1
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Giardina SF, Valdambrini E, Singh PK, Bacolod MD, Babu-Karunakaran G, Peel M, Warren JD, Barany F. Combinatorial Ubiquitination REal-time PROteolysis (CURE-PROs): A Modular Platform for Generating Reversible, Self-Assembling Bifunctional Targeted Degraders. J Med Chem 2024; 67:5473-5501. [PMID: 38554135 DOI: 10.1021/acs.jmedchem.3c02097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2024]
Abstract
Proteolysis-Targeting Chimeras (PROTACs) are bifunctional molecules that bring a target protein and an E3 ubiquitin ligase into proximity to append ubiquitin, thus directing target degradation. Although numerous PROTACs have entered clinical trials, their development remains challenging, and their large size can produce poor drug-like properties. To overcome these limitations, we have modified our Coferon platform to generate Combinatorial Ubiquitination REal-time PROteolysis (CURE-PROs). CURE-PROs are small molecule degraders designed to self-assemble through reversible bio-orthogonal linkers to form covalent heterodimers. By modifying known ligands for Cereblon, MDM2, VHL, and BRD with complementary phenylboronic acid and diol/catechol linkers, we have successfully created CURE-PROs that direct degradation of BRD4 both in vitro and in vivo. The combinatorial nature of our platform significantly reduces synthesis time and effort to identify the optimal linker length and E3 ligase partner to each target and is readily amenable to screening for new targets.
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Affiliation(s)
- Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Elena Valdambrini
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Pradeep K Singh
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
| | - Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | | | - Michael Peel
- MRP Pharma LLC, Chapel Hill, North Carolina 27514, United States
| | - J David Warren
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
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2
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Papadimitropoulou A, Makri M, Zoidis G. MYC the oncogene from hell: Novel opportunities for cancer therapy. Eur J Med Chem 2024; 267:116194. [PMID: 38340508 DOI: 10.1016/j.ejmech.2024.116194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Cancer comprises a heterogeneous disease, characterized by diverse features such as constitutive expression of oncogenes and/or downregulation of tumor suppressor genes. MYC constitutes a master transcriptional regulator, involved in many cellular functions and is aberrantly expressed in more than 70 % of human cancers. The Myc protein belongs to a family of transcription factors whose structural pattern is referred to as basic helix-loop-helix-leucine zipper. Myc binds to its partner, a smaller protein called Max, forming an Myc:Max heterodimeric complex that interacts with specific DNA recognition sequences (E-boxes) and regulates the expression of downstream target genes. Myc protein plays a fundamental role for the life of a cell, as it is involved in many physiological functions such as proliferation, growth and development since it controls the expression of a very large percentage of genes (∼15 %). However, despite the strict control of MYC expression in normal cells, MYC is often deregulated in cancer, exhibiting a key role in stimulating oncogenic process affecting features such as aberrant proliferation, differentiation, angiogenesis, genomic instability and oncogenic transformation. In this review we aim to meticulously describe the fundamental role of MYC in tumorigenesis and highlight its importance as an anticancer drug target. We focus mainly on the different categories of novel small molecules that act as inhibitors of Myc function in diverse ways hence offering great opportunities for an efficient cancer therapy. This knowledge will provide significant information for the development of novel Myc inhibitors and assist to the design of treatments that would effectively act against Myc-dependent cancers.
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Affiliation(s)
- Adriana Papadimitropoulou
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Maria Makri
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece
| | - Grigoris Zoidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece.
