Diffuse large B cell lymphomas (DLBCLs) arise from proliferating B cells transiting different stages of the germinal center reaction. In activated B cell DLBCLs (ABC-DLBCLs), a class of DLBCLs that respond poorly to current therapies, chromosomal translocations and amplification lead to constitutive expression of the B cell lymphoma 6 (BCL6) oncogene. The role of BCL6 in maintaining these lymphomas has not been investigated. Here, we designed small-molecule inhibitors that display higher affinity for BCL6 than its endogenous corepressor ligands to evaluate their therapeutic efficacy for targeting ABC-DLBCL. We used an in silico drug design functional-group mapping approach called SILCS to create a specific BCL6 inhibitor called FX1 that has 10-fold greater potency than endogenous corepressors and binds an essential region of the BCL6 lateral groove. FX1 disrupted formation of the BCL6 repression complex, reactivated BCL6 target genes, and mimicked the phenotype of mice engineered to express BCL6 with corepressor binding site mutations. Low doses of FX1 induced regression of established tumors in mice bearing DLBCL xenografts. Furthermore, FX1 suppressed ABC-DLBCL cells in vitro and in vivo, as well as primary human ABC-DLBCL specimens ex vivo. These findings indicate that ABC-DLBCL is a BCL6-dependent disease that can be targeted by rationally designed inhibitors that exceed the binding affinity of natural BCL6 ligands.

A variety of organisms, such as bacteria, fungi, and plants, produce secondary metabolites, also known as natural products. Natural products have been a prolific source and an inspiration for numerous medical agents with widely divergent chemical structures and biological activities, including antimicrobial, immunosuppressive, anticancer, and anti-inflammatory activities, many of which have been developed as treatments and have potential therapeutic applications for human diseases. Aside from natural products, the recent development of recombinant DNA technology has sparked the development of a wide array of biopharmaceutical products, such as recombinant proteins, offering significant advances in treating a broad spectrum of medical illnesses and conditions. Herein, we will introduce the structures and diverse biological activities of natural products and recombinant proteins that have been exploited as valuable molecules in medicine, agriculture and insect control. In addition, we will explore past and ongoing efforts along with achievements in the development of robust and promising microorganisms as cell factories to produce biologically active molecules. Furthermore, we will review multi-disciplinary and comprehensive engineering approaches directed at improving yields of microbial production of natural products and proteins and generating novel molecules. Throughout this article, we will suggest ways in which microbial-derived biologically active molecular entities and their analogs could continue to inspire the development of new therapeutic agents in academia and industry.

Mycobacterium tuberculosis is thought to undergo transformation into its non-replicating persistence state under the influence of hypoxia or nitric oxide (NO). This transformation is thought to be mediated via two sensor histidine kinases, DosS and DosT, each of which contains two GAF domains that are responsible for detecting oxygen tension. In this study we determined the crystal structures of the first GAF domain (GAF-A) of DosS, which shows an interaction with a heme. A b-type heme was embedded in a hydrophobic cavity of the GAF-A domain and was roughly perpendicular to the ␤-sheet of the GAF domain. The heme iron was liganded by His-149 at the proximal heme axial position. The iron, in the oxidized form, was sixcoordinated with a water molecule at the distal position. Upon reduction, the iron, in ferrous form, was five-coordinated, and when the GAF domain was exposed to atmospheric O 2 , the ferrous form was oxidized to generate the Met form rather than a ferrous O 2 -bound form. Because the heme is isolated inside the GAF domain, its accessibility is restricted. However, a defined hydrogen bond network found at the heme site could accelerate the electron transferability and would explain why DosS was unable to bind O 2 . Flavin nucleotides were shown to reduce the heme iron of DosS while NADH was unable to do so. These results suggest that DosS is a redox sensor and detects hypoxic conditions by its reduction.Mycobacterium tuberculosis is still one of the most dreaded pathogens in existence, and one of the reasons for its success as a pathogen lies in its ability to persist for years within its host. One-third of the world population is estimated to carry M. tuberculosis in the dormant form (1), and while in this state, the pathogen is insensitive to most available chemotherapy. M. tuberculosis has been shown to undergo a metabolic transformation to its non-replicating persistence state under the influence of environmental stimuli such as hypoxia or nitric oxide (2). Recent studies have implied that CO is also an environmental trigger of mycobacterial persistence (3, 4).A two-component regulatory system mediates the genetic response to oxygen limitation and NO exposure in M. tuberculosis (5). The regulatory system consists of two sensor proteins, DosS and DosT and the cognate response regulator DosR (6, 7). DosS and DosR are also known as DevS and DevR (6). DosS and DosT are histidine kinases that undergo autophosphorylation in response to an environmental change, and subsequently transduce the signal to DosR (a transcriptional regulator). DosS and DosT each contain two GAF domains at the N-terminal sensory domain and an HATPase (histidine kinase-like ATPase) domain at its C terminus (8). Hypoxia sensing by DosS or DosT is presumably carried out through the GAF domains.GAF domains are small molecule binding domains found in many proteins from various organisms and are known to play important roles as regulatory elements. Many GAF-containing proteins have two GAF domains in tandem and the two domains have s...

Background: GST domains have been found in diverse proteins involved in translational systems. Results: Four GST domains from human methionyl-tRNA synthetase, glutaminyl-prolyl-tRNA synthetase, ARS-interacting multifunctional protein (AIMP) 2, and AIMP3 are complexed in an ordered fashion. Conclusion: Four components in the human multisynthetase complex are assembled through a GST domain tetrameric complex. Significance: GST domain assemblies act as scaffolds for the formation of multicomponent protein complexes.

