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  1. Article ; Online: Advances in covalent drug discovery.

    Boike, Lydia / Henning, Nathaniel J / Nomura, Daniel K

    Nature reviews. Drug discovery

    2022  Volume 21, Issue 12, Page(s) 881–898

    Abstract: Covalent drugs have been used to treat diseases for more than a century, but tools that facilitate the rational design of covalent drugs have emerged more recently. The purposeful addition of reactive functional groups to existing ligands can enable ... ...

    Abstract Covalent drugs have been used to treat diseases for more than a century, but tools that facilitate the rational design of covalent drugs have emerged more recently. The purposeful addition of reactive functional groups to existing ligands can enable potent and selective inhibition of target proteins, as demonstrated by the covalent epidermal growth factor receptor (EGFR) and Bruton's tyrosine kinase (BTK) inhibitors used to treat various cancers. Moreover, the identification of covalent ligands through 'electrophile-first' approaches has also led to the discovery of covalent drugs, such as covalent inhibitors for KRAS(G12C) and SARS-CoV-2 main protease. In particular, the discovery of KRAS(G12C) inhibitors validates the use of covalent screening technologies, which have become more powerful and widespread over the past decade. Chemoproteomics platforms have emerged to complement covalent ligand screening and assist in ligand discovery, selectivity profiling and target identification. This Review showcases covalent drug discovery milestones with emphasis on the lessons learned from these programmes and how an evolving toolbox of covalent drug discovery techniques facilitates success in this field.
    MeSH term(s) Humans ; Drug Discovery/methods ; Ligands ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use ; Proto-Oncogene Proteins p21(ras)/metabolism ; SARS-CoV-2 ; Structure-Activity Relationship ; COVID-19 Drug Treatment
    Chemical Substances Ligands ; Protein Kinase Inhibitors ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; BTK protein, human (EC 2.7.10.2) ; EGFR protein, human (EC 2.7.10.1)
    Language English
    Publishing date 2022-08-25
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2062954-0
    ISSN 1474-1784 ; 1474-1776
    ISSN (online) 1474-1784
    ISSN 1474-1776
    DOI 10.1038/s41573-022-00542-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Tyrosinase-Mediated Synthesis of Nanobody-Cell Conjugates.

    Maza, Johnathan C / García-Almedina, Derek M / Boike, Lydia E / Hamlish, Noah X / Nomura, Daniel K / Francis, Matthew B

    ACS central science

    2022  Volume 8, Issue 7, Page(s) 955–962

    Abstract: A convenient enzymatic strategy is reported for the modification of cell surfaces. Using a tyrosinase enzyme isolated ... ...

    Abstract A convenient enzymatic strategy is reported for the modification of cell surfaces. Using a tyrosinase enzyme isolated from
    Language English
    Publishing date 2022-06-22
    Publishing country United States
    Document type Journal Article
    ISSN 2374-7943
    ISSN 2374-7943
    DOI 10.1021/acscentsci.1c01265
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication.

    Han, Hesong / Gracia, Albert Vallejo / Røise, Joachim J / Boike, Lydia / Leon, Kristoffer / Schulze-Gahmen, Ursula / Stentzel, Michael R / Bajaj, Teena / Chen, Dake / Li, I-Che / He, Maomao / Behrouzi, Kamyar / Khodabakhshi, Zahra / Nomura, Daniel K / Mofrad, Mohammad R K / Kumar, G Renuka / Ott, Melanie / Murthy, Niren

    RSC advances

    2023  Volume 13, Issue 16, Page(s) 10636–10641

    Abstract: Covalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 have great potential as antivirals, but their non-specific reactivity with thiols has limited their development. In this report, we performed an 8000 molecule electrophile screen ... ...

    Abstract Covalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 have great potential as antivirals, but their non-specific reactivity with thiols has limited their development. In this report, we performed an 8000 molecule electrophile screen against PLpro and identified an α-chloro amide fragment, termed compound 1, which inhibited SARS-CoV-2 replication in cells, and also had low non-specific reactivity with thiols. Compound 1 covalently reacts with the active site cysteine of PLpro, and had an IC50 of 18 μM for PLpro inhibition. Compound 1 also had low non-specific reactivity with thiols and reacted with glutathione 1-2 orders of magnitude slower than other commonly used electrophilic warheads. Finally, compound 1 had low toxicity in cells and mice and has a molecular weight of only 247 daltons and consequently has great potential for further optimization. Collectively, these results demonstrate that compound 1 is a promising lead fragment for future PLpro drug discovery campaigns.
    Language English
    Publishing date 2023-04-04
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d3ra00426k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors.