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3
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Gui W, Giardina SF, Balzarini M, Barany F, Kodadek T. Reversible Assembly of Proteolysis Targeting Chimeras. ACS Chem Biol 2023; 18:1582-1593. [PMID: 37422908 DOI: 10.1021/acschembio.3c00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are of significant current interest for the development of probe molecules and drug leads. However, they suffer from certain limitations. PROTACs are rule-breaking molecules with sub-optimal cellular permeability, solubility, and other drug-like properties. In particular, they exhibit an unusual dose-response curve where high concentrations of the bivalent molecule inhibit degradation activity, a phenomenon known as the hook effect. This will likely complicate their use in vivo. In this study, we explore a novel approach to create PROTACs that do not exhibit a hook effect. This is achieved by equipping the target protein and E3 ubiquitin ligase ligands with functionalities that undergo rapid and reversible covalent assembly in cellulo. We report the development of Self-Assembled Proteolysis Targeting Chimeras that mediate the degradation of the Von Hippel-Lindau E3 ubiquitin ligase and do not evince a hook effect.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Madeline Balzarini
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
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4
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Song S, Gao P, Sun L, Kang D, Kongsted J, Poongavanam V, Zhan P, Liu X. Recent developments in the medicinal chemistry of single boron atom-containing compounds. Acta Pharm Sin B 2021; 11:3035-3059. [PMID: 34729302 PMCID: PMC8546671 DOI: 10.1016/j.apsb.2021.01.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Various boron-containing drugs have been approved for clinical use over the past two decades, and more are currently in clinical trials. The increasing interest in boron-containing compounds is due to their unique binding properties to biological targets; for example, boron substitution can be used to modulate biological activity, pharmacokinetic properties, and drug resistance. In this perspective, we aim to comprehensively review the current status of boron compounds in drug discovery, focusing especially on progress from 2015 to December 2020. We classify these compounds into groups showing anticancer, antibacterial, antiviral, antiparasitic and other activities, and discuss the biological targets associated with each activity, as well as potential future developments.
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Key Words
- ACTs, artemisinin combination therapies
- ADCs, Acinetobacter-derived cephalosporinases
- AML, acute myeloid leukemia
- AMT, aminopterin
- BLs, β-lactamases
- BNCT, boron neutron capture therapy
- BNNPs, boron nitride nanoparticles
- BNNTs, boron nitride nanotubes
- Boron-containing compounds
- CEs, carboxylesterases
- CIA, collagen-induced arthritis
- COVID-19, coronavirus disease 2019
- ClpP, casein protease P
- Covalent inhibitors
- GSH, glutathione
- HADC1, class I histone deacetylase
- HBV, hepatitis B virus
- HCV, hepatitis C virus
- HIV, human immunodeficiency virus
- LeuRS, leucyl-tRNA synthetase
- Linker components
- MBLs, metal β-lactamases
- MDR-TB, multidrug-resistant tuberculosis
- MERS, Middle East respiratory syndrome
- MIDA, N-methyliminodiacetic acid
- MM, multiple myeloma
- MTX, methotrexate
- Mcl-1, myeloid cell leukemia 1
- Mtb, Mycobacterium tuberculosis
- NA, neuraminidase
- NS5B, non-nucleoside polymerase
- OBORT, oxaborole tRNA capture
- OPs, organophosphate
- PBA, phenylboronic acid
- PDB, Protein Data Bank
- PPI, protein–protein interaction
- Prodrug
- QM, quinone methide
- RA, rheumatoid arthritis
- ROS, reactive oxygen species
- SARS-CoV-2, syndrome coronavirus 2
- SBLs, serine β-lactamases
- SERD, selective estrogen receptor downregulator
- SHA, salicyl hydroxamic acid
- SaClpP, Staphylococcus aureus caseinolytic protease P
- TB, tuberculosis
- TTR, transthyretin
- U4CR, Ugi 4-component reaction
- cUTI, complex urinary tract infection
- dCTPase, dCTPase pyrophosphatase
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Affiliation(s)
- Shu Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
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5
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Gene Transactivation and Transrepression in MYC-Driven Cancers. Int J Mol Sci 2021; 22:ijms22073458. [PMID: 33801599 PMCID: PMC8037706 DOI: 10.3390/ijms22073458] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
MYC is a proto-oncogene regulating a large number of genes involved in a plethora of cellular functions. Its deregulation results in activation of MYC gene expression and/or an increase in MYC protein stability. MYC overexpression is a hallmark of malignant growth, inducing self-renewal of stem cells and blocking senescence and cell differentiation. This review summarizes the latest advances in our understanding of MYC-mediated molecular mechanisms responsible for its oncogenic activity. Several recent findings indicate that MYC is a regulator of cancer genome and epigenome: MYC modulates expression of target genes in a site-specific manner, by recruiting chromatin remodeling co-factors at promoter regions, and at genome-wide level, by regulating the expression of several epigenetic modifiers that alter the entire chromatin structure. We also discuss novel emerging therapeutic strategies based on both direct modulation of MYC and its epigenetic cofactors.
