency restores functional β-cells and normoglycemia. The identification of MST1 inhibitors represents a promising approach for a β-cell-protective diabetes therapy. Here, we identify neratinib, an FDA-approved drug targeting HER2/EGFR dual kinases, as a potent MST1 inhibitor, which improves β-cell survival under multiple diabetogenic conditions in human islets and INS-1E cells. In a pre-clinical study, neratinib attenuates hyperglycemia and improves β-cell function, survival and β-cell mass in type 1 (streptozotocin) and type 2 (obese Leprdb/db) diabetic mouse models. In summary, neratinib is a previously unrecognized inhibitor of MST1 and represents a potential β-cell-protective drug with proof-of-concept in vitro in human islets and in vivo in rodent models of both type 1 and type 2 diabetes. Type 1 as well as type 2 diabetes are characterized by a loss of insulin-producing β-cells. Here the authors show that the FDA-approved drug neratinib has beneficial effects on β-cell survival, insulin secretion, and glycemic control in mouse models of diabetes.
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Affiliation(s)
- Amin Ardestani
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany.
| | - Sijia Li
- Calibr at Scripps Research, La Jolla, CA, USA
| | - Karthika Annamalai
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
| | - Blaz Lupse
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
| | - Shirin Geravandi
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
| | | | - Shan Yu
- Calibr at Scripps Research, La Jolla, CA, USA
| | - Siying Zhu
- Calibr at Scripps Research, La Jolla, CA, USA
| | | | | | - Janina Oetjen
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany.,Center for Industrial Mathematics, University of Bremen, Bremen, Germany.,MALDI Imaging Lab, University of Bremen, Bremen, Germany
| | - Lena Hauberg-Lotte
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany
| | - Raquel Herranz
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
| | - Sushil Awal
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
| | - Delsi Altenhofen
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
| | | | - Sean Joseph
- Calibr at Scripps Research, La Jolla, CA, USA
| | | | | | | | | | - Weijun Shen
- Calibr at Scripps Research, La Jolla, CA, USA.
| | - Kathrin Maedler
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany.
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23
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Koh M, Yao A, Gleason PR, Mills JH, Schultz PG. A General Strategy for Engineering Noncanonical Amino Acid Dependent Bacterial Growth. J Am Chem Soc 2019; 141:16213-16216. [PMID: 31580059 DOI: 10.1021/jacs.9b08491] [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: 01/08/2023]
Abstract
Synthetic auxotrophy in which bacterial viability depends on the presence of a synthetic amino acid provides a robust strategy for the containment of genetically modified organisms and the development of safe, live vaccines. However, a simple, general strategy to evolve essential proteins to be dependent on synthetic amino acids is lacking. Using a temperature-sensitive selection system, we evolved an Escherichia coli (E. coli) sliding clamp variant with an orthogonal protein-protein interface, which contains a Leu273 to p-benzoylphenyl alanine (pBzF) mutation. The E. coli strain with this variant DNA clamp has a very low escape frequency (<10-10), and its growth is strictly dependent on the presence of pBzF. This selection strategy can be generally applied to create ncAA dependence of other organisms with DNA clamp homologues.
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Affiliation(s)
- Minseob Koh
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Anzhi Yao
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Patrick R Gleason
- School of Molecular Sciences and The Biodesign Center for Molecular Design and Biomimetics , Arizona State University , Tempe , Arizona 85281 , United States
| | - Jeremy H Mills
- School of Molecular Sciences and The Biodesign Center for Molecular Design and Biomimetics , Arizona State University , Tempe , Arizona 85281 , United States
| | - Peter G Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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24
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Abstract
Based on the endosymbiotic theory, one of the key events that occurred during mitochondrial evolution was an extensive loss of nonessential genes from the protomitochondrial endosymbiont genome and transfer of some of the essential endosymbiont genes to the host nucleus. We have developed an approach to recapitulate various aspects of endosymbiont genome minimization using a synthetic system consisting of Escherichia coli endosymbionts within host yeast cells. As a first step, we identified a number of E. coli auxotrophs of central metabolites that can form viable endosymbionts within yeast cells. These studies provide a platform to identify nonessential biosynthetic pathways that can be deleted in the E. coli endosymbionts to investigate the evolutionary adaptations in the host and endosymbiont during the evolution of mitochondria.
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Affiliation(s)
- Angad P Mehta
- The Department of Chemistry , Scripps Research , La Jolla , California 92037 , United States
| | - Yeonjin Ko
- The Department of Chemistry , Scripps Research , La Jolla , California 92037 , United States
| | - Lubica Supekova
- The Department of Chemistry , Scripps Research , La Jolla , California 92037 , United States
| | - Kersi Pestonjamasp
- The Core Microscopy Facility , Scripps Research , La Jolla , California 92037 , United States
| | - Jack Li
- The Department of Chemistry , Scripps Research , La Jolla , California 92037 , United States
| | - Peter G Schultz
- The Department of Chemistry , Scripps Research , La Jolla , California 92037 , United States
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25
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Abstract
We have genetically encoded a dithiolane containing amino acid (dtF) in Escherichia coli (E. coli) using a polyspecific aminoacyl-tRNA synthetase (aaRS)/amber suppressor tRNA pair. To demonstrate the utility of dtF for bioapplications, we synthesized gold nanoparticle (AuNP) constructs with a mutant superfolder green fluorescent protein (sfGFP) [sfGFP-AuNP] as a model for the protein-metal conjugation. The resulting sfGFP-AuNP constructs show directional homogeneity and enhanced chemical durability compared to their cysteine analogues toward excess environmental 1,4-dithiothreitol (DTT).
