Crystal Structure of Glycosomal Glyceraldehyde-3-phosphate Dehydrogenase from Leishmania mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site

Biochemistry ◽  
1995 ◽  
Vol 34 (46) ◽  
pp. 14975-14986 ◽  
Author(s):  
Hidong Kim ◽  
Ingeborg K. Feil ◽  
Christophe L. M. J. Verlinde ◽  
Philip H. Petra ◽  
Wim G. J. Hol
Keyword(s):  
Crystal Structure ◽  
Drug Design ◽  
Binding Site ◽  
Inorganic Phosphate ◽  
Leishmania Mexicana ◽  
Phosphate Binding ◽  
Structure Based Drug Design

Phosphate Binding to Isolated Chloroplast Coupling Factor (CF1)

1988 ◽  
Vol 43 (3-4) ◽  
pp. 213-218 ◽  
Author(s):  
Bernhard Huchzermeyer
Keyword(s):  
Atpase Activity ◽  
Binding Site ◽  
Inorganic Phosphate ◽  
Coupling Factor ◽  
Binding Domain ◽  
Atp Binding ◽  
Phosphate Binding ◽  
Chloroplast Coupling Factor ◽  
Single Binding Site ◽  
Site Binding

A single binding site for phosphate was found on isolated chloroplast coupling factor in the absence of nucleotides. In our experiments the phosphate binding site showed a Kd of 170 μᴍ. We did not observe any differences whether the ATPase activity of CF] had been activated or not. If the enzyme was incubated with [γ-32P]ATP the amount of 32P bound per CF1 depended on the pretreatment of the enzyme: In the presence of ADP no ATP or phosphate was bound to CF,. After activation of ATPase activity one mol of ATP per mol CF, was rapidly bound and hydrolyzed while there was a slowly occurring binding of another phosphate without concomitant nucleotide binding. We conclude that there are two different types of phosphate binding observed in our experiments: 1) Inorganic phosphate can be bound by one catalytic site per mol of CF1 2) The γ-phosphate of ATP is able to bind to an ATP binding domain of the enzyme if this domain can exchange substrates with the incubation medium. This ATP binding domain appears to differ from the site binding inorganic phosphate, because at least a portion of the coupling factor contains more than one labelled phosphate during our ATPase tests.

3D U-Net: A voxel-based method in binding site prediction of protein structure

2021 ◽  
Vol 19 (02) ◽  
pp. 2150006
Author(s):  
Fatemeh Nazem ◽  
Fahimeh Ghasemi ◽  
Afshin Fassihi ◽  
Alireza Mehri Dehnavi
Keyword(s):  
Drug Design ◽  
Binding Site ◽  
Binding Sites ◽  
Semantic Segmentation ◽  
Structure Based Drug Design ◽  
Site Prediction ◽  
Binding Site Prediction ◽  
Novel Proteins ◽  
Proposed Model ◽  
Deep Learning Model

Binding site prediction for new proteins is important in structure-based drug design. The identified binding sites may be helpful in the development of treatments for new viral outbreaks in the world when there is no information available about their pockets with COVID-19 being a case in point. Identification of the pockets using computational methods, as an alternative method, has recently attracted much interest. In this study, the binding site prediction is viewed as a semantic segmentation problem. An improved 3D version of the U-Net model based on the dice loss function is utilized to predict the binding sites accurately. The performance of the proposed model on the independent test datasets and SARS-COV-2 shows the segmentation model could predict the binding sites with a more accurate shape than the recently published deep learning model, i.e. DeepSite. Therefore, the model may help predict the binding sites of proteins and could be used in drug design for novel proteins.

