Validation of Protein–Ligand Crystal Structure Models: Small Molecule and Peptide Ligands

2017 ◽  
pp. 611-625 ◽  
Author(s):  
Edwin Pozharski ◽  
Marc C. Deller ◽  
Bernhard Rupp
Keyword(s):  
Crystal Structure ◽  
Small Molecule ◽  
Peptide Ligands

scholarly journals Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate

2015 ◽  
Vol 71 (2) ◽  
pp. 199-205 ◽  
Author(s):  
George T. Lountos ◽  
Scott Cherry ◽  
Joseph E. Tropea ◽  
David S. Waugh
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Phosphatase Activity ◽  
Small Molecule ◽  
Molecular Basis ◽  
Protein Tyrosine Phosphatases ◽  
Simple Method ◽  
Dual Specificity Phosphatase ◽  
Dual Specificity ◽  
Nitrophenyl Phosphate

4-Nitrophenyl phosphate (p-nitrophenyl phosphate, pNPP) is widely used as a small molecule phosphotyrosine-like substrate in activity assays for protein tyrosine phosphatases. It is a colorless substrate that upon hydrolysis is converted to a yellow 4-nitrophenolate ion that can be monitored by absorbance at 405 nm. Therefore, the pNPP assay has been widely adopted as a quick and simple method to assess phosphatase activity and is also commonly used in assays to screen for inhibitors. Here, the first crystal structure is presented of a dual-specificity phosphatase, human dual-specificity phosphatase 22 (DUSP22), in complex with pNPP. The structure illuminates the molecular basis for substrate binding and may also facilitate the structure-assisted development of DUSP22 inhibitors.

scholarly journals Metal Complex Geometries in Small-Molecule Crystals

1998 ◽  
Vol 54 (6) ◽  
pp. 1194-1198 ◽  
Author(s):  
A. Guy Orpen
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Metal Complex ◽  
Small Molecule ◽  
Structure Determination ◽  
Complex Geometries ◽  
Bond Lengths ◽  
Structural Database ◽  
Metal Ligand ◽  
Ligand Bond

The origins, scope and utility of compilations of metal–ligand and intraligand bond lengths based on the Cambridge Structural Database are discussed. The limitations on the apparent uncertainty of metal–ligand bond lengths derived from crystallographic data and recent evidence of metal-assisted hydrogen bonding involving ligands are reviewed in the light of the transferability of bond-length values from one crystal structure determination.

scholarly journals Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals

2008 ◽  
Vol 71 (4) ◽  
pp. 2091-2096 ◽  
Author(s):  
Suk-Youl Park ◽  
Woo-Ram Lee ◽  
Suk-Chan Lee ◽  
Myung-Hee Kwon ◽  
Yong-Sung Kim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Small Molecule ◽  
Active Site ◽  
Single Domain ◽  
Complex Structures ◽  
3D8 Scfv ◽  
Binding Antibody

scholarly journals eCrystals: a route for open access to small molecule crystal structure data

2006 ◽  
Vol 62 (a1) ◽  
pp. s119-s119
Author(s):  
S. Coles ◽  
M. Hursthouse ◽  
J. Frey ◽  
A. Milsted ◽  
L. Carr ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Open Access ◽  
Small Molecule ◽  
Structure Data ◽  
Crystal Structure Data

scholarly journals Computational Identification of Tractable Drug-like Inhibitors of eIF4A1

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 5802-5802
Author(s):  
Derek Essegian ◽  
Tyler A. Cunningham ◽  
Jonathan H. Schatz ◽  
Stephan Schurer
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Cell Lines ◽  
Small Molecule ◽  
Nucleotide Binding ◽  
Hematologic Malignancies ◽  
Dead Box ◽  
Binding Cleft ◽  
Homology Models