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Affiliation(s)
- Minseob Koh
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
| | - Hyeon-Yeol Cho
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , Piscataway , New Jersey 08854 , United States
| | - Chenguang Yu
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
| | - Seihyun Choi
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , Piscataway , New Jersey 08854 , United States.,Department of Life and Nanopharmaceutical Science, College of Pharmacy , Kyung Hee University , Seoul 02447 , Republic of Korea
| | - Peter G Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
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26
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Zhang Y, Fang C, Wang RE, Wang Y, Guo H, Guo C, Zhao L, Li S, Li X, Schultz PG, Cao YJ, Wang F. A tumor-targeted immune checkpoint blocker. Proc Natl Acad Sci U S A 2019; 116:15889-15894. [PMID: 31332018 PMCID: PMC6689898 DOI: 10.1073/pnas.1905646116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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] [Indexed: 01/22/2023] Open
Abstract
To direct checkpoint inhibition to the tumor microenvironment, while avoiding systemic immune activation, we have synthesized a bispecific antibody [norleucine4, d-Phe7]-melanocyte stimulating hormone (NDP-MSH)-antiprogrammed cell death-ligand 1 antibody (αPD-L1) by conjugating a melanocyte stimulating hormone (α-MSH) analog to the antiprogrammed cell death-ligand 1 to (αPD-L1) antibody avelumab. This bispecific antibody can bind to both the melanocortin-1 receptor (MC1R) and to PD-L1 expressed on melanoma cells and shows enhanced specific antitumor efficacy in a syngeneic B16-SIY melanoma mouse model compared with the parental antibody at a 5 mg/kg dose. Moreover, the bispecific antibody showed increased infiltrated T cells in the tumor microenvironment. These results suggest that a tumor-targeted PD-L1-blocking bispecific antibody could have a therapeutic advantage in vivo, especially when used in combination with other checkpoint inhibitors.
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Affiliation(s)
- Yuhan Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Changming Fang
- California Institute for Biomedical Research (Calibr), La Jolla, CA 92037
| | - Rongsheng E Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Ying Wang
- California Institute for Biomedical Research (Calibr), La Jolla, CA 92037
| | - Hui Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Chao Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- School of Ocean, Shandong University, 264209 Weihai, China
| | - Lijun Zhao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, 518055 Shenzhen, China
| | - Shuhong Li
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, 518055 Shenzhen, China
| | - Xia Li
- School of Ocean, Shandong University, 264209 Weihai, China
| | - Peter G Schultz
- California Institute for Biomedical Research (Calibr), La Jolla, CA 92037;
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, 518055 Shenzhen, China
| | - Feng Wang
- Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China;
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Li JC, Nastertorabi F, Xuan W, Han GW, Stevens RC, Schultz PG. A Single Reactive Noncanonical Amino Acid Is Able to Dramatically Stabilize Protein Structure. ACS Chem Biol 2019; 14:1150-1153. [PMID: 31181898 DOI: 10.1021/acschembio.9b00002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A p-isothiocyanate phenylalanine mutant of the homodimeric protein homoserine o-succinyltransferase (MetA) was isolated in a temperature dependent selection from a library of metA mutants containing noncanonical amino acids. This mutant protein has a dramatic increase of 24 °C in thermal stability compared to the wild type protein. Peptide mapping experiments revealed that the isothiocyanate group forms a thiourea cross-link to the N terminal proline of the other monomer, despite the two positions being >30 Å apart in the X-ray crystal structure of the wild type protein. These results show that an expanded set of building blocks beyond the canonical 20 amino acids can lead to significant changes in the properties of proteins.
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Affiliation(s)
- Jack C. Li
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Fariborz Nastertorabi
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Weimin Xuan
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gye Won Han
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Raymond C. Stevens
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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28
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Bakowski MA, Shiroodi RK, Liu R, Olejniczak J, Yang B, Gagaring K, Guo H, White PM, Chappell L, Debec A, Landmann F, Dubben B, Lenz F, Struever D, Ehrens A, Frohberger SJ, Sjoberg H, Pionnier N, Murphy E, Archer J, Steven A, Chunda VC, Fombad FF, Chounna PW, Njouendou AJ, Metuge HM, Ndzeshang BL, Gandjui NV, Akumtoh DN, Kwenti TDB, Woods AK, Joseph SB, Hull MV, Xiong W, Kuhen KL, Taylor MJ, Wanji S, Turner JD, Hübner MP, Hoerauf A, Chatterjee AK, Roland J, Tremblay MS, Schultz PG, Sullivan W, Chu XJ, Petrassi HM, McNamara CW. Discovery of short-course antiwolbachial quinazolines for elimination of filarial worm infections. Sci Transl Med 2019; 11:11/491/eaav3523. [DOI: 10.1126/scitranslmed.aav3523] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/18/2019] [Indexed: 12/21/2022]
Abstract
Parasitic filarial nematodes cause debilitating infections in people in resource-limited countries. A clinically validated approach to eliminating worms uses a 4- to 6-week course of doxycycline that targetsWolbachia, a bacterial endosymbiont required for worm viability and reproduction. However, the prolonged length of therapy and contraindication in children and pregnant women have slowed adoption of this treatment. Here, we describe discovery and optimization of quinazolines CBR417 and CBR490 that, with a single dose, achieve >99% elimination ofWolbachiain the in vivoLitomosoides sigmodontisfilarial infection model. The efficacious quinazoline series was identified by pairing a primary cell-based high-content imaging screen with an orthogonal ex vivo validation assay to rapidly quantifyWolbachiaelimination inBrugia pahangifilarial ovaries. We screened 300,368 small molecules in the primary assay and identified 288 potent and selective hits. Of 134 primary hits tested, only 23.9% were active in the worm-based validation assay, 8 of which contained a quinazoline heterocycle core. Medicinal chemistry optimization generated quinazolines with excellent pharmacokinetic profiles in mice. Potent antiwolbachial activity was confirmed inL. sigmodontis,Brugia malayi, andOnchocerca ochengiin vivo preclinical models of filarial disease and in vitro selectivity againstLoa loa(a safety concern in endemic areas). The favorable efficacy and in vitro safety profiles of CBR490 and CBR417 further support these as clinical candidates for treatment of filarial infections.
