The SKS of the KMSKS signature of class I aminoacyl-tRNA synthetases corresponds to the GKT/S sequence characteristic of the ATP-binding site of many proteins

AbstractThe polyketide natural product reveromycin A (RM-A) exhibits antifungal, anticancer, anti-bone metastasis, anti-periodontitis and anti-osteoporosis activities by selectively inhibiting eukaryotic cytoplasmic isoleucyl-tRNA synthetase (IleRS). Herein, a co-crystal structure suggests that the RM-A molecule occupies the substrate tRNAIle binding site of Saccharomyces cerevisiae IleRS (ScIleRS), by partially mimicking the binding of tRNAIle. RM-A binding is facilitated by the copurified intermediate product isoleucyl-adenylate (Ile-AMP). The binding assays confirm that RM-A competes with tRNAIle while binding synergistically with l-isoleucine or intermediate analogue Ile-AMS to the aminoacylation pocket of ScIleRS. This study highlights that the vast tRNA binding site of the Rossmann-fold catalytic domain of class I aminoacyl-tRNA synthetases could be targeted by a small molecule. This finding will inform future rational drug design.

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Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

10.1101/198846 ◽

2017 ◽

Cited By ~ 1

Author(s):

Florian Kaiser ◽

Sebastian Bittrich ◽

Sebastian Salentin ◽

Christoph Leberecht ◽

V. Joachim Haupt ◽

...

Keyword(s):

Class Ii ◽

Class I ◽

General Mechanism ◽

Atp Binding ◽

Structural Level ◽

Ligand Interaction ◽

Binding Motifs ◽

Trna Synthetases ◽

Aminoacyl Trna Synthetases ◽

Arginine Residues

AbstractThe origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes.Author summaryAminoacyl tRNA synthetases (aaRS) are primordial enzymes essential for interpretation and transfer of genetic information. Understanding the origin of the peculiarities observed with aaRS can explain what constituted the earliest life forms and how the genetic code was established. The increasing amount of experimentally determined three-dimensional structures of aaRS opens up new avenues for high-throughput analyses of molecular mechanisms. In this study, we present an exhaustive structural analysis of ATP binding motifs. We unveil an oppositional implementation of enzyme substrate binding in each aaRS Class. While Class I binds via interactions mediated by backbone hydrogen bonds, Class II uses a pair of arginine residues to establish salt bridges to its ATP ligand. We show how nature realized the binding of the same ligand species with completely different mechanisms. In addition, we demonstrate that sequence or even structure analysis for conserved residues may miss important functional aspects which can only be revealed by ligand interaction studies. Additionally, the placement of those key residues in the structure supports a popular hypothesis, which states that prototypic aaRS were once coded on complementary strands of the same gene.

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New Mechanistic Insight on the PIM-1 Kinase Inhibitor AZD1208 Using Multidrug Resistant Human Erythroleukemia Cell Lines and Molecular Docking Simulations

Current Topics in Medicinal Chemistry ◽

10.2174/1568026619666190509121606 ◽

2019 ◽

Vol 19 (11) ◽

pp. 914-926 ◽

Cited By ~ 2

Author(s):

Maiara Bernardes Marques ◽

Michael González-Durruthy ◽

Bruna Félix da Silva Nornberg ◽

Bruno Rodrigues Oliveira ◽

Daniela Volcan Almeida ◽

...

Keyword(s):

