Development of small molecule CREBBP bromodomain ligands using medicinal chemistry-based approaches

This work explores medicinal chemistry-based approaches to develop CREBBP bromodomain ligands, using protein-ligand X-ray crystallography to enable structure-guided drug design. Here, we report the improvement of affinity and selectivity for a previously reported CREBBP bromodomain inhibitor through; (i) bioisosteric modifications to remove unfavourable enthalpic contributions to binding; and (ii) macrocyclic drug design to favour the CREBBP bromodomain binding mode. These improved ligands were also incorporated into (iii) PROTACs to develop full-length CREBBP degraders as a proof-of-concept for this target. In collaboration with Prof. Dario Neri’s group (ETH Zurich), we use (iv) DNA-encoded chemical library technology to identify novel CREBBP bromodomain fragments and scaffolds. This work has provided valuable insight in the development of selective inhibitors for the CREBBP bromodomain and sets the foundations for applying new technologies to identify novel inhibitors and degraders for this target protein.</p

Short Frame Length Approximation for IRSA

In this letter, we propose a short-frame (SF) approximation for the packet loss rate of Irregular Repetition Slotted ALOHA (IRSA) particularly suitable for very short frames, up to 50 slots. The reason for limiting the frame size is to allow low-latency communications, a typical requirement in Industrial Internet of Things (IIoT) applications. We extend the approximation of [1] (named EF) through a recursive evaluation of inter-related stopping sets (STs). The tighter approximation yields the user degree distribution that minimizes the packet loss rate (PLR). For a scenario with 10 slots and 5 users, the degree distribution optimized adopting the SF approximation results in a 20% lower PLR compared to the one optimized with the EF approximation

System Level Integration of Irregular Repetition Slotted ALOHA for Industrial IoT in 5G New Radio

Automation is a key part of the new industrial revolution, that will be enabled by the deployment of thousands of sensors and actuators. The flexible deployment of these devices requires wireless connectivity which is labeled as industrial internet of things, IIoT. The sporadic activity pattern of IIoT devices naturally suggest the use of random access techniques, albeit posing new and unexplored challenges for the current wireless networks. On top of the demand for new access protocols, the latency-reliability requirements further challenge the existing random access protocols. In this work we investigate the adaptation of a well known modern random access algorithm, Irregular Repetition Slotted ALOHA (IRSA) to IIoT in 5G New Radio. The key contribution of the paper is the proposed system level protocol, Adaptive-Multichannel IRSA, that can fulfill the latency-reliability requirements. On top of this, the definition and solution of the resource allocation problem as a resource efficiency optimization guarantees that the algorithm minimizes the system resources. We show that for a set of specific requirements, AMC-IRSA can fulfill the requirements in an a lot resource efficient manner. Lastly, we analyze most critical parameters to consider for integration of IRSA for 5G NR

Chemical epigenetics: the impact of chemical and chemical biology techniques on bromodomain target validation

Epigenetics is currently the focus of intense research interest across a broad range of disciplines due to its importance in a multitude of biological processes and disease states. Epigenetic functions result partly from modification of the nucleobases in DNA and RNA, and/or post‐translational modifications of histone proteins. These modifications are dynamic, with cellular machinery identified to modulate and interpret the marks. Our focus is on bromodomains, which bind to acetylated lysine residues. Progress in the study of bromodomains, and the development of bromodomain ligands, has been rapid. These advances have been underpinned by many disciplines, but chemistry and chemical biology have undoubtedly played a significant role. Herein, we review the key chemistry and chemical biology approaches that have furthered our study of bromodomains, enabled the development of bromodomain ligands, and played a critical role in the validation of bromodomains as therapeutic targets

Chemical epigenetics: the impact of chemical- and chemical biology techniques on bromodomain target validation

Epigenetics is currently the focus of intense research across a broad range of disciplines due to its involvement in a multitude of biological processes and disease states. At the molecular level, epigenetic functions result partly from modification of the nucleobases in DNA and RNA, and/or post-translational modifications (PTMs) of histone proteins. Much evidence has emerged to demonstrate that these modifications are dynamic, with cellular machinery identified to modulate and interpret the marks. Our focus is on bromodomains that bind to acetylated lysine (KAc) residues. Progress in the study of bromodomains, and the development of bromodomain ligands, has been rapid. These advances have been underpinned by many disciplines, but chemistry and chemical biology techniques have undoubtedly played a very significant role. Here we review the key chemistry and chemical biology techniques and approaches that have furthered our study of bromodomains, enabled the development of bromodomain ligands, and played a critical role in the validation of bromodomains as therapeutic targets