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Abstract
The ability to add noncanonical amino acids to the genetic code may allow one to evolve proteins with new or enhanced properties using a larger set of building blocks. To this end, we have been able to select mutant proteins with enhanced thermal properties from a library of E. coli homoserine O-succinyltransferase ( metA) mutants containing randomly incorporated noncanonical amino acids. Here, we show that substitution of Phe 21 with ( p-benzoylphenyl)alanine (pBzF), increases the melting temperature of E. coli metA by 21 °C. This dramatic increase in thermal stability, arising from a single mutation, likely results from a covalent adduct between Cys 90 and the keto group of pBzF that stabilizes the dimeric form of the enzyme. These experiments show that an expanded genetic code can provide unique solutions to the evolution of proteins with enhanced properties.
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Affiliation(s)
- Jack C Li
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Tao Liu
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Yan Wang
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Angad P Mehta
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Peter G Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
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30
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Ahmed N, De Graaf JF, Ahmed N, Foss DV, Delcorde J, Schultz PG, Pezacki JP. Visualization of the Delivery and Release of Small RNAs Using Genetic Code Expansion and Unnatural RNA-Binding Proteins. Bioconjug Chem 2018; 29:3982-3986. [DOI: 10.1021/acs.bioconjchem.8b00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Noreen Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Joanna Fréderique De Graaf
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Nadine Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Dana V. Foss
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Julie Delcorde
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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31
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Janes J, Young ME, Chen E, Rogers NH, Burgstaller-Muehlbacher S, Hughes LD, Love MS, Hull MV, Kuhen KL, Woods AK, Joseph SB, Petrassi HM, McNamara CW, Tremblay MS, Su AI, Schultz PG, Chatterjee AK. The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis. Proc Natl Acad Sci U S A 2018; 115:10750-10755. [PMID: 30282735 PMCID: PMC6196526 DOI: 10.1073/pnas.1810137115] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [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] [Indexed: 02/01/2023] Open
Abstract
The chemical diversity and known safety profiles of drugs previously tested in humans make them a valuable set of compounds to explore potential therapeutic utility in indications outside those originally targeted, especially neglected tropical diseases. This practice of "drug repurposing" has become commonplace in academic and other nonprofit drug-discovery efforts, with the appeal that significantly less time and resources are required to advance a candidate into the clinic. Here, we report a comprehensive open-access, drug repositioning screening set of 12,000 compounds (termed ReFRAME; Repurposing, Focused Rescue, and Accelerated Medchem) that was assembled by combining three widely used commercial drug competitive intelligence databases (Clarivate Integrity, GVK Excelra GoStar, and Citeline Pharmaprojects), together with extensive patent mining of small molecules that have been dosed in humans. To date, 12,000 compounds (∼80% of compounds identified from data mining) have been purchased or synthesized and subsequently plated for screening. To exemplify its utility, this collection was screened against Cryptosporidium spp., a major cause of childhood diarrhea in the developing world, and two active compounds previously tested in humans for other therapeutic indications were identified. Both compounds, VB-201 and a structurally related analog of ASP-7962, were subsequently shown to be efficacious in animal models of Cryptosporidium infection at clinically relevant doses, based on available human doses. In addition, an open-access data portal (https://reframedb.org) has been developed to share ReFRAME screen hits to encourage additional follow-up and maximize the impact of the ReFRAME screening collection.
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Affiliation(s)
- Jeff Janes
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Megan E Young
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Emily Chen
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Nicole H Rogers
- California Institute for Biomedical Research, La Jolla, CA 92037
| | | | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Melissa S Love
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Mitchell V Hull
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Kelli L Kuhen
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Ashley K Woods
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Sean B Joseph
- California Institute for Biomedical Research, La Jolla, CA 92037
| | | | - Case W McNamara
- California Institute for Biomedical Research, La Jolla, CA 92037
| | | | - Andrew I Su
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Peter G Schultz
- California Institute for Biomedical Research, La Jolla, CA 92037;
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32
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Bollong MJ, Lee G, Coukos JS, Yun H, Zambaldo C, Chang JW, Chin EN, Ahmad I, Chatterjee AK, Lairson LL, Schultz PG, Moellering RE. A metabolite-derived protein modification integrates glycolysis with KEAP1-NRF2 signalling. Nature 2018; 562:600-604. [PMID: 30323285 PMCID: PMC6444936 DOI: 10.1038/s41586-018-0622-0] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 08/21/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Michael J Bollong
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Gihoon Lee
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - John S Coukos
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Hwayoung Yun
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.,College of Pharmacy, Pusan National University, Busan, South Korea
| | - Claudio Zambaldo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jae Won Chang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Emily N Chin
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Insha Ahmad
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Arnab K Chatterjee
- California Institute for Biomedical Research (Calibr), La Jolla, CA, USA
| | - Luke L Lairson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,California Institute for Biomedical Research (Calibr), La Jolla, CA, USA.