Molecular Docking ◽

Binding Site ◽

Cell Lines ◽

Chemotherapeutic Agents ◽

Atp Binding ◽

Human Leukemia ◽

Atp Binding Site ◽

Mechanistic Insight ◽

Multiple Drugs

Background:PIM-1 is a kinase which has been related to the oncogenic processes like cell survival, proliferation, and multidrug resistance (MDR). This kinase is known for its ability to phosphorylate the main extrusion pump (ABCB1) related to the MDR phenotype.Objective:In the present work, we tested a new mechanistic insight on the AZD1208 (PIM-1 specific inhibitor) under interaction with chemotherapy agents such as Daunorubicin (DNR) and Vincristine (VCR).Materials and Methods:In order to verify a potential cytotoxic effect based on pharmacological synergism, two MDR cell lines were used: Lucena (resistant to VCR) and FEPS (resistant to DNR), both derived from the K562 non-MDR cell line, by MTT analyses. The activity of Pgp was ascertained by measuring accumulation and the directional flux of Rh123. Furthermore, we performed a molecular docking simulation to delve into the molecular mechanism of PIM-1 alone, and combined with chemotherapeutic agents (VCR and DNR).Results:Our in vitro results have shown that AZD1208 alone decreases cell viability of MDR cells. However, co-exposure of AZD1208 and DNR or VCR reverses this effect. When we analyzed the ABCB1 activity AZD1208 alone was not able to affect the pump extrusion. Differently, co-exposure of AZD1208 and DNR or VCR impaired ABCB1 activity, which could be explained by compensatory expression of abcb1 or other extrusion pumps not analyzed here. Docking analysis showed that AZD1208 is capable of performing hydrophobic interactions with PIM-1 ATP- binding-site residues with stronger interaction-based negative free energy (FEB, kcal/mol) than the ATP itself, mimicking an ATP-competitive inhibitory pattern of interaction. On the same way, VCR and DNR may theoretically interact at the same biophysical environment of AZD1208 and also compete with ATP by the PIM-1 active site. These evidences suggest that AZD1208 may induce pharmacodynamic interaction with VCR and DNR, weakening its cytotoxic potential in the ATP-binding site from PIM-1 observed in the in vitro experiments.Conclusion:Finally, the current results could have a pre-clinical relevance potential in the rational polypharmacology strategies to prevent multiple-drugs resistance in human leukemia cancer therapy.

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Identification of the ATP binding site in tyrocidine synthetase 1 by selective modification with fluorescein 5'-isothiocyanate.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)36560-2 ◽

1994 ◽

Vol 269 (21) ◽

pp. 14962-14966

Author(s):

M. Pavela-Vrancic ◽

E. Pfeifer ◽

W. Schröder ◽

H. von Döhren ◽

H. Kleinkauf

Keyword(s):

Binding Site ◽

Atp Binding ◽

Atp Binding Site

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Crizotinib acts as ABL1 inhibitor combining ATP-binding with allosteric inhibition and is active against native BCR-ABL1 and its resistance and compound mutants BCR-ABL1T315I and BCR-ABL1T315I-E255K

Annals of Hematology ◽

10.1007/s00277-020-04357-z ◽

2021 ◽

Author(s):

Afsar Ali Mian ◽

Isabella Haberbosch ◽

Hazem Khamaisie ◽

Abed Agbarya ◽

Larissa Pietsch ◽

...

Keyword(s):

Binding Site ◽

Kinase Inhibitors ◽

Therapeutic Potential ◽

Lymphoblastic Leukemia ◽

Philadelphia Chromosome ◽

Binding Pocket ◽

Atp Binding ◽

Atp Binding Site ◽

Lung Cancer Patients

AbstractResistance remains the major clinical challenge for the therapy of Philadelphia chromosome–positive (Ph+) leukemia. With the exception of ponatinib, all approved tyrosine kinase inhibitors (TKIs) are unable to inhibit the common “gatekeeper” mutation T315I. Here we investigated the therapeutic potential of crizotinib, a TKI approved for targeting ALK and ROS1 in non-small cell lung cancer patients, which inhibited also the ABL1 kinase in cell-free systems, for the treatment of advanced and therapy-resistant Ph+ leukemia. By inhibiting the BCR-ABL1 kinase, crizotinib efficiently suppressed growth of Ph+ cells without affecting growth of Ph− cells. It was also active in Ph+ patient-derived long-term cultures (PD-LTCs) independently of the responsiveness/resistance to other TKIs. The efficacy of crizotinib was confirmed in vivo in syngeneic mouse models of BCR-ABL1- or BCR-ABL1T315I-driven chronic myeloid leukemia–like disease and in BCR-ABL1-driven acute lymphoblastic leukemia (ALL). Although crizotinib binds to the ATP-binding site, it also allosterically affected the myristol binding pocket, the binding site of GNF2 and asciminib (former ABL001). Therefore, crizotinib has a seemingly unique double mechanism of action, on the ATP-binding site and on the myristoylation binding pocket. These findings strongly suggest the clinical evaluation of crizotinib for the treatment of advanced and therapy-resistant Ph+ leukemia.

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