Targeting protein-protein interaction between MLL1 and reciprocal proteins for leukemia therapy

Recent advances in targeting the "undruggable" proteins: from drug discovery to clinical trials

Undruggable proteins are a class of proteins that are often characterized by large, complex structures or functions that are difficult to interfere with using conventional drug design strategies. Targeting such undruggable targets has been considered also a great opportunity for treatment of human diseases and has attracted substantial efforts in the field of medicine. Therefore, in this review, we focus on the recent development of drug discovery targeting "undruggable" proteins and their application in clinic. To make this review well organized, we discuss the design strategies targeting the undruggable proteins, including covalent regulation, allosteric inhibition, protein-protein/DNA interaction inhibition, targeted proteins regulation, nucleic acid-based approach, immunotherapy and others.

MLL1:EZH2 Ratio in Uterine Secretions and Endometrial Receptivity in Patients with Endometriosis

OBJECTIVE

To establish a novel approach for diagnosing endometriosis (EM) in patients with impaired endometrial receptivity.

METHOD

Mixed lineage leukemia 1 (MLL1) and enhancer of zeste homolog 2 (EZH2) levels were analyzed. The MLL1:EZH2 ratio in identifying impaired endometrial receptivity has been established and validated.

RESULTS

In normal endometrial tissue, the MLL1:EZH2 ratio increased significantly in the midsecretory phase, compared with that in the proliferative phase. In the midsecretory phase, the MLL1:EZH2 ratio in endometrial tissues and uterine secretions accurately identifies patients with EM who have impaired endometrial receptivity. In the validation group, the sensitivity and specificity of the MLL1:EZH2 ratio in the uterine secretions of the midsecretory phase, in diagnosing patients EM who have impaired endometrial receptivity, were 100% and 96.55%, respectively.

CONCLUSIONS

The MLL1:EZH2 ratio in uterine secretions of the midsecretory phase may serve as a marker to diagnose EM in patients with impaired endometrial receptivity.

Bistable Photoswitch Allows in Vivo Control of Hematopoiesis

Optical control has enabled functional modulation in cell culture with unparalleled spatiotemporal resolution. However, current tools for in vivo manipulation are scarce. Here, we design and implement a genuine on-off optochemical probe capable of achieving hematopoietic control in zebrafish. Our photopharmacological approach first developed conformationally strained visible light photoswitches (CS-VIPs) as inhibitors of the histone methyltransferase MLL1 (KMT2A). In blood homeostasis MLL1 plays a crucial yet controversial role. CS-VIP 8 optimally fulfils the requirements of a true bistable functional system in vivo under visible-light irradiation, and with unprecedented stability. These properties are exemplified via hematopoiesis photoinhibition with a single isomer in zebrafish. The present interdisciplinary study uncovers the mechanism of action of CS-VIPs. Upon WDR5 binding, CS-VIP 8 causes MLL1 release with concomitant allosteric rearrangements in the WDR5/RbBP5 interface. Since our tool provides on-demand reversible control without genetic intervention or continuous irradiation, it will foster hematopathology and epigenetic investigations. Furthermore, our workflow will enable exquisite photocontrol over other targets inhibited by macrocycles.

Discovery of as a Potent and Orally Bioavailable Inhibitor of the WDR5-Mixed Lineage Leukemia 1 Protein-Protein Interaction for the Treatment of MLL Fusion Leukemia

WD repeat-containing protein 5 (WDR5) is essential for the stability and methyltransferase activity of the mixed lineage leukemia 1 (MLL1) complex. Dysregulation of the MLL1 gene is associated with human acute leukemias, and the direct disruption of the WDR5-MLL1 protein-protein interaction (PPI) is emerging as an alternative strategy for MLL-rearranged cancers. Here, we represent a new aniline pyrimidine scaffold for WDR5-MLL1 inhibitors. A comprehensive structure-activity analysis identified a potent inhibitor 63 (DDO-2213), with an IC50 of 29 nM in a competitive fluorescence polarization assay and a Kd value of 72.9 nM for the WDR5 protein. Compound 63 selectively inhibited MLL histone methyltransferase activity and the proliferation of MLL translocation-harboring cells. Furthermore, 63 displayed good pharmacokinetic properties and suppressed the growth of MV4-11 xenograft tumors in mice after oral administration, first verifying the in vivo efficacy of targeting the WDR5-MLL1 PPI by small molecules.