Abstract Targeted signaling inhibitors for hematologic malignancies often lead to limited clinical efficacy due to the outgrowth of subpopulations with alternative pathways independent of the drug target. The eIF4F complex responsible for translation initiation is a convergence point for many cancer-promoting signaling pathways and its inhibition leads to decreased expression of key oncoproteins and apoptosis. Lymphomas and leukemias show particular dependence on constitutive eIF4F activation. Indeed, natural compounds targeting the eIF4F enzymatic component, eIF4A1, demonstrate activities both in vitro and in vivo against lymphoma and leukemia model systems, among other tumor types. eIF4A1 is a noteworthy target for hematologic malignancies based on the finding that BCR stimulation leads to increased mRNA translation primary CLL patient samples. Additionally, eIF4F components eIF4A1 and eIF4G1 had increased expression upon IgM-induced BCR activation. The natural compound silvestrol is a potent inhibitor of eIF4A1, results in cancer cell cytotoxicity, and has an established therapeutic window in vivo. Silvestrol shows potent antitumor activity against 924 pan-cancer tumor cell lines with 830/924 (90%) sensitive at IC50 <100nM with lymphoma and leukemia cell lines being particularly sensitive. Silvestrol and other natural compounds, however, lack core drug-like properties and synthetic tractability. To discover new, specific and tractable inhibitors of eIF4A1 that are more drug-like, we have constructed several molecular models that we used to virtually screen more than 20 million compounds. eIF4A1 is the founding member of the DEAD-box RNA helicases, which include its paralogs eIF4A2 (91% amino-acid identity with eIF4A1) and eIF4A3 (60% identity). All DEAD-box helicases contain two RecA-like domains separated by a flexible linker. The cleft between these domains is lined with helicase motifs that mediate nucleotide binding and hydrolysis. In an absence of RNA or nucleotide, eIF4A proteins adopt diffuse open conformations; binding of RNA and ATP triggers transition to a more stable closed state. Modeling small-molecule interactions in the nucleotide cleft of eIF4A1 therefore assesses ability of molecules to lock eIF4A1 in a conformation unable to cycle through ATPase and helicase activities. Although no experimentally derived structure of human eIF4A1 co-crystalized with ATP exists, crystal structures of other DEAD-box family members with similar motifs permit detailed studies of nucleotide and ligand-binding and the development of homology models. We have used four available high-resolution crystal structures to build models predicting interactions of small molecules in the interdomain nucleotide-binding cleft. We identified nucleotide binding-site residues and accurately reproduced ATP interactions for all four models (derived from PDB: 2J0S, 1FUU, 2VSO, 2DB3). We then performed all-atom explicit-water molecular dynamics (MD) simulations for 500-700 ns to study conformational dynamics and atomic interactions of ATP-bound and ATP-unbound states. Yeast eif4A crystal structure (PDB:1FUU) in the open state, for example, illustrated closure of the two RecA domains upon ATP binding. As expected, ATP makes strong interactions with the N-terminal, while phosphate groups extend to the C-terminal interacting with arginines, bringing the two RecA domains together. In contrast, we did not observe domain closure in the same simulation with 1FUU without ATP bound. We also assessed 2J0S, a crystal structure of human closed eIF4A3 bound to ANP. ATP docked to this active site followed by 500 ns MD held the protein in the closed state with several interdomain interactions. Upon nucleotide removal, marked RecA separation occurred. We observed similar domain closure and opening for PDB: 2VSO and 2DB3. Pooling these results, we constructed two homology models of human eIF4A1 with both open (2VSO, 1FUU) and closed conformations (2J0S) as structural templates. We therefore have developed accurate and novel in silico models of eIF4A1 highly useful in assessing interactions of small-molecule ATPase inhibitors, with focus on the ATP-binding cleft. Disclosures No relevant conflicts of interest to declare.

scholarly journals Varying experimental conditions to study interactions in the solid state

2014 ◽  
Vol 70 (a1) ◽  
pp. C631-C631
Author(s):  
Elena Boldyreva
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Small Molecule ◽  
Variable Temperature ◽  
Variable Pressure ◽  
Continuous Lattice ◽  
Experimental Conditions ◽  
Different Types

Supramolecular interactions in the solid state attract much attention. Different experimental and computational approaches are used, to predict and to design crystal structures, to predict the properties based on molecular and crystal structures, to range different types of intermolecular interactions. Analysis of the crystal structures at fixed (e.g. ambient) temperature and pressure conditions is most common for experiments, whereas most DFT calculations are limited to 0 K, to minimize computational costs. At the same time, evolution of a crystal structure as a function of experimental conditions can contribute significantly to understanding the structure-forming role and relative energies of different types of intermolecular interactions in the same crystal structure and of similar interactions in a series of different but structurally or chemically related compounds. In the present invited contribution I attempt to illustrate this using several selected examples from my own practice and from the papers published by other research groups. I consider, in particular, the results of variable-temperature and variable-pressure studies of continuous lattice strain and phase transitions in small-molecule organic compounds, the results of variable-temperature and variable-pressure crystallization, the results of comparing the dissolution profiles of mono- and multi-component small-molecule organic crystals. I shall also discuss how variable-temperature and variable-pressure experimental diffraction data can assist in optimizing the calculations aimed at comparing the relative stability of polymorphs and predicting polymorph transitions. The study was supported by Russian Ministry of Science and Education and Russian Academy of Sciences.

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