Bromodomains: A New Target Class for Drug Development

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 10728

Special Issue Editors

Dana-Farber Cancer Insitute, 450 Brookline Ave. Boston, MA 02215, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
Interests: bromodomain; epigenetics; drug discovery

E-Mail Website
Guest Editor
St. Jude Children’s Research Hospital, 262 Danny Thomas Pl., Memphis, TN 38105, USA
Interests: epigenetics; transcription; drug discovery

Special Issue Information

Dear Colleagues,

Epigenetic proteins, including histone writers, readers and erasers, modulate the epigenetic landscape of cells which impacts upon gene expression and cell state. Increasing evidence suggests that epigenetic protein function can be dysregulated in neoplastic cell states. Intensive studies by many groups have focused on the bromodomain, an epigenetic reader domain that recognizes acetylated protein and is broadly dysregulated in distinct cancer and disease states. Thus, bromodomains have enormous potential as targets for novel therapeutic development in cancer. An explosion of interest in these proteins was facilitated by the establishment of small molecule inhibitors with great selectivity and potency both in vitro and in vivo. Widespread use of these molecules, especially JQ1 and I-BET762 (Filippakopoulos et al., 2010; Nicodeme et al., 2010), to probe cell responses has led to widely applicable insights into the mechanisms of how inhibition of epigenetic readers impacts transcriptional programs in cancer cells, resulting in differentiation and apoptosis. On the basis of these promising early results, BET inhibitors have entered human clinical investigations for the treatment of different cancers and other diseases (Alqahtani et al., 2019). Next-generation compounds targeting BET bromodomains have been generated using proteolysis-targeted chimera (PROTAC) chemistry, in order to induce targeted degradation of BET proteins (Winter et al., 2015). In parallel, further non-BET bromodomains have been identified as targets for novel therapy in cancers and other diseases. This Special Issue will focus on recent advancements in understanding bromodomain function, ranging from structure to function, and identifying opportunities for drug development for this intriguing class of proteins.

Dr. Jun Qi
Dr. Adam David Durbin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pharmaceuticals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • epigenetic targets
  • inhibitor
  • degrader
  • transcription factor
  • drug development

Published Papers (4 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

12 pages, 2252 KiB  
Article
BET Bromodomain Degradation Disrupts Function but Not 3D Formation of RNA Pol2 Clusters
by Diana H. Chin, Issra Osman, Jadon Porch, Hyunmin Kim, Kristen K. Buck, Javier Rodriguez, Bianca Carapia, Deborah Yan, Stela B. Moura, Jantzen Sperry, Jonathan Nakashima, Kasey Altman, Delsee Altman and Berkley E. Gryder
Pharmaceuticals 2023, 16(2), 199; https://doi.org/10.3390/ph16020199 - 29 Jan 2023
Cited by 2 | Viewed by 2755
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) is driven by a translocation that creates the chimeric transcription factor PAX3-FOXO1 (P3F), which assembles de novo super enhancers to drive high levels of transcription of other core regulatory transcription factors (CRTFs). P3F recruits co-regulatory factors to super enhancers such [...] Read more.
Fusion-positive rhabdomyosarcoma (FP-RMS) is driven by a translocation that creates the chimeric transcription factor PAX3-FOXO1 (P3F), which assembles de novo super enhancers to drive high levels of transcription of other core regulatory transcription factors (CRTFs). P3F recruits co-regulatory factors to super enhancers such as BRD4, which recognizes acetylated lysines via BET bromodomains. In this study, we demonstrate that inhibition or degradation of BRD4 leads to global decreases in transcription, and selective downregulation of CRTFs. We also show that the BRD4 degrader ARV-771 halts transcription while preserving RNA Polymerase II (Pol2) loops between super enhancers and their target genes, and causes the removal of Pol2 only past the transcriptional end site of CRTF genes, suggesting a novel effect of BRD4 on Pol2 looping. We finally test the most potent molecule, inhibitor BMS-986158, in an orthotopic PDX mouse model of FP-RMS with additional high-risk mutations, and find that it is well tolerated in vivo and leads to an average decrease in tumor size. This effort represents a partnership with an FP-RMS patient and family advocates to make preclinical data rapidly accessible to the family, and to generate data to inform future patients who develop this disease. Full article
(This article belongs to the Special Issue Bromodomains: A New Target Class for Drug Development)
Show Figures