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,California Institute for Biomedical Research (Calibr), La Jolla, CA, USA.
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
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33
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Crnovcic I, Gan F, Yang D, Dong LB, Schultz PG, Shen B. Activities of recombinant human bleomycin hydrolase on bleomycins and engineered analogues revealing new opportunities to overcome bleomycin-induced pulmonary toxicity. Bioorg Med Chem Lett 2018; 28:2670-2674. [PMID: 29730026 DOI: 10.1016/j.bmcl.2018.04.065] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 02/08/2023]
Abstract
The bleomycins (BLMs) are widely used in combination therapies for the treatment of various cancers. Dose-dependent and cumulative pulmonary toxicity is the major cause of BLM-associated morbidity, limiting the broad uses of BLMs as anticancer drugs. The organ specificity of BLM-induced toxicity has been correlated with the expression of the hBLMH gene, encoding the human bleomycin hydrolase (hBLMH), which is poorly expressed in the lung. hBLMH hydrolyzes BLMs into the biologically inactive deamido BLMs, thereby protecting organs from BLM-induced toxicity. Here we report (i) expression of hBLMH and production and isolation of recombinant human bleomycin hydrolase (rhBLMH) from E. coli, (ii) structural characterization of deamido BLM A2 and B2 isolated from rhBLMH-catalyzed hydrolysis of BLM A2 and B2, and (iii) kinetic characterization of the rhBLMH-catalyzed hydrolysis of BLM A2 and B2, in comparison with five BLM analogues. rhBLMH from E. coli catalyzes rapid and efficient hydrolysis of all BLMs tested, exhibiting a superior catalytic efficiency for BLM B2. These findings reveal new opportunities to overcome BLM-induced pulmonary toxicity in chemotherapies, potentially by exploring BLM B2 as the preferred congener, engineering designer BLMs with optimized activity for rhBLMH, or co-administrating rhBLMH directly into the lung as a potential protein therapeutic.
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Affiliation(s)
- Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Fei Gan
- California Institute for Biomedical Research, La Jolla, CA 92037, United States
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Liao-Bin Dong
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Peter G Schultz
- California Institute for Biomedical Research, La Jolla, CA 92037, United States; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, United States.
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34
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Zhong L, Tran T, Baguley TD, Lee SJ, Henke A, To A, Li S, Yu S, Grieco FA, Roland J, Schultz PG, Eizirik DL, Rogers N, Chartterjee AK, Tremblay MS, Shen W. A novel inhibitor of inducible NOS dimerization protects against cytokine-induced rat beta cell dysfunction. Br J Pharmacol 2018; 175:3470-3485. [PMID: 29888783 PMCID: PMC6086989 DOI: 10.1111/bph.14388] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 05/14/2018] [Accepted: 05/28/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND AND PURPOSE Beta cell apoptosis is a major feature of type 1 diabetes, and pro-inflammatory cytokines are key drivers of the deterioration of beta cell mass through induction of apoptosis. Mitochondrial stress plays a critical role in mediating apoptosis by releasing cytochrome C into the cytoplasm, directly activating caspase-9 and its downstream signalling cascade. We aimed to identify new compounds that protect beta cells from cytokine-induced activation of the intrinsic (mitochondrial) pathway of apoptosis. EXPERIMENTAL APPROACH Diabetogenic media, composed of IL-1β, IFN-γ and high glucose, were used to induce mitochondrial stress in rat insulin-producing INS1E cells, and a high-content image-based screen of small molecule modulators of Casp9 pathway was performed. KEY RESULTS A novel small molecule, ATV399, was identified from a high-content image-based screen for compounds that inhibit cleaved caspase-9 activation and subsequent beta cell apoptosis induced by a combination of IL-1β, IFN-γ and high glucose, which together mimic the pathogenic diabetic milieu. Through medicinal chemistry optimization, potency was markedly improved (6-30 fold), with reduced inhibitory effects on CYP3A4. Improved analogues, such as CAT639, improved beta cell viability and insulin secretion in cytokine-treated rat insulin-producing INS1E cells and primary dispersed islet cells. Mechanistically, CAT639 reduced the production of NO by allosterically inhibiting dimerization of inducible NOS (iNOS) without affecting its mRNA levels. CONCLUSION AND IMPLICATIONS Taken together, these studies demonstrate a successful phenotypic screening campaign resulting in identification of an inhibitor of iNOS dimerization that protects beta cell viability and function through modulation of mitochondrial stress induced by cytokines.