    Moon, Patrick / Zammit, Charlotte M / Shao, Qian / Dovala, Dustin / Boike, Lydia / Henning, Nathaniel J / Knapp, Mark / Spradlin, Jessica N / Ward, Carl C / Wolleb, Helene / Fuller, Daniel / Blake, Gabrielle / Murphy, Jason P / Wang, Feng / Lu, Yipin / Moquin, Stephanie A / Tandeske, Laura / Hesse, Matthew J / McKenna, Jeffrey M /
    Tallarico, John A / Schirle, Markus / Toste, F Dean / Nomura, Daniel K

    Chembiochem : a European journal of chemical biology

    2023  Volume 24, Issue 11, Page(s) e202300116

    Abstract: While vaccines and antivirals are now being deployed for the current SARS-CoV-2 pandemic, we require additional antiviral therapeutics to not only effectively combat SARS-CoV-2 and its variants, but also future coronaviruses. All coronaviruses have ... ...

    Abstract While vaccines and antivirals are now being deployed for the current SARS-CoV-2 pandemic, we require additional antiviral therapeutics to not only effectively combat SARS-CoV-2 and its variants, but also future coronaviruses. All coronaviruses have relatively similar genomes that provide a potential exploitable opening to develop antiviral therapies that will be effective against all coronaviruses. Among the various genes and proteins encoded by all coronaviruses, one particularly "druggable" or relatively easy-to-drug target is the coronavirus Main Protease (3CL
    MeSH term(s) Humans ; SARS-CoV-2 ; COVID-19 ; Cysteine ; Antiviral Agents/pharmacology ; Antiviral Agents/chemistry ; Protease Inhibitors/pharmacology ; Protease Inhibitors/chemistry ; Molecular Docking Simulation
    Chemical Substances 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Cysteine (K848JZ4886) ; Antiviral Agents ; Protease Inhibitors
    Language English
    Publishing date 2023-05-03
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202300116
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Chemoproteomics-enabled discovery of covalent RNF114-based degraders that mimic natural product function.

    Luo, Mai / Spradlin, Jessica N / Boike, Lydia / Tong, Bingqi / Brittain, Scott M / McKenna, Jeffrey M / Tallarico, John A / Schirle, Markus / Maimone, Thomas J / Nomura, Daniel K

    Cell chemical biology

    2021  Volume 28, Issue 4, Page(s) 559–566.e15

    Abstract: The translation of functionally active natural products into fully synthetic small-molecule mimetics has remained an important process in medicinal chemistry. We recently discovered that the terpene natural product nimbolide can be utilized as a covalent ...

    Abstract The translation of functionally active natural products into fully synthetic small-molecule mimetics has remained an important process in medicinal chemistry. We recently discovered that the terpene natural product nimbolide can be utilized as a covalent recruiter of the E3 ubiquitin ligase RNF114 for use in targeted protein degradation-a powerful therapeutic modality within modern-day drug discovery. Using activity-based protein profiling-enabled covalent ligand-screening approaches, here we report the discovery of fully synthetic RNF114-based recruiter molecules that can also be exploited for PROTAC applications, and demonstrate their utility in degrading therapeutically relevant targets, such as BRD4 and BCR-ABL, in cells. The identification of simple and easily manipulated drug-like scaffolds that can mimic the function of a complex natural product is beneficial in further expanding the toolbox of E3 ligase recruiters, an area of great importance in drug discovery and chemical biology.
    MeSH term(s) Biological Products/chemistry ; Biological Products/metabolism ; Humans ; Molecular Structure ; Proteomics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
    Chemical Substances Biological Products ; RNF114 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2021-01-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2451-9448
    ISSN (online) 2451-9448
    DOI 10.1016/j.chembiol.2021.01.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Discovery of a Functional Covalent Ligand Targeting an Intrinsically Disordered Cysteine within MYC.

    Boike, Lydia / Cioffi, Alexander G / Majewski, Felix C / Co, Jennifer / Henning, Nathaniel J / Jones, Michael D / Liu, Gang / McKenna, Jeffrey M / Tallarico, John A / Schirle, Markus / Nomura, Daniel K

    Cell chemical biology

    2020  Volume 28, Issue 1, Page(s) 4–13.e17

    Abstract: MYC is a major oncogenic transcriptional driver of most human cancers that has remained intractable to direct targeting because much of MYC is intrinsically disordered. Here, we have performed a cysteine-reactive covalent ligand screen to identify ... ...

    Abstract MYC is a major oncogenic transcriptional driver of most human cancers that has remained intractable to direct targeting because much of MYC is intrinsically disordered. Here, we have performed a cysteine-reactive covalent ligand screen to identify compounds that could disrupt the binding of MYC to its DNA consensus sequence in vitro and also impair MYC transcriptional activity in situ in cells. We have identified a covalent ligand, EN4, that targets cysteine 171 of MYC within a predicted intrinsically disordered region of the protein. We show that EN4 directly targets MYC in cells, reduces MYC and MAX thermal stability, inhibits MYC transcriptional activity, downregulates multiple MYC transcriptional targets, and impairs tumorigenesis. We also show initial structure-activity relationships of EN4 and identify compounds that show improved potency. Overall, we identify a unique ligandable site within an intrinsically disordered region of MYC that leads to inhibition of MYC transcriptional activity.
    MeSH term(s) Cells, Cultured ; Cysteine/antagonists & inhibitors ; Cysteine/metabolism ; Dose-Response Relationship, Drug ; Humans ; Ligands ; Molecular Structure ; Proto-Oncogene Proteins c-myc/antagonists & inhibitors ; Proto-Oncogene Proteins c-myc/genetics ; Proto-Oncogene Proteins c-myc/metabolism
    Chemical Substances Ligands ; Proto-Oncogene Proteins c-myc ; Cysteine (K848JZ4886)
    Language English
    Publishing date 2020-09-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2451-9448
    ISSN (online) 2451-9448
    DOI 10.1016/j.chembiol.2020.09.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Deubiquitinase-targeting chimeras for targeted protein stabilization.