Graphical abstract

15 pages, 3583 KiB  
Article
Mechanistic Analysis of Chemically Diverse Bromodomain-4 Inhibitors Using Balanced QSAR Analysis and Supported by X-ray Resolved Crystal Structures
by Magdi E. A. Zaki, Sami A. Al-Hussain, Aamal A. Al-Mutairi, Vijay H. Masand, Abdul Samad and Rahul D. Jawarkar
Pharmaceuticals 2022, 15(6), 745; https://doi.org/10.3390/ph15060745 - 14 Jun 2022
Cited by 2 | Viewed by 1980
Abstract
Bromodomain-4 (BRD-4) is a key enzyme in post-translational modifications, transcriptional activation, and many other cellular processes. Its inhibitors find their therapeutic usage in cancer, acute heart failure, and inflammation to name a few. In the present study, a dataset of 980 molecules with [...] Read more.
Bromodomain-4 (BRD-4) is a key enzyme in post-translational modifications, transcriptional activation, and many other cellular processes. Its inhibitors find their therapeutic usage in cancer, acute heart failure, and inflammation to name a few. In the present study, a dataset of 980 molecules with a significant diversity of structural scaffolds and composition was selected to develop a balanced QSAR model possessing high predictive capability and mechanistic interpretation. The model was built as per the OECD (Organisation for Economic Co-operation and Development) guidelines and fulfills the endorsed threshold values for different validation parameters (R2tr = 0.76, Q2LMO = 0.76, and R2ex = 0.76). The present QSAR analysis identified that anti-BRD-4 activity is associated with structural characters such as the presence of saturated carbocyclic rings, the occurrence of carbon atoms near the center of mass of a molecule, and a specific combination of planer or aromatic nitrogen with ring carbon, donor, and acceptor atoms. The outcomes of the present analysis are also supported by X-ray-resolved crystal structures of compounds with BRD-4. Thus, the QSAR model effectively captured salient as well as unreported hidden pharmacophoric features. Therefore, the present study successfully identified valuable novel pharmacophoric features, which could be beneficial for the future optimization of lead/hit compounds for anti-BRD-4 activity. Full article
(This article belongs to the Special Issue Bromodomains: A New Target Class for Drug Development)
Show Figures

Graphical abstract

Review

Jump to: Research

18 pages, 1039 KiB  
Review
Roles of Bromodomain Extra Terminal Proteins in Metabolic Signaling and Diseases
by Dayu Wu and Qiong Duan
Pharmaceuticals 2022, 15(8), 1032; https://doi.org/10.3390/ph15081032 - 22 Aug 2022
Cited by 1 | Viewed by 2263
Abstract
BET proteins, which recognize and bind to acetylated histones, play a key role in transcriptional regulation. The development of chemical BET inhibitors in 2010 greatly facilitated the study of these proteins. BETs play crucial roles in cancer, inflammation, heart failure, and fibrosis. In [...] Read more.
BET proteins, which recognize and bind to acetylated histones, play a key role in transcriptional regulation. The development of chemical BET inhibitors in 2010 greatly facilitated the study of these proteins. BETs play crucial roles in cancer, inflammation, heart failure, and fibrosis. In particular, BETs may be involved in regulating metabolic processes, such as adipogenesis and metaflammation, which are under tight transcriptional regulation. In addition, acetyl-CoA links energy metabolism with epigenetic modification through lysine acetylation, which creates docking sites for BET. Given this, it is possible that the ambient energy status may dictate metabolic gene transcription via a BET-dependent mechanism. Indeed, recent studies have reported that various BET proteins are involved in both metabolic signaling regulation and disease. Here, we discuss some of the most recent information on BET proteins and their regulation of the metabolism in both cellular and animal models. Further, we summarize data from some randomized clinical trials evaluating BET inhibitors for the treatment of metabolic diseases. Full article
(This article belongs to the Special Issue Bromodomains: A New Target Class for Drug Development)
Show Figures

Figure 1

16 pages, 2928 KiB  
Review
Bromodomain and Extra-Terminal Protein Inhibitors: Biologic Insights and Therapeutic Potential in Pediatric Brain Tumors
by Andrew Groves, Jessica Clymer and Mariella G. Filbin
Pharmaceuticals 2022, 15(6), 665; https://doi.org/10.3390/ph15060665 - 26 May 2022
Cited by 6 | Viewed by 2794
Abstract
Pediatric brain tumors have surpassed leukemia as the leading cause of cancer-related death in children. Several landmark studies from the last two decades have shown that many pediatric brain tumors are driven by epigenetic dysregulation within specific developmental contexts. One of the major [...] Read more.
Pediatric brain tumors have surpassed leukemia as the leading cause of cancer-related death in children. Several landmark studies from the last two decades have shown that many pediatric brain tumors are driven by epigenetic dysregulation within specific developmental contexts. One of the major determinants of epigenetic control is the histone code, which is orchestrated by a number of enzymes categorized as writers, erasers, and readers. Bromodomain and extra-terminal (BET) proteins are reader proteins that bind to acetylated lysines in histone tails and play a crucial role in regulating gene transcription. BET inhibitors have shown efficacy in a wide range of cancers, and a number have progressed to clinical phase testing. Here, we review the evidence for BET inhibitors in pediatric brain tumor experimental models, as well as their translational potential. Full article
(This article belongs to the Special Issue Bromodomains: A New Target Class for Drug Development)
Show Figures

Graphical abstract

Back to TopTop