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Affiliation(s)
- Linlin Zhong
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Tuan Tran
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Tyler D Baguley
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Sang Jun Lee
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Adam Henke
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Andrew To
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Sijia Li
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Shan Yu
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Fabio A Grieco
- ULB Center for Diabetes ResearchUniversite´ Libre de Bruxelles (ULB)Brussels1070Belgium
| | - Jason Roland
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | - Peter G Schultz
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
- Department of ChemistryThe Scripps Research InstituteLa JollaCA92037USA
| | - Decio L Eizirik
- ULB Center for Diabetes ResearchUniversite´ Libre de Bruxelles (ULB)Brussels1070Belgium
| | - Nikki Rogers
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
| | | | | | - Weijun Shen
- California Institute for Biomedical Research (Calibr)La JollaCA92037USA
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35
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Mehta AP, Wang Y, Reed SA, Supekova L, Javahishvili T, Chaput JC, Schultz PG. Bacterial Genome Containing Chimeric DNA–RNA Sequences. J Am Chem Soc 2018; 140:11464-11473. [DOI: 10.1021/jacs.8b07046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Angad P. Mehta
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yiyang Wang
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sean A. Reed
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lubica Supekova
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tsotne Javahishvili
- Bay Area Innovation Center, Corteva Agriscience, 4010 Point Eden Way, Hayward, California 94545, United States
| | | | - Peter G. Schultz
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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36
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Abdeen S, Kunkle T, Salim N, Ray AM, Mammadova N, Summers C, Stevens M, Ambrose AJ, Park Y, Schultz PG, Horwich AL, Hoang QQ, Chapman E, Johnson SM. Sulfonamido-2-arylbenzoxazole GroEL/ES Inhibitors as Potent Antibacterials against Methicillin-Resistant Staphylococcus aureus (MRSA). J Med Chem 2018; 61:7345-7357. [PMID: 30060666 DOI: 10.1021/acs.jmedchem.8b00989] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Extending from a study we recently published examining the antitrypanosomal effects of a series of GroEL/ES inhibitors based on a pseudosymmetrical bis-sulfonamido-2-phenylbenzoxazole scaffold, here, we report the antibiotic effects of asymmetric analogs of this scaffold against a panel of bacteria known as the ESKAPE pathogens ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). While GroEL/ES inhibitors were largely ineffective against K. pneumoniae, A. baumannii, P. aeruginosa, and E. cloacae (Gram-negative bacteria), many analogs were potent inhibitors of E. faecium and S. aureus proliferation (Gram-positive bacteria, EC50 values of the most potent analogs were in the 1-2 μM range). Furthermore, even though some compounds inhibit human HSP60/10 biochemical functions in vitro (IC50 values in the 1-10 μM range), many of these exhibited moderate to low cytotoxicity to human liver and kidney cells (CC50 values > 20 μM).
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Affiliation(s)
- Sanofar Abdeen
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Trent Kunkle
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Nilshad Salim
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Anne-Marie Ray
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Najiba Mammadova
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Corey Summers
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Mckayla Stevens
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Andrew J Ambrose
- College of Pharmacy, Department of Pharmacology and Toxicology , The University of Arizona , 1703 East Mabel Street , P.O. Box 210207, Tucson , Arizona 85721 , United States
| | - Yangshin Park
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States.,Stark Neurosciences Research Institute , Indiana University School of Medicine , 320 West 15th Street, Suite 414 , Indianapolis , Indiana 46202 , United States.,Department of Neurology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Peter G Schultz
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Arthur L Horwich
- HHMI, Department of Genetics, Yale School of Medicine , Boyer Center for Molecular Medicine , 295 Congress Avenue , New Haven , Connecticut 06510 , United States
| | - Quyen Q Hoang
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States.,Stark Neurosciences Research Institute , Indiana University School of Medicine , 320 West 15th Street, Suite 414 , Indianapolis , Indiana 46202 , United States.,Department of Neurology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology , The University of Arizona , 1703 East Mabel Street , P.O. Box 210207, Tucson , Arizona 85721 , United States
| | - Steven M Johnson
- Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , 635 Barnhill Drive , Indianapolis , Indiana 46202 , United States
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37
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Miglianico M, Eldering M, Slater H, Ferguson N, Ambrose P, Lees RS, Koolen KMJ, Pruzinova K, Jancarova M, Volf P, Koenraadt CJM, Duerr HP, Trevitt G, Yang B, Chatterjee AK, Wisler J, Sturm A, Bousema T, Sauerwein RW, Schultz PG, Tremblay MS, Dechering KJ. Repurposing isoxazoline veterinary drugs for control of vector-borne human diseases. Proc Natl Acad Sci U S A 2018; 115:E6920-E6926. [PMID: 29967151 PMCID: PMC6055183 DOI: 10.1073/pnas.1801338115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [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] [Indexed: 01/24/2023] Open
Abstract
Isoxazolines are oral insecticidal drugs currently licensed for ectoparasite control in companion animals. Here we propose their use in humans for the reduction of vector-borne disease incidence. Fluralaner and afoxolaner rapidly killed Anopheles, Aedes, and Culex mosquitoes and Phlebotomus sand flies after feeding on a drug-supplemented blood meal, with IC50 values ranging from 33 to 575 nM, and were fully active against strains with preexisting resistance to common insecticides. Based on allometric scaling of preclinical pharmacokinetics data, we predict that a single human median dose of 260 mg (IQR, 177-407 mg) for afoxolaner, or 410 mg (IQR, 278-648 mg) for fluralaner, could provide an insecticidal effect lasting 50-90 days against mosquitoes and Phlebotomus sand flies. Computational modeling showed that seasonal mass drug administration of such a single dose to a fraction of a regional population would dramatically reduce clinical cases of Zika and malaria in endemic settings. Isoxazolines therefore represent a promising new component of drug-based vector control.