Structure-Based Drug Design of c-Kit Inhibitors for Use in the Treatment of Acute Myeloid Leukemia.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1906-1906
Author(s):  
David S. Maxwell ◽  
Ashutosh Pal ◽  
Zhenghong Peng ◽  
Alexandr Shavrin ◽  
Stefan Faderl ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Acute Myeloid Leukemia ◽  
Drug Design ◽  
Cell Lines ◽  
Myeloid Leukemia ◽  
Kinase Inhibitors ◽  
Kinase Assay ◽  
Structure Based Drug Design ◽  
Acute Myeloid

Abstract Inhibitors of c-Kit kinase have shown clinical relevance in various myeloid disorders, including acute myeloid leukemia (AML). Research in our lab has been oriented towards structure-based drug design of c-Kit inhibitors based on the available crystal structure. We describe the design, synthesis, and preliminary results from the in-vitro testing of several c-Kit kinase inhibitors in both enzymatic and cell-based assays. The design resulted from in-silico screening of several targeted libraries via docking to the crystal structure of c-Kit, followed by aggressive post-filtering by several criteria to significantly bias synthesis efforts towards candidate compounds with best chance for success. This led to 128 structures built from 8 common structural cores, from which 2 cores were initially selected based on the synthetic feasibility. Five compounds were initially synthesized, and were immediately followed by 60 compounds with variations to probe local structure-activity relationships. The initial set of compounds, designated APCKxxx, was tested in a c-Kit kinase assay; two compounds were found to have an IC50 in the high nM to low uM range. These compounds have been tested in a MTT-based assay using OCIM2 and OCI/AML3 cell lines. In the c-Kit expressing OCI/AML3 cell line, all five compounds possessed an EC50 < 500 nM and two had and EC50 ~100 nM. Our most recent results show that these compounds also show efficacy in some imatinib-resistant cell lines. We will discuss these results and our strategies for the second generation of compounds that are optimized for better activity, selectivity, and ADME properties.

Binding Site Detection and Druggability Prediction of Protein Targets for Structure- Based Drug Design

2013 ◽  
Vol 19 (12) ◽  
pp. 2326-2333 ◽  
Author(s):  
Yaxia Yuan ◽  
Jianfeng Pei ◽  
Luhua Lai
Keyword(s):  
Drug Design ◽  
Binding Site ◽  
Structure Based Drug Design ◽  
Protein Targets

scholarly journals Allosteric interactions of glycogen phosphorylase b. A crystallographic study of glucose 6-phosphate and inorganic phosphate binding to di-imidate-cross-linked phosphorylase b

1984 ◽  
Vol 218 (1) ◽  
pp. 45-60 ◽  
Author(s):  
A Lorek ◽  
K S Wilson ◽  
M S P Sansom ◽  
D I Stuart ◽  
E A Stura ◽  
...  
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Inorganic Phosphate ◽  
Glycogen Phosphorylase ◽  
Phosphate Binding ◽  
Binding Studies ◽  
Structural Explanation ◽  
Alpha Helices ◽  
Allosteric Effector ◽  
Glycogen Phosphorylase B

The binding to glycogen phosphorylase b of glucose 6-phosphate and inorganic phosphate (respectively allosteric inhibitor and substrate/activator of the enzyme) were studied in the crystal at 0.3 nm (3A) resolution. Glucose 6-phosphate binds in the alpha-configuration at a site that is close to the AMP allosteric effector site at the subunit-subunit interface and promotes several conformational changes. The phosphate-binding site of the enzyme for glucose 6-phosphate involves contacts to two cationic residues, Arg-309 and Lys-247. This site is also occupied in the inorganic-phosphate-binding studies and is therefore identified as a high-affinity phosphate-binding site. It is distinct from the weaker phosphate-binding site of the enzyme for AMP, which is 0.27 nm (2.7A) away. The glucose moiety of glucose 6-phosphate and the adenosine moiety of AMP do not overlap. The results provide a structural explanation for the kinetic observations that glucose 6-phosphate inhibition of AMP activation of phosphorylase b is partially competitive and highly co-operative. The results suggest that the transmission of allosteric conformational changes involves an increase in affinity at phosphate-binding sites and relative movements of alpha-helices. In order to study glucose 6-phosphate and phosphate binding it was necessary to cross-link the crystals. The use of dimethyl malondi-imidate as a new cross-linking reagent in protein crystallography is discussed.