Stereo- and regiodefined DNA-encoded chemical libraries enable efficient tumour-targeting applications

The encoding of chemical compounds with amplifiable DNA tags facilitates the discovery of small-molecule ligands for proteins. To investigate the impact of stereo- and regiochemistry on ligand discovery, we synthesized a DNA-encoded library of 670,752 derivatives based on 2-azido-3-iodophenylpropionic acids. The library was selected against multiple proteins and yielded specific ligands. The selection fingerprints obtained for a set of protein targets of pharmaceutical relevance clearly showed the preferential enrichment of ortho-, meta- or para-regioisomers, which was experimentally verified by affinity measurements in the absence of DNA. The discovered ligands included novel selective enzyme inhibitors and binders to tumour-associated antigens, which enabled conditional chimeric antigen receptor T-cell activation and tumour targeting

BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability

Ligands for the bromodomain and extra-terminal domain (BET) family of bromodomains have shown promise as useful therapeutic agents for treating a range of cancers and inflammation. Here we report that our previously developed 3,5-dimethylisoxazole-based BET bromodomain ligand (OXFBD02) inhibits interactions of BRD4(1) with the RelA subunit of NF-κB, in addition to histone H4. This ligand shows a promising profile in a screen of the NCI-60 panel but was rapidly metabolised (t½ = 39.8 min). Structure-guided optimisation of compound properties led to the development of the 3-pyridyl-derived OXFBD04. Molecular dynamics simulations assisted our understanding of the role played by an internal hydrogen bond in altering the affinity of this series of molecules for BRD4(1). OXFBD04 shows improved BRD4(1) affinity (IC50 = 166 nM), optimised physicochemical properties (LE = 0.43; LLE = 5.74; SFI = 5.96), and greater metabolic stability (t½ = 388 min)

BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability

Ligands for the bromodomain and extra-terminal domain (BET) family of bromodomains have shown promise as useful therapeutic agents for treating a range of cancers and inflammation. Here we report that our previously developed 3,5-dimethylisoxazole-based BET bromodomain ligand (OXFBD02) inhibits interactions of BRD4(1) with the RelA subunit of NF-κB, in addition to histone H4. This ligand shows a promising profile in a screen of the NCI-60 panel but was rapidly metabolised (t½ = 39.8 min). Structure-guided optimisation of compound properties led to the development of the 3-pyridyl-derived OXFBD04. Molecular dynamics simulations assisted our understanding of the role played by an internal hydrogen bond in altering the affinity of this series of molecules for BRD4(1). OXFBD04 shows improved BRD4(1) affinity (IC50 = 166 nM), optimised physicochemical properties (LE = 0.43; LLE = 5.74; SFI = 5.96), and greater metabolic stability (t½ = 388 min)

Controlling intramolecular interactions in the design of selective, high-affinity, ligands for the CREBBP Bromodomain

CREBBP (CBP/KAT3A) and its paralogue EP300 (KAT3B) are lysine acetyltransferases (KATs) that are essential for human development. They each comprise ten domains through which they interact with >400 proteins, making them important transcriptional coactivators, and key nodes in the human protein-protein interactome. The bromodomains of CREBBP and EP300 enable binding of acetylated lysine residues from histones, and a number of other important proteins, including p53, p73, E2F and GATA1. Here we report work to develop a high affinity, small molecule, ligand for the CREBBP and EP300 bromodomains [(−)-OXFBD05] that shows >100-fold selectivity over a representative member of the BET bromodomains, BRD4(1). Cellular studies using this ligand demonstrate that inhibition of the CREBBP/EP300 bromodomain in HCT116 colon cancer cells results in lowered levels of c-Myc, and a reduction in H3K18 and H3K27 acetylation. In hypoxia (<0.1% O2), inhibition of the CREBBP/EP300 bromodomain results in enhanced stabilization of HIF-1α