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Affiliation(s)
| | | | - Hannah Slater
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Neil Ferguson
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Pauline Ambrose
- The Liverpool Insect Testing Establishment, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Rosemary S Lees
- The Liverpool Insect Testing Establishment, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | | | - Katerina Pruzinova
- Department of Parasitology, Faculty of Science, Charles University, 116 36 Prague, Czech Republic
| | - Magdalena Jancarova
- Department of Parasitology, Faculty of Science, Charles University, 116 36 Prague, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, 116 36 Prague, Czech Republic
| | | | | | | | - Baiyuan Yang
- California Institute for Biomedical Research, La Jolla, CA 92037
| | | | - John Wisler
- California Institute for Biomedical Research, La Jolla, CA 92037
| | | | - Teun Bousema
- Department of Medical Microbiology, Radboud University Medical Center, 6525 Nijmegen, The Netherlands
| | - Robert W Sauerwein
- TropIQ Health Sciences, 6534 Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, 6525 Nijmegen, The Netherlands
| | - Peter G Schultz
- California Institute for Biomedical Research, La Jolla, CA 92037;
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38
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Abstract
RG-7916 is a first-in-class drug candidate for the treatment of spinal muscular atrophy (SMA) that functions by modulating pre-mRNA splicing of the SMN2 gene, resulting in a 2.5-fold increase in survival of motor neuron (SMN) protein level, a key protein lacking in SMA patients. RG-7916 is currently in three interventional phase 2 clinical trials for various types of SMA. In this report, we show that SMN-C2 and -C3, close analogs of RG-7916, act as selective RNA-binding ligands that modulate pre-mRNA splicing. Chemical proteomic and genomic techniques reveal that SMN-C2 directly binds to the AGGAAG motif on exon 7 of the SMN2 pre-mRNA, and promotes a conformational change in two to three unpaired nucleotides at the junction of intron 6 and exon 7 in both in vitro and in-cell models. This change creates a new functional binding surface that increases binding of the splicing modulators, far upstream element binding protein 1 (FUBP1) and its homolog, KH-type splicing regulatory protein (KHSRP), to the SMN-C2/C3-SMN2 pre-mRNA complex and enhances SMN2 splicing. These findings underscore the potential of small-molecule drugs to selectively bind RNA and modulate pre-mRNA splicing as an approach to the treatment of human disease.
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Affiliation(s)
- Jingxin Wang
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Peter G Schultz
- California Institute for Biomedical Research, La Jolla, CA 92037;
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
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39
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Supekova L, Zambaldo C, Choi S, Lim R, Luo X, Kazane SA, Young TS, Schultz PG. The genetic incorporation of p-azidomethyl-l-phenylalanine into proteins in yeast. Bioorg Med Chem Lett 2018; 28:1570-1573. [DOI: 10.1016/j.bmcl.2018.03.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 11/24/2022]
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40
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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41
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Yao A, Reed SA, Koh M, Yu C, Luo X, Mehta AP, Schultz PG. Progress toward a reduced phage genetic code. Bioorg Med Chem 2018; 26:5247-5252. [PMID: 29609949 DOI: 10.1016/j.bmc.2018.03.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 02/22/2018] [Revised: 03/14/2018] [Accepted: 03/23/2018] [Indexed: 12/23/2022]
Abstract
All known living organisms use at least 20 amino acids as the basic building blocks of life. Efforts to reduce the number of building blocks in a replicating system to below the 20 canonical amino acids have not been successful to date. In this work, we use filamentous phage as a model system to investigate the feasibility of removing methionine (Met) from the proteome. We show that all 24 elongation Met sites in the M13 phage genome can be replaced by other canonical amino acids. Most of these changes involve substitution of methionine by leucine (Leu), but in some cases additional compensatory mutations are required. Combining Met substituted sites in the proteome generally led to lower viability/infectivity of the mutant phages, which remains the major challenge in eliminating all methionines from the phage proteome. To date a total of 15 (out of all 24) elongation Mets have been simultaneously deleted from the M13 proteome, providing a useful foundation for future efforts to minimize the genetic code.
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Affiliation(s)
- Anzhi Yao
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Sean A Reed
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Minseob Koh
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Chenguang Yu
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Xiaozhou Luo
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Angad P Mehta
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Peter G Schultz
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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42
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Yang PY, Zou H, Lee C, Muppidi A, Chao E, Fu Q, Luo X, Wang D, Schultz PG, Shen W. Stapled, Long-Acting Glucagon-like Peptide 2 Analog with Efficacy in Dextran Sodium Sulfate Induced Mouse Colitis Models. J Med Chem 2018. [PMID: 29528634 DOI: 10.1021/acs.jmedchem.7b00768] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glucagon-like peptide 2 (GLP-2) is a hormone that has been shown to stimulate intestinal growth and attenuate intestinal inflammation. Despite being efficacious in a variety of animal models of disease, its therapeutic potential is hampered by the short half-life in vivo. We now describe a highly potent, stapled long-acting GLP-2 analog, peptide 10, that has a more than 10-fold longer half-life than teduglutide and improved intestinotrophic and anti-inflammatory effects in mouse models of DSS-induced colitis.
