Fragment optimization and elaboration strategies - the discovery of two lead series of PRMT5/MTA inhibitors from five fragment hits

Here we describe the early stages of a fragment-based lead discovery (FBLD) project for a recently elucidated synthetic lethal target, the PRMT5/MTA complex, for the treatment of MTAP-deleted cancers. Starting with five fragment/PRMT5/MTA X-ray co-crystal structures, we employed a two-phase fragment elaboration process encompassing optimization of fragment hits and subsequent fragment growth to increase potency, assess synthetic tractability, and enable structure-based drug design. Two lead series were identified, one of which led to the discovery of the clinical candidate MRTX1719.

Analyzing the relationship between the cytokine profile of invasive breast carcinoma, its histopathological characteristics and metastasis to regional lymph nodes

This study was aimed at analyzing the relations of metastasis to regional lymph nodes (RLNs) with histopathological indicators of invasive breast carcinoma of no special type (IC-NST) and its cytokine profile. Enzyme-linked immunosorbent assays were performed to determine concentrations of IL-2, IL-6, IL-8, IL-10, IL-17, IL-18, IL-1β, IL-1Ra, TNF-α, IFN-γ, G-CSF, GM-CSF, VEGF-A, and MCP-1 in the culture supernatant of IC-NST samples from 48 female patients. Histopathological indicators (degree of tumor cell differentiation, mitoses, and others) and ER, PR, Her2/neu, Ki-67, and CD34 expression levels were determined. By means of three types of neural network models, it was shown that for different parameters of the output layer, different groups of parameters are involved that have predictive value regarding metastasis to RLNs. As a result of multi-dimensional cluster analysis, three clusters were formed with different cytokines profiles of IC-NST. Different correlations between indicators of cytokine production by IC-NST and its histopathological parameters were revealed in groups with different cytokine profiles. It was shown that at simultaneous evaluation of the production of even two cytokines, the importance of which relationship with metastasis was revealed by neural network modeling, can increase the probability of determining the presence of metastasis in the RLNs.

Structural Aspects of Photopharmacology: Insight into the Binding of Photoswitchable and Photocaged Inhibitors to the Glutamate Transporter Homologue

Photopharmacology addresses the challenge of drug selectivity and side effects through creation of photoresponsive molecules activated with light with high spatiotemporal precision. This is achieved through incorporation of molecular photoswitches and photocages into the pharmacophore. However, the structural basis for the light-induced modulation of inhibitory potency in general is still missing, which poses a major design challenge for this emerging field of research. Here we solved crystal structures of the glutamate transporter homologue Glt_Tk in complex with photoresponsive transport inhibitors—azobenzene derivative of TBOA (both in trans and cis configuration) and with the photocaged compound ONB-hydroxyaspartate. The essential role of glutamate transporters in the functioning of the central nervous system renders them potential therapeutic targets in the treatment of neurodegenerative diseases. The obtained structures provide a clear structural insight into the origins of photocontrol in photopharmacology and lay the foundation for application of photocontrolled ligands to study the transporter dynamics by using time-resolved X-ray crystallography.

The Relationship Between Cytokine Production, CSF2RA, and IL1R2 Expression in Mammary Adenocarcinoma, Tumor Histopathological Parameters, and Lymph Node Metastasis

Objective:

The aim of this study was to evaluate the relationship between cytokine production, GM-CSF receptor (CSF2RA), and IL-1 receptor (IL1R2) expression in mammary adenocarcinoma and their association with it histopathological parameters and lymph node metastasis.

Methods:

We analyzed tumor biopsy samples (cultured in vitro) from 50 women (aged 43-75) with invasive ductal mammary adenocarcinomas. Enzyme-linked immunosorbent assay method the concentrations of interleukin 2, interleukin 6, interleukin 8, interleukin 10, interleukin 17, interleukin 18, interleukin 1β, interleukin 1Ra, tumor necrosis factor α, interferon γ, granulocyte colony-stimulating factor, granulocyte macrophage colony-stimulating factor, and vascular endothelial growth factor A were determined in culture supernatants. The expression of CSF2RA and IL1R2 in tumor biopsy was evaluated by immunohistochemical method.