    Henning, Nathaniel J / Boike, Lydia / Spradlin, Jessica N / Ward, Carl C / Liu, Gang / Zhang, Erika / Belcher, Bridget P / Brittain, Scott M / Hesse, Matthew J / Dovala, Dustin / McGregor, Lynn M / Valdez Misiolek, Rachel / Plasschaert, Lindsey W / Rowlands, David J / Wang, Feng / Frank, Andreas O / Fuller, Daniel / Estes, Abigail R / Randal, Katelyn L /
    Panidapu, Anoohya / McKenna, Jeffrey M / Tallarico, John A / Schirle, Markus / Nomura, Daniel K

    Nature chemical biology

    2022  Volume 18, Issue 4, Page(s) 412–421

    Abstract: Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), ... ...

    Abstract Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), heterobifunctional small molecules consisting of a deubiquitinase recruiter linked to a protein-targeting ligand, to stabilize the levels of specific proteins degraded in a ubiquitin-dependent manner. Using chemoproteomic approaches, we discovered the covalent ligand EN523 that targets a non-catalytic allosteric cysteine C23 in the K48-ubiquitin-specific deubiquitinase OTUB1. We showed that a DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR), robustly stabilized ΔF508-CFTR protein levels, leading to improved chloride channel conductance in human cystic fibrosis bronchial epithelial cells. We also demonstrated stabilization of the tumor suppressor kinase WEE1 in hepatoma cells. Our study showcases covalent chemoproteomic approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS.
    MeSH term(s) Chimera/metabolism ; Cystic Fibrosis/drug therapy ; Cystic Fibrosis/metabolism ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; Cystic Fibrosis Transmembrane Conductance Regulator/metabolism ; Deubiquitinating Enzymes/metabolism ; Deubiquitinating Enzymes/therapeutic use ; Humans ; Ligands ; Ubiquitin/metabolism
    Chemical Substances Ligands ; Ubiquitin ; Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6) ; Deubiquitinating Enzymes (EC 3.4.19.12)
    Language English
    Publishing date 2022-02-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-022-00971-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors

    Moon, Patrick / Boike, Lydia / Dovala, Dustin / Henning, Nathaniel J / Knapp, Mark / Spradlin, Jessica N / Ward, Carl C / Wolleb, Helen / Zammit, Charlotte M / Fuller, Daniel / Blake, Gabrielle / Murphy, Jason P / Wang, Feng / Lu, Yipin / Moquin, Stephanie A / Tandeske, Laura / Hesse, Matthew J / McKenna, Jeffrey M / Tallarico, John /
    Schirle, Markus / Toste, F. Dean / Nomura, Daniel K

    bioRxiv

    Abstract: While vaccines and antivirals are now being deployed for the current SARS-CoV-2 pandemic, we require additional antiviral therapeutics to not only effectively combat SARS-CoV-2 and its variants, but also future coronaviruses. All coronaviruses have ... ...

    Abstract While vaccines and antivirals are now being deployed for the current SARS-CoV-2 pandemic, we require additional antiviral therapeutics to not only effectively combat SARS-CoV-2 and its variants, but also future coronaviruses. All coronaviruses have relatively similar genomes that provide a potential exploitable opening to develop antiviral therapies that will be effective against all coronaviruses. Among the various genes and proteins encoded by all coronaviruses, one particularly druggable or relatively easy-to-drug target is the coronavirus Main Protease (3CLpro or Mpro), an enzyme that is involved in cleaving a long peptide translated by the viral genome into its individual protein components that are then assembled into the virus to enable viral replication in the cell. Inhibiting Mpro with a small-molecule antiviral would effectively stop the ability of the virus to replicate, providing therapeutic benefit. In this study, we have utilized activity-based protein profiling (ABPP)-based chemoproteomic approaches to discover and further optimize cysteine-reactive pyrazoline-based covalent inhibitors for the SARS-CoV-2 Mpro. Structure-guided medicinal chemistry and modular synthesis of di- and tri-substituted pyrazolines bearing either chloroacetamide or vinyl sulfonamide cysteine-reactive warheads enabled the expedient exploration of structure-activity relationships (SAR), yielding nanomolar potency inhibitors against Mpro from not only SARS-CoV-2, but across many other coronaviruses. Our studies highlight promising chemical scaffolds that may contribute to future pan-coronavirus inhibitors.
    Keywords covid19
    Language English
    Publishing date 2022-03-07
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.03.05.483025
    Database COVID19

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