Summary Pan-NOTCH inhibitors are poorly tolerated in clinical trials because NOTCH signals are crucial for intestinal homeostasis. These inhibitors may also promote cancer as NOTCH can act as a tumor suppressor. We previously reported that the PIAS-like coactivator ZMIZ1 is frequently co-expressed with activated NOTCH1 in T-cell acute lymphoblastic leukemia (T-ALL). Here, we show that similar to Notch1, Zmiz1 was important for T-cell development and controlled the expression of certain Notch target genes, such as Myc. However, unlike Notch, Zmiz1 had no major role in intestinal homeostasis or myeloid suppression. Deletion of Zmiz1 impaired the initiation and maintenance of Notch-induced T-ALL. Zmiz1 directly interacted with Notch1 via a tetratricopeptide repeat domain at a special class of Notch-regulatory sites. In contrast to the Notch cofactor Maml, which is nonselective, Zmiz1 was selective. Thus, targeting the NOTCH1-ZMIZ1 interaction may combat leukemic growth while avoiding the intolerable toxicities of NOTCH inhibitors.

The NSD family of histone methyltransferases is associated with various malignancies, including aggressive acute leukemia with NUP98-NSD1 translocation. While NSD proteins represent attractive drug targets, their catalytic SET domains exist in autoinhibited conformation, presenting significant challenges for inhibitor development. Here, we employed a fragment-based screening strategy followed by chemical optimization, which resulted in development of the first-in-class irreversible small molecule inhibitors of the NSD1 SET domain. The crystal structure of NSD1 in complex with covalently bound ligand reveals conformational change in the autoinhibitory loop of the SET domain and formation of a channel-like pocket suitable for targeting with small molecules. Our covalent lead, compound BT5, demonstrates on-target activity in NUP98-NSD1 leukemia cells, including inhibition of H3K36 dimethylation and downregulation of target genes, and impairs colony formation in NUP98-NSD1 patient sample. This study will facilitate development of the next generation of potent and selective inhibitors of the NSD histone methyltransferases.

The DevS histidine kinase of Mycobacterium smegmatis contains tandem GAF domains (GAF-A and GAF-B) in its N-terminal sensory domain. The heme iron of DevS is in the ferrous state when purified and is resistant to autooxidation from a ferrous to a ferric state in the presence of O 2 . The redox property of the heme and the results of sequence comparison analysis indicate that DevS of M. smegmatis is more closely related to DosT of Mycobacterium tuberculosis than DevS of M. tuberculosis. The binding of O 2 to the deoxyferrous heme led to a decrease in the autokinase activity of DevS, whereas NO binding did not. The regulation of DevS autokinase activity in response to O 2 and NO was not observed in the DevS derivatives lacking its heme, indicating that the ligand-binding state of the heme plays an important role in the regulation of DevS kinase activity. The redox state of the quinone/quinol pool of the respiratory electron transport chain appears not to be implicated in the regulation of DevS activity. Neither cyclic GMP (cGMP) nor cAMP affected DevS autokinase activity, excluding the possibility that the cyclic nucleotides serve as the effector molecules to modulate DevS kinase activity. The three-dimensional structure of the putative GAF-B domain revealed that it has a GAF folding structure without cyclic nucleotide binding capacity.Mycobacterium smegmatis is a nonpathogenic and fast-growing mycobacterium whose adaptive response to a gradual decrease in oxygen tension and exposure to NO is similar to that of Mycobacterium tuberculosis (7). This adaptive capability of mycobacteria has been suggested to allow them to persist in a latent state in the immune-competent host, especially in the case of M. tuberculosis (14,24,35,52). The hypoxic conditions within granulomas, although this is controversial (1), and the NO synthesized by activated macrophages have been proposed to serve as possible signals for the transition of mycobacteria to the nonreplicating, latent state (35, 50, 52).The DevSR (DosSR) two-component system plays a crucial role in the adaptation of mycobacteria to hypoxic and NO conditions. Approximately 48 genes of M. tuberculosis were reported to be induced under hypoxic conditions, as well as on exposure to NO. The upregulation of these genes is mediated by the DevSR system (35, 38, 39, 52). The DevSR two-component system consists of the DevS histidine kinase (HK) and its cognate response regulator (39, 40). In addition to DevS, the DosT HK was found to cross talk with DevR and to be functional in M. tuberculosis (39,40). DevS and DosT show high sequence similarity to each other over the length of their primary structures. The N-terminal sensory domains of DevS and DosT contain two putative GAF domains. The first GAF domain (GAF-A) serves as a heme-binding domain, while the function of the second one (GAF-B) remains to be revealed (18,22,43,46). It was recently demonstrated that either the binding of O 2 to the ferrous form of hemes of both DevS and DosT or the oxidation of Fe 2ϩ within the heme to...

BMI1 is a core component of the polycomb repressive complex 1 (PRC1) and emerging data support a role of BMI1 in cancer. The central domain of BMI1 is involved in protein–protein interactions and is essential for its oncogenic activity. Here, we present the structure of BMI1 bound to the polyhomeotic protein PHC2 illustrating that the central domain of BMI1 adopts an ubiquitin-like (UBL) fold and binds PHC2 in a β-hairpin conformation. Unexpectedly, we find that the UBL domain is involved in homo-oligomerization of BMI1. We demonstrate that both the interaction of BMI1 with polyhomeotic proteins and homo-oligomerization via UBL domain are necessary for H2A ubiquitination activity of PRC1 and for clonogenic potential of U2OS cells. Here, we also emphasize need for joint application of NMR spectroscopy and X-ray crystallography to determine the overall structure of the BMI1–PHC2 complex.