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6
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Madden SK, de Araujo AD, Gerhardt M, Fairlie DP, Mason JM. Taking the Myc out of cancer: toward therapeutic strategies to directly inhibit c-Myc. Mol Cancer 2021; 20:3. [PMID: 33397405 PMCID: PMC7780693 DOI: 10.1186/s12943-020-01291-6] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023] Open
Abstract
c-Myc is a transcription factor that is constitutively and aberrantly expressed in over 70% of human cancers. Its direct inhibition has been shown to trigger rapid tumor regression in mice with only mild and fully reversible side effects, suggesting this to be a viable therapeutic strategy. Here we reassess the challenges of directly targeting c-Myc, evaluate lessons learned from current inhibitors, and explore how future strategies such as miniaturisation of Omomyc and targeting E-box binding could facilitate translation of c-Myc inhibitors into the clinic.
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Affiliation(s)
- Sarah K Madden
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Aline Dantas de Araujo
- Division of Chemistry and Structural Biology and ARC 1066 Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mara Gerhardt
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - David P Fairlie
- Division of Chemistry and Structural Biology and ARC 1066 Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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7
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Giardina SF, Werner DS, Pingle M, Feinberg PB, Foreman KW, Bergstrom DE, Arnold LD, Barany F. Novel, Self-Assembling Dimeric Inhibitors of Human β Tryptase. J Med Chem 2020; 63:3004-3027. [PMID: 32057241 DOI: 10.1021/acs.jmedchem.9b01689] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
β-Tryptase, a homotetrameric serine protease, has four identical active sites facing a central pore, presenting an optimized setting for the rational design of bivalent inhibitors that bridge two adjacent sites. Using diol, hydroxymethyl phenols or benzoyl methyl hydroxamates, and boronic acid chemistries to reversibly join two [3-(1-acylpiperidin-4-yl)phenyl]methanamine core ligands, we have successfully produced a series of self-assembling heterodimeric inhibitors. These heterodimeric tryptase inhibitors demonstrate superior activity compared to monomeric modes of inhibition. X-ray crystallography validated the dimeric mechanism of inhibition, and compounds demonstrated high selectivity against related proteases, good target engagement, and tryptase inhibition in HMC1 xenograft models. Screening 3872 possible combinations from 44 boronic acid and 88 diol derivatives revealed several combinations that produced nanomolar inhibition, and seven unique pairs produced greater than 100-fold improvement in potency over monomeric inhibition. These heterodimeric tryptase inhibitors demonstrate the power of target-driven combinatorial chemistry to deliver bivalent drugs in a small molecule form.