Epigenetic Control of Infant B Cell Precursor Acute Lymphoblastic Leukemia

B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a highly aggressive malignancy, with poorer prognosis in infants than in adults. A genetic signature has been associated with this outcome but, remarkably, leukemogenesis is commonly triggered by genetic alterations of embryonic origin that involve the deregulation of chromatin remodelers. This review considers in depth how the alteration of epigenetic profiles (at DNA and histone levels) induces an aberrant phenotype in B lymphocyte progenitors by modulating the oncogenic drivers and tumor suppressors involved in key cancer hallmarks. DNA methylation patterns have been widely studied in BCP-ALL and their correlation with survival has been established. However, the effect of methylation on histone residues can be very different. For instance, methyltransferase KMT2A gene participates in chromosomal rearrangements with several partners, imposing an altered pattern of methylated H3K4 and H3K79 residues, enhancing oncogene promoter activation, and conferring a worse outcome on affected infants. In parallel, acetylation processes provide an additional layer of epigenetic regulation and can alter the chromatin conformation, enabling the binding of regulatory factors. Therefore, an integrated knowledge of all epigenetic disorders is essential to understand the molecular basis of BCP-ALL and to identify novel entry points that can be exploited to improve therapeutic options and disease prognosis.

The Development of Inhibitors Targeting the Mixed Lineage Leukemia 1 (MLL1)-WD Repeat Domain 5 Protein (WDR5) Protein- Protein Interaction

Mixed Lineage Leukemia 1 (MLL1), an important member of Histone Methyltransferases (HMT) family, is capable of catalyzing mono-, di-, and trimethylation of Histone 3 lysine 4 (H3K4). The optimal catalytic activity of MLL1 requires the formation of a core complex consisting of MLL1, WDR5, RbBP5, and ASH2L. The Protein-Protein Interaction (PPI) between WDR5 and MLL1 plays an important role in abnormal gene expression during tumorigenesis, and disturbing this interaction may have a potential for the treatment of leukemia harboring MLL1 fusion proteins. In this review, we will summarize recent progress in the development of inhibitors targeting MLL1- WDR5 interaction.

Tranylcypromine and 6-trifluoroethyl thienopyrimidine hybrid as LSD1 inhibitor

Tranylcypromine moiety extracted from LSD1 inhibitors and 6-trifluoroethyl thienopyrimidine moiety from menin-MLL1 PPI inhibitors were merged to give new chemotypes for medicinal chemistry study. Among 15 new compounds prepared in this work, some exhibited nanomolar LSD1 activity and good selectivity over MAO-A/B, low micromolar menin-MLL1 PPI inhibitory activity, as well as submicromolar MV4-11 antiprofilative activities. Intracellular LSD1 engagement of compounds with higher enzymatic and antiproliferative activities was confirmed by CD86 mRNA up-regulation experiments.

Drug-Target Interaction Prediction via Dual Laplacian Graph Regularized Matrix Completion

Drug-target interactions play an important role for biomedical drug discovery and development. However, it is expensive and time-consuming to accomplish this task by experimental determination. Therefore, developing computational techniques for drug-target interaction prediction is urgent and has practical significance. In this work, we propose an effective computational model of dual Laplacian graph regularized matrix completion, referred to as DLGRMC briefly, to infer the unknown drug-target interactions. Specifically, DLGRMC transforms the task of drug-target interaction prediction into a matrix completion problem, in which the potential interactions between drugs and targets can be obtained based on the prediction scores after the matrix completion procedure. In DLGRMC, the drug pairwise chemical structure similarities and the target pairwise genomic sequence similarities are fully exploited to serve the matrix completion by using a dual Laplacian graph regularization term; i.e., drugs with similar chemical structure are more likely to have interactions with similar targets and targets with similar genomic sequence similarity are more likely to have interactions with similar drugs. In addition, during the matrix completion process, an indicator matrix with binary values which indicates the indices of the observed drug-target interactions is deployed to preserve the experimental confirmed interactions. Furthermore, we develop an alternative iterative strategy to solve the constrained matrix completion problem based on Augmented Lagrange Multiplier algorithm. We evaluate DLGRMC on five benchmark datasets and the results show that DLGRMC outperforms several state-of-the-art approaches in terms of 10-fold cross validation based AUPR values and PR curves. In addition, case studies also demonstrate that DLGRMC can successfully predict most of the experimental validated drug-target interactions.

Architects meets Repairers: The interplay between homeobox genes and DNA repair

Homeobox genes are widely considered the major protagonists of embryonic development and tissue formation. For the past decades, it was established that the deregulation of these genes is intimately related to developmental abnormalities and a broad range of diseases in adults. Since the proper regulation and expression of homeobox genes are necessary for a successful developmental program and tissue function, their relation to DNA repair mechanisms become a necessary discussion. However, important as it is, studies focused on the interplay between homeobox genes and DNA repair are scarce, and there is no critical discussion on the subject. Hence, in this work, I aim to provide the first review of the current knowledge of the interplay between homeobox genes and DNA repair mechanisms, and offer future perspectives on this, yet, young ground for new researches. Critical discussion is conducted, together with a careful assessment of each reviewed topic.