scholarly journals The crystal structure of alanine racemase from Streptococcus pneumoniae, a target for structure-based drug design

2011 ◽  
Vol 11 (1) ◽  
pp. 116 ◽  
Author(s):  
Hookang Im ◽  
Miriam L Sharpe ◽  
Ulrich Strych ◽  
Milya Davlieva ◽  
Kurt L Krause
Keyword(s):  
Crystal Structure ◽  
Streptococcus Pneumoniae ◽  
Drug Design ◽  
Alanine Racemase ◽  
Structure Based Drug Design

Glycogen phosphorylase revisited: extending the resolution of the R- and T-state structures of the free enzyme and in complex with allosteric activators

2021 ◽  
Vol 77 (9) ◽  
pp. 303-311
Author(s):  
Demetres D. Leonidas ◽  
Spyros E. Zographos ◽  
Katerina E. Tsitsanou ◽  
Vassiliki T. Skamnaki ◽  
George Stravodimos ◽  
...  
Keyword(s):  
Drug Design ◽  
Binding Site ◽  
Crystal Structures ◽  
Glycogen Phosphorylase ◽  
Structural Features ◽  
Terminal Segment ◽  
Structure Based Drug Design ◽  
Allosteric Transition ◽  
Α Helix ◽  
T State

The crystal structures of free T-state and R-state glycogen phosphorylase (GP) and of R-state GP in complex with the allosteric activators IMP and AMP are reported at improved resolution. GP is a validated pharmaceutical target for the development of antihyperglycaemic agents, and the reported structures may have a significant impact on structure-based drug-design efforts. Comparisons with previously reported structures at lower resolution reveal the detailed conformation of important structural features in the allosteric transition of GP from the T-state to the R-state. The conformation of the N-terminal segment (residues 7–17), the position of which was not located in previous T-state structures, was revealed to form an α-helix (now termed α0). The conformation of this segment (which contains Ser14, phosphorylation of which leads to the activation of GP) is significantly different between the T-state and the R-state, pointing in opposite directions. In the T-state it is packed between helices α4 and α16 (residues 104–115 and 497–508, respectively), while in the R-state it is packed against helix α1 (residues 22′–38′) and towards the loop connecting helices α4′ and α5′ of the neighbouring subunit. The allosteric binding site where AMP and IMP bind is formed by the ordering of a loop (residues 313–326) which is disordered in the free structure, and adopts a conformation dictated mainly by the type of nucleotide that binds at this site.

scholarly journals Crystal structure of pyrimidine-nucleoside phosphorylase fromBacillus subtilisin complex with imidazole and sulfate

2018 ◽  
Vol 74 (4) ◽  
pp. 193-197 ◽  
Author(s):  
V. V. Balaev ◽  
I. I. Prokofev ◽  
A. G. Gabdoulkhakov ◽  
C. Betzel ◽  
A. A. Lashkov
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Drug Design ◽  
Binding Site ◽  
Anticancer Drug ◽  
Imidazole Ring ◽  
Pyrimidine Nucleoside ◽  
Nucleoside Phosphorylase ◽  
Pyrimidine Nucleoside Phosphorylase

Pyrimidine-nucleoside phosphorylase catalyzes the phosphorolytic cleavage of thymidine and uridine with equal activity. Investigation of this protein is essential for anticancer drug design. Here, the structure of this protein fromBacillus subtilisin complex with imidazole and sulfate is reported at 1.9 Å resolution, which is an improvement on the previously reported structure at 2.6 Å resolution. The localization and position of imidazole in the nucleoside-binding site reflects the possible binding of ligands that possess an imidazole ring.

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