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Affiliation(s)
- Peng-Yu Yang
- California Institute for Biomedical Research , La Jolla , California 92037 , United States.,Department of Chemistry, The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Huafei Zou
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Candy Lee
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Avinash Muppidi
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Elizabeth Chao
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Qiangwei Fu
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Xiaozhou Luo
- Department of Chemistry, The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Danling Wang
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Peter G Schultz
- California Institute for Biomedical Research , La Jolla , California 92037 , United States.,Department of Chemistry, The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Weijun Shen
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
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43
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Abstract
![]()
Here,
we report the site-specific incorporation of a thioester
containing noncanonical amino acid (ncAA) into recombinantly expressed
proteins. Specifically, we genetically encoded a thioester-activated
aspartic acid (ThioD) in bacteria in good yield and with high fidelity
using an orthogonal nonsense suppressor tRNA/aminoacyl-tRNA synthetase
(aaRS) pair. To demonstrate the utility of ThioD, we used native chemical
ligation to label green fluorescent protein with a fluorophore in
good yield.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Daniel Collins
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Minseob Koh
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Sida Shao
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Anzhi Yao
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Han Xiao
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip Garner
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
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44
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Gan F, Liu R, Wang F, Schultz PG. Functional Replacement of Histidine in Proteins To Generate Noncanonical Amino Acid Dependent Organisms. J Am Chem Soc 2018; 140:3829-3832. [DOI: 10.1021/jacs.7b13452] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Fei Gan
- California Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Renhe Liu
- California Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Feng Wang
- California Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Peter G. Schultz
- California Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, La Jolla, California 92037, United States
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45
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Sun SB, Sen S, Kim NJ, Magliery TJ, Schultz PG, Wang F. Retraction of "Mutational Analysis of 48G7 Reveals that Somatic Hypermutation Affects Both Antibody Stability and Binding Affinity". J Am Chem Soc 2018; 140:1976. [PMID: 29376652 DOI: 10.1021/jacs.7b08106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Du J, Cao Y, Liu Y, Wang Y, Zhang Y, Fu G, Zhang Y, Lu L, Luo X, Kim CH, Schultz PG, Wang F. Engineering Bifunctional Antibodies with Constant Region Fusion Architectures. J Am Chem Soc 2017; 139:18607-18615. [PMID: 29186655 DOI: 10.1021/jacs.7b09641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report a method to generate bifunctional antibodies by grafting full-length proteins into constant region loops of a full-length antibody or an antigen-binding fragment (Fab). The fusion proteins retain the antigen binding activity of the parent antibody but have an additional activity associated with the protein insert. The engineered antibodies have excellent in vitro activity, physiochemical properties, and stability. Among these, a Her2 × CD3 bispecific antibody (BsAb) was constructed by inserting an anti-Her2 single-chain variable fragment (ScFv) into an anti-CD3 Fab. This bispecific antibody efficiently induces targeted cell lysis in the presence of effector cells at as low as sub-picomolar concentrations in vitro. Moreover, the Her2 × CD3 BsAb shows potent in vivo antitumor activity in mouse Her22+ and Her21+ xenograft models. These results demonstrate that insertion of a full-length protein into non-CDR loops of antibodies provides a feasible approach to generate multifunctional antibodies for therapeutic applications.
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Affiliation(s)
- Juanjuan Du
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Yu Cao
- Department of Chemistry, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Yan Liu
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Wang
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Zhang
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Guangsen Fu
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Yuhan Zhang
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Lucy Lu
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Xiaozhou Luo
- Department of Chemistry, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Chan Hyuk Kim
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Feng Wang
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
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47
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Choi SH, Mahankali M, Lee SJ, Hull M, Petrassi HM, Chatterjee AK, Schultz PG, Jones KA, Shen W. Targeted Disruption of Myc-Max Oncoprotein Complex by a Small Molecule. ACS Chem Biol 2017; 12:2715-2719. [PMID: 28976731 DOI: 10.1021/acschembio.7b00799] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Myc plays important roles in cell cycle progression, cell growth, and stem cell self-renewal. Although dysregulation of Myc expression is a hallmark of human cancers, there is no Myc targeted therapy yet. Here, we report sAJM589, a novel small molecule Myc inhibitor, identified from a PCA-based high-throughput screen. sAJM589 potently disrupts the Myc-Max heterodimer in a dose dependent manner with an IC50 of 1.8 ± 0.03 μM. sAJM589 preferentially inhibits transcription of Myc target genes in a Burkitt lymphoma cell model, P493-6. Genome-wide transcriptome analysis showed that sAJM589 treatment and Myc depletion induced similar gene expression profiles. Consistently, sAJM589 suppressed cellular proliferation in diverse Myc-dependent cancer cell lines and anchorage independent growth of Raji cells. Disruption of the Myc-Max interaction by sAJM589 reduced Myc protein levels, possibly by promoting ubiquitination and degradation of Myc. Collectively, these results suggest that sAJM589 may be a basis for the development of potential inhibitors of Myc-dependent cell growth.
