scholarly journals New Millennium Antivirals against Pandemic and Epidemic Influenza: The Neuraminidase Inhibitors

2002 ◽  
Vol 13 (4) ◽  
pp. 205-217 ◽  
Author(s):  
John S Oxford ◽  
Patricia Novelli ◽  
Armine Sefton ◽  
Robert Lambkin
Keyword(s):  
Active Site ◽  
Therapeutic Effects ◽  
Neuraminidase Inhibitors ◽  
X Ray ◽  
Enzyme Active Site ◽  
X Ray Crystallography ◽  
Substrate Analogues ◽  
Near Future ◽  
Acid Substrate ◽  
Nasal Fluid

The mushroom shaped outer spike protein of influenza, neuraminidase, was first discovered nearly 60 years ago. Its importance in viral replication was soon recognised both at the point of viral release from the cell and also enabling passage of virus through nasal fluid to reach the cell. The enzyme active site was identified by x-ray crystallography, allowing an atomic study of interaction of enzyme with the sialic acid substrate. Analogues could then be identified and synthesized and became a focused target for antivirals. With the current threat of bioterrorism and the potential for the emergence of a new pandemic strain in the near future, efforts are underway to develop more potent second-generation anti-neuraminidase inhibitors with enhanced protective and therapeutic effects. Here we review older and newer neuraminidase inhibitors and the role that they will play in the fight against influenza in its epidemic and pandemic face.

scholarly journals Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

2020 ◽  
Vol 117 (52) ◽  
pp. 33204-33215
Author(s):  
Filip Yabukarski ◽  
Justin T. Biel ◽  
Margaux M. Pinney ◽  
Tzanko Doukov ◽  
Alexander S. Powers ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Enzyme Design ◽  
Reaction Cycle ◽  
New Era ◽  
X