Results:

We showed that the “cytokine profile” of a tumor (the ability of tumor cells and its microenvironment to produce different cytokines) is very individual. It has been shown that the features of the cytokine profile of the mammary adenocarcinoma are important for the formation and realization of the metastatic potential of the mammary adenocarcinoma. We found correlations between some histopathological parameters of mammary adenocarcinoma and coefficients K_{GM-CSF/CSF2RA} and K_IL-1β/IL1R2, which are the ratios of concentrations of granulocyte macrophage colony-stimulating factor and interleukin -1β to expression of CSF2RA and IL1R2, respectively. K_{GM-CSF/CSF2RA} positively correlated with highly differentiated cells, and K_IL-1β/IL1R2 positively correlated with the number of mitoses, poorly differentiated cells, and a number of lymph nodes with metastases. K_{GM-CSF/CSF2RA} positively correlated with the concentrations of interleukin 6, interleukin 8, interleukin 1Ra, and granulocyte colony-stimulating factor. K_IL-1β/IL1R2 positively correlated with concentrations of interleukin 1β and interferon γ and negative correlated with the concentrations of vascular endothelial growth factor A and tumor necrosis factor α. It is shown that K_IL-1β/IL1R2 can be considered as a prognostic indicator predicting the probability of mammary adenocarcinoma metastasis to regional lymph nodes.

Conclusions:

The ratios of granulocyte macrophage colony-stimulating factor and interleukin 1β cytokines, produced in tumor, to the expression of CSF2RA and IL1R2 depend on levels of interleukin 6, interleukin 8, tumor necrosis factor α, interferon γ, granulocyte colony-stimulating factor, and vascular endothelial growth factor A and are important factors affecting the progression and metastasis of the breast cancer.

Structural ensemble of a glutamate transporter homologue in lipid nanodisc environment

Glutamate transporters are cation-coupled secondary active membrane transporters that clear the neurotransmitter L-glutamate from the synaptic cleft. These transporters are homotrimers, with each protomer functioning independently by an elevator-type mechanism, in which a mobile transport domain alternates between inward- and outward-oriented states. Using single-particle cryo-EM we have determined five structures of the glutamate transporter homologue Glt_Tk, a Na⁺- L-aspartate symporter, embedded in lipid nanodiscs. Dependent on the substrate concentrations used, the protomers of the trimer adopt a variety of asymmetrical conformations, consistent with the independent movement. Six of the 15 resolved protomers are in a hitherto elusive state of the transport cycle in which the inward-facing transporters are loaded with Na⁺ ions. These structures explain how substrate-leakage is prevented - a strict requirement for coupled transport. The belt protein of the lipid nanodiscs bends around the inward oriented protomers, suggesting that membrane deformations occur during transport.

Binding and transport of D-aspartate by the glutamate transporter homolog GltTk

Mammalian glutamate transporters are crucial players in neuronal communication as they perform neurotransmitter reuptake from the synaptic cleft. Besides L-glutamate and L-aspartate, they also recognize D-aspartate, which might participate in mammalian neurotransmission and/or neuromodulation. Much of the mechanistic insight in glutamate transport comes from studies of the archeal homologs Glt_Ph from Pyrococcus horikoshii and Glt_Tk from Thermococcus kodakarensis. Here, we show that Glt_Tk transports D-aspartate with identical Na⁺: substrate coupling stoichiometry as L-aspartate, and that the affinities (K_d and K_m) for the two substrates are similar. We determined a crystal structure of Glt_Tk with bound D-aspartate at 2.8 Å resolution. Comparison of the L- and D-aspartate bound Glt_Tk structures revealed that D-aspartate is accommodated with only minor rearrangements in the structure of the binding site. The structure explains how the geometrically different molecules L- and D-aspartate are recognized and transported by the protein in the same way.