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Affiliation(s)
- Seung H. Choi
- Regulatory
Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Madhupriya Mahankali
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Sang Jun Lee
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Mitchell Hull
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - H. Michael Petrassi
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Arnab K. Chatterjee
- California Institute for Biomedical Research, La Jolla, California 92037, United States
| | - Peter G. Schultz
- California Institute for Biomedical Research, La Jolla, California 92037, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, California 92037, United States
| | - Katherine A. Jones
- Regulatory
Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Weijun Shen
- California Institute for Biomedical Research, La Jolla, California 92037, United States
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48
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Laborda E, Mazagova M, Shao S, Wang X, Quirino H, Woods AK, Hampton EN, Rodgers DT, Kim CH, Schultz PG, Young TS. Development of A Chimeric Antigen Receptor Targeting C-Type Lectin-Like Molecule-1 for Human Acute Myeloid Leukemia. Int J Mol Sci 2017; 18:ijms18112259. [PMID: 29077054 PMCID: PMC5713229 DOI: 10.3390/ijms18112259] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 12/17/2022] Open
Abstract
The treatment of patients with acute myeloid leukemia (AML) with targeted immunotherapy is challenged by the heterogeneity of the disease and a lack of tumor-exclusive antigens. Conventional immunotherapy targets for AML such as CD33 and CD123 have been proposed as targets for chimeric antigen receptor (CAR)-engineered T-cells (CAR-T-cells), a therapy that has been highly successful in the treatment of B-cell leukemia and lymphoma. However, CD33 and CD123 are present on hematopoietic stem cells, and targeting with CAR-T-cells has the potential to elicit long-term myelosuppression. C-type lectin-like molecule-1 (CLL1 or CLEC12A) is a myeloid lineage antigen that is expressed by malignant cells in more than 90% of AML patients. CLL1 is not expressed by healthy Hematopoietic Stem Cells (HSCs), and is therefore a promising target for CAR-T-cell therapy. Here, we describe the development and optimization of an anti-CLL1 CAR-T-cell with potent activity on both AML cell lines and primary patient-derived AML blasts in vitro while sparing healthy HSCs. Furthermore, in a disseminated mouse xenograft model using the CLL1-positive HL60 cell line, these CAR-T-cells completely eradicated tumor, thus supporting CLL1 as a promising target for CAR-T-cells to treat AML while limiting myelosuppressive toxicity.
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MESH Headings
- Animals
- Antigens, Neoplasm/immunology
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- Disease Models, Animal
- Female
- Humans
- Immunotherapy, Adoptive/methods
- Lectins, C-Type/antagonists & inhibitors
- Lectins, C-Type/immunology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/therapy
- Mice
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Mitogen/antagonists & inhibitors
- Receptors, Mitogen/immunology
- Recombinant Fusion Proteins
- Single-Chain Antibodies/genetics
- Single-Chain Antibodies/immunology
- Single-Chain Antibodies/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Eduardo Laborda
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
| | - Magdalena Mazagova
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
| | - Sida Shao
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 11119, USA.
| | - Xinxin Wang
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
| | - Herlinda Quirino
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
| | - Ashley K Woods
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
| | - Eric N Hampton
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
| | - David T Rodgers
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
| | - Chan Hyuk Kim
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Peter G Schultz
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 11119, USA.
| | - Travis S Young
- Department of Biology, California Institute for Biomedical Research (Calibr), La Jolla, CA 11119, USA.
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49
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Abstract
Sirtuins are NAD+ dependent protein deacetylases, which are involved in many biological processes. We now report a novel genetically encoded fluorescent probe (EGFP-K85AcK) that responds to sirtuins in living cells. The probe design exploits a lysyl residue in EGFP that is essential for chromophore maturation, and is also an efficient deacetylation substrate for sirtuins. Analysis of activity in Escherichia coli ΔcobB revealed that the probe can respond to various human sirtuins, including SIRT1, SIRT2, SIRT3 and SIRT5. We also directly monitored SIRT1 and SIRT2 activity in HEK293T cells with an mCherry fusion of EGFP-K85AcK, and showed that this approach can be extended to other fluorescent proteins. Finally, we demonstrate that this approach can be used to examine the activity of sirtuins toward additional lysyl posttranslational modifications, and show that sirtuins can act as erasers of HibK modified proteins.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry and Skaggs Institute for Chemical Biology, the Scripps Research Institute , 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Anzhi Yao
- Department of Chemistry and Skaggs Institute for Chemical Biology, the Scripps Research Institute , 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, the Scripps Research Institute , 10550 N Torrey Pines Road, La Jolla, California 92037, United States
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50
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Abstract
Nisin is a complex lanthipeptide that has broad spectrum antibacterial activity. In efforts to broaden the structural diversity of this ribosomally synthesized lantibiotic, we now report the recombinant expression of Nisin variants that incorporate noncanonical amino acids (ncAAs) at discrete positions. This is achieved by expressing the nisA structural gene, cyclase (nisC) and dehydratase (nisB), together with an orthogonal nonsense suppressor tRNA/aminoacyl-tRNA synthetase pair in Escherichia coli. A number of ncAAs with novel chemical reactivity were genetically incorporated into NisA, including an α-chloroacetamide-containing ncAA that allowed for the expression of Nisin variants with novel macrocyclic topologies. This methodology should allow for the exploration of lanthipeptide variants with new or enhanced activities.
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Affiliation(s)
- Claudio Zambaldo
- The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA - 92037
| | - Xiaozhou Luo
- The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA - 92037
| | - Angad P. Mehta
- The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA - 92037
| | - Peter G. Schultz
- The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA - 92037
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