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Affiliation(s)
- Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Douglas S Werner
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Maneesh Pingle
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States.,Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Kenneth W Foreman
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Donald E Bergstrom
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall, West Lafa-yette, Indiana 47907, United States
| | - Lee D Arnold
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
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8
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Wang XN, Su XX, Cheng SQ, Sun ZY, Huang ZS, Ou TM. MYC modulators in cancer: a patent review. Expert Opin Ther Pat 2019; 29:353-367. [PMID: 31068032 DOI: 10.1080/13543776.2019.1612878] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION The important role of MYC in tumorigenesis makes it particularly important to design MYC modulators. Over the past decade, researchers have raised a number of strategies for designing MYC modulators, some of which are already in clinical trials. This paper aims to review the patents of MYC modulators. AREAS COVERED The important biological relevance of c-MYC and the regulation pathways related to c-MYC are briefly introduced. Base on that, the MYC modulators reported in published patents and references primarily for cancer treatment are outlined, highlighting the structures and biological activities. EXPERT OPINION There has been a growing awareness of finding and designing MYC modulators as novel anticancer drugs over recent years. Patents involving the discovery, synthesis, and application of MYC modulators are particularly important for further development in this field. Although finding direct MYC inhibitors or binders is challenging, MYC cannot be simply defined as an undruggable target. There is still substantial evidence proving the concept that MYC modulators can benefit to the treatment of both human hematological malignancies and solid tumors. More efforts should be taken to improve the activity and specificity of MYC modulators.
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Affiliation(s)
- Xiao-Na Wang
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Xiao-Xuan Su
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Sui-Qi Cheng
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Zhi-Yin Sun
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Zhi-Shu Huang
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Tian-Miao Ou
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
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9
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Carabet LA, Rennie PS, Cherkasov A. Therapeutic Inhibition of Myc in Cancer. Structural Bases and Computer-Aided Drug Discovery Approaches. Int J Mol Sci 2018; 20:E120. [PMID: 30597997 PMCID: PMC6337544 DOI: 10.3390/ijms20010120] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/08/2018] [Accepted: 12/21/2018] [Indexed: 12/23/2022] Open
Abstract
Myc (avian myelocytomatosis viral oncogene homolog) represents one of the most sought after drug targets in cancer. Myc transcription factor is an essential regulator of cell growth, but in most cancers it is overexpressed and associated with treatment-resistance and lethal outcomes. Over 40 years of research and drug development efforts did not yield a clinically useful Myc inhibitor. Drugging the "undruggable" is problematic, as Myc inactivation may negatively impact its physiological functions. Moreover, Myc is a disordered protein that lacks effective binding pockets on its surface. It is well established that the Myc function is dependent on dimerization with its obligate partner, Max (Myc associated factor X), which together form a functional DNA-binding domain to activate genomic targets. Herein, we provide an overview of the knowledge accumulated to date on Myc regulation and function, its critical role in cancer, and summarize various strategies that are employed to tackle Myc-driven malignant transformation. We focus on important structure-function relationships of Myc with its interactome, elaborating structural determinants of Myc-Max dimer formation and DNA recognition exploited for therapeutic inhibition. Chronological development of small-molecule Myc-Max prototype inhibitors and corresponding binding sites are comprehensively reviewed and particular emphasis is placed on modern computational drug design methods. On the outlook, technological advancements may soon provide the so long-awaited Myc-Max clinical candidate.
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Affiliation(s)
- Lavinia A Carabet
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
| | - Paul S Rennie
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
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10
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Giardina SF, Werner DS, Pingle M, Foreman KW, Bergstrom DE, Arnold LD, Barany F. Target-Directed Self-Assembly of Homodimeric Drugs Against β-Tryptase. ACS Med Chem Lett 2018; 9:827-831. [PMID: 30128075 PMCID: PMC6088348 DOI: 10.1021/acsmedchemlett.8b00204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/05/2018] [Indexed: 02/05/2023] Open
Abstract
![]()
Tryptase,
a serine protease released from mast cells, is implicated
in many allergic and inflammatory disorders. Human tryptase is a donut-shaped
tetramer with the active sites facing inward forming a central pore.
Bivalent ligands spanning two active sites potently inhibit this configuration,
but these large compounds have poor drug-like properties. To overcome
some of these challenges, we developed self-assembling molecules,
called coferons, which deliver a larger compound in two parts. Using
a pharmacophoric core and reversibly binding linkers to span two active
sites, we have successfully produced three novel homodimeric tryptase
inhibitors. Upon binding to tryptase, compounds reassembled into flexible
homodimers, with significant improvements in IC50 (0.19
± 0.08 μM) over controls (5.50 ± 0.09 μM), and
demonstrate good activity in mast cell lines. These studies provide
validation for this innovative technology that is especially well-suited
for the delivery of dimeric drugs to modulate intracellular macromolecular
targets.