VEGF-R2 and TNF-R1 expression and cytokine production by samples of mammary adenocarcinomas and correlations with histopathological parameters of these malignant tumors

Currently, the role of cytokines in the tumor progression, including breast cancer, is universally recognized. At the same time, there are still many questions concerning the role of individual cytokines and receptors for cytokines in various morphogenetic processes underlying the tumor progression. The objective of this work was to study cytokine production and vascular endothelial growth factor (VEGF)-R2 and VEGF-R1 expression by mammary adenocarcinoma (MAC) and the correlations with histopathological parameters of malignant tumors. The object of the study was cultured tumor biopsy samples from 47 women aged 43-75 years with invasive ductal carcinoma, which was classified as grade II-III adenocarcinoma. It was shown that the cytokine profiles of the supernatants of MAC samples from patients differ greatly. A correlation between the levels of VEGF-R2 and tumor necrosis factor (TNF)-R1 expression was observed. Correlations were also revealed during analysis of the relations of histopathological MAC indicators with K_{VEGF-R2/VEGF-A} and K_{TNF-R1/TNF-α} coefficients, which are equal, respectively, to the ratio of expression values of receptors VEGF-R2 and TNF-R1 to the concentrations of the relevant cytokines (VEGF-A and TNF-α) in the culture supernatants of the same MAC samples. A direct correlation was identified between K_{VEGF-R/VEGF-A} and some histopathological MAC characteristics: proportion of cells undergoing mitosis or pathological mitosis in MAC and poorly differentiated cells. K_{VEGF-R2/VEGF-A} directly correlated with the concentration in supernatant interleukin (IL)-18 and interferon (IFN)-γ. K_{TNF-R1/TNF-α} was inversely correlated with the concentration in supernatant of IL-1Ra, IL-8, and granulocyte-macrophage colony-stimulating factor (GM-CSF). The data obtained show that the high-level production of IL-18 and IL-1β by MAC, overexpression of VEGF-R2 in tumor (at relatively low VEGF-A production), and the high level of IFN-γ production are attributed factors contributing to the formation of a population of low-grade cells in the tumor. The factors regulating the population of moderately differentiated cells in the tumor are referred to as IL-1Ra, IL-8, and GM-CSF.

Analysis of the quality of crystallographic data and the limitations of structural models

Arkhipova et al. caution that the limitations of structural models be taken into account when interpreting crystallographic data.

Crystal structures provide visual models of biological macromolecules, which are widely used to interpret data from functional studies and generate new mechanistic hypotheses. Because the quality of the collected x-ray diffraction data directly affects the reliability of the structural model, it is essential that the limitations of the models are carefully taken into account when making interpretations. Here we use the available crystal structures of members of the glutamate transporter family to illustrate the importance of inspecting the data that underlie the structural models. Crystal structures of glutamate transporters in multiple different conformations have been solved, but most structures were determined at relatively low resolution, with deposited models based on crystallographic data of moderate quality. We use these examples to demonstrate the extent to which mechanistic interpretations can be made safely.

Cytokine production in mammary adenocarcinoma and its microenvironmental cells in patients with or without metastases in regional lymph nodes

In recent years, the concept of formation of a sufficiently autonomous cytokine network in a malignant tumour has emerged. In this regard, the data on the role of this network and its signalling pathways in the process of metastasis are an interesting topic. The aim of this study was to evaluate the in vitro cytokine-producing potential of mammary adenocarcinoma (MAC; and cells of its microenvironment) from patients with or without metastases in regional lymph nodes (LNs). By enzyme-linked immunosorbent assays of culture supernatants, we studied the cytokine production by biopsy samples of MAC: spontaneous and stimulated by polyclonal activators (PAs: phytohaemagglutinin, concanavalin A and lipopolysaccharide). The levels of spontaneous production of interleukin (IL)-10 and granulocyte colony-stimulating factor (G-CSF) and the amounts of IL-2, IL-10, G-CSF and monocyte chemoattractant protein-1 (MCP-1) produced during stimulation by PAs, as well as the index of stimulation by polyclonal activators (ISPA) for IL-2 production, were lower for MAC with LN metastasis than for MAC without LN metastasis. The levels of spontaneous production of IL-2 and interferon (IFN)-γ and the ISPA for granulocyte-macrophage colony-stimulating factor (GM-CSF) production were higher for MAC with LN metastasis. There were only three pairwise correlations between the produced cytokines that were specific to MAC with LN metastasis: IL-2 and IFN-γ, IL-6 and GM-CSF, and IL-8 and GM-CSF. There were 10 pairwise correlations between the produced cytokines that were specific to nonmetastasising MAC: IL-6 and IL-10, IL-6 and MCP-1, IL-8 and IL-10, IL-8 and MCP-1, IL-10 and G-CSF, IL-10 and MCP-1, IFN-γ and MCP-1, MCP-1 and G-CSF, G-CSF and IL-1Ra, and GM-CSF and tumour necrosis factor (TNF)-α. Our data indicate that metastatic tumours show desynchronisation of many pathways of induction and synthesis of cytokines that are characteristic of nonmetastatic tumours.

Water clusters in the nucleotide-binding pocket of the protein aIF2γ from the archaeon Sulfolobus solfataricus: Proton transmission

In Archaea and Eukaryotes, the binding of Met-tRNAi(Met) to the P-site of the ribosome is mediated by translation initiation factor 2 (a/eIF2) which consists of three subunits: α, β and γ. Here, we present the high-resolution structure of intact aIF2γ from Sulfolobus solfataricus (SsoIF2γ) in complex with GTP analog, GDPCP. The comparison of the nucleotide-binding pockets in this structure and in the structure of the ribosome-bound form of EF-Tu reveals their close conformation similarity. The nucleotide-binding pocket conformation observed in this structure could be consider as corresponding to intermediate conformation of EF-Tu nucleotide-binding pocket in its transition from the GTP-bound form to the GDP-bound one. Three clusters of well defined water molecules are associated with amino acid residues of the SsoIF2γ nucleotide-binding pocket and stabilize its conformation. We suppose that two water bridges between the oxygen atoms of the GTP γ-phosphate and negatively charged residues of the pocket can serve as ways to transmit protons arising from the catalytic reaction.

Binding of the 5'-Triphosphate End of mRNA to the γ-Subunit of Translation Initiation Factor 2 of the Crenarchaeon Sulfolobus solfataricus

The heterotrimeric archaeal IF2 orthologue of eukaryotic translation initiation factor 2 consists of the α-subunit, β-subunit and γ-subunit. Previous studies showed that the γ-subunit of aIF2, besides its central role in Met-tRNAi binding, has an additional function: it binds to the 5'-triphosphorylated end of mRNA and protects its 5'-part from degradation. Competition studies with nucleotides and mRNA, as well as structural and kinetic analyses of aIF2γ mutants, strongly implicate the canonical GTP/GDP-binding pocket in binding to the 5'-triphosphate end of mRNAs. The biological implication of these findings is being discussed.

Conformational transitions in the γ subunit of the archaeal translation initiation factor 2

In eukaryotes and archaea, the heterotrimeric translation initiation factor 2 (e/aIF2) is pivotal for the delivery of methionylated initiator tRNA (Met-tRNA(i)) to the ribosome. It acts as a molecular switch that cycles between inactive (GDP-bound) and active (GTP-bound) states. Recent studies show that eIF2 can also exist in a long-lived eIF2γ-GDP-P(i) (inorganic phosphate) active state. Here, four high-resolution crystal structures of aIF2γ from Sulfolobus solfataricus are reported: aIF2γ-GDPCP (a nonhydrolyzable GTP analogue), aIF2γ-GDP-formate (in which a formate ion possibly mimics P(i)), aIF2γ-GDP and nucleotide-free aIF2γ. The structures describe the different states of aIF2γ and demonstrate the conformational transitions that take place in the aIF2γ `life cycle'.

Crystal structure of the archaeal translation initiation factor 2 in complex with a GTP analogue and Met-tRNAf(Met.)

Heterotrimeric aIF2αβγ (archaeal homologue of the eukaryotic translation initiation factor 2) in its GTP-bound form delivers Met-tRNAi(Met) to the small ribosomal subunit. It is known that the heterodimer containing the GTP-bound γ subunit and domain 3 of the α subunit of aIF2 is required for the formation of a stable complex with Met-tRNAi. Here, the crystal structure of an incomplete ternary complex including aIF2αD3γ⋅GDPNP⋅Met-tRNAf(Met) has been solved at 3.2Å resolution. This structure is in good agreement with biochemical and hydroxyl radical probing data. The analysis of the complex shows that despite the structural similarity of aIF2γ and the bacterial translation elongation factor EF-Tu, their modes of tRNA binding are very different. Remarkably, the recently published 5.0-Å-resolution structure of almost the same ternary initiation complex differs dramatically from the structure presented. Reasons for this discrepancy are discussed.