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Affiliation(s)
- Sarah F. Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Douglas S. Werner
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Maneesh Pingle
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Kenneth W. Foreman
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Donald E. Bergstrom
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall, West Lafayette, Indiana 47907, United States
| | - Lee D. Arnold
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
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11
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Wiedemann B, Weisner J, Rauh D. Chemical modulation of transcription factors. MEDCHEMCOMM 2018; 9:1249-1272. [PMID: 30151079 PMCID: PMC6097187 DOI: 10.1039/c8md00273h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/10/2018] [Indexed: 12/12/2022]
Abstract
Transcription factors (TFs) constitute a diverse class of sequence-specific DNA-binding proteins, which are key to the modulation of gene expression. TFs have been associated with human diseases, including cancer, Alzheimer's and other neurodegenerative diseases, which makes this class of proteins attractive targets for chemical biology and medicinal chemistry research. Since TFs lack a common binding site or structural similarity, the development of small molecules to efficiently modulate TF biology in cells and in vivo is a challenging task. This review highlights various strategies that are currently being explored for the identification and development of modulators of Myc, p53, Stat, Nrf2, CREB, ER, AR, HIF, NF-κB, and BET proteins.
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Affiliation(s)
- Bianca Wiedemann
- Technische Universität Dortmund , Fakultät für Chemie und Chemische Biologie , Otto-Hahn-Strasse 4a , D-44227 Dortmund , Germany . ; ; Tel: +49 (0)231 755 7080
| | - Jörn Weisner
- Technische Universität Dortmund , Fakultät für Chemie und Chemische Biologie , Otto-Hahn-Strasse 4a , D-44227 Dortmund , Germany . ; ; Tel: +49 (0)231 755 7080
| | - Daniel Rauh
- Technische Universität Dortmund , Fakultät für Chemie und Chemische Biologie , Otto-Hahn-Strasse 4a , D-44227 Dortmund , Germany . ; ; Tel: +49 (0)231 755 7080
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12
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Foreman KW. A general model for predicting the binding affinity of reversibly and irreversibly dimerized ligands. PLoS One 2017; 12:e0188134. [PMID: 29166663 PMCID: PMC5699851 DOI: 10.1371/journal.pone.0188134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/01/2017] [Indexed: 01/13/2023] Open
Abstract
Empirical data has shown that bivalent inhibitors can bind a given target protein significantly better than their monomeric counterparts. However, predicting the corresponding theoretical fold improvements has been challenging. The current work builds off the reacted-site probability approach to provide a straightforward baseline reference model for predicting fold-improvements in effective affinity of dimerized ligands over their monomeric counterparts. For the more familiar irreversibly linked bivalents, the model predicts a weak dependence on tether length and a scaling of the effective affinity with the 3/2 power of the monomer’s affinity. For the previously untreated case of the emerging technology of reversibly linking dimers, the effective affinity is also significantly improved over the affinity of the non-dimerizing monomers. The model is related back to experimental quantities, such as EC50s, and the approaches to fully characterize the system given the assumptions of the model. Because of the predicted significant potency gains, both irreversibly and reversibly linked bivalent ligands offer the potential to be a disruptive technology in pharmaceutical research.
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13
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Reverte M, Barvik I, Vasseur JJ, Smietana M. RNA-directed off/on switch of RNase H activity using boronic ester formation. Org Biomol Chem 2017; 15:8204-8210. [DOI: 10.1039/c7ob02145c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new concept to modulate RNase H activity is presented based on the boronic acid/boronate switch.
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Affiliation(s)
- Maëva Reverte
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Ivan Barvik
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | - Jean-Jacques Vasseur
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Michael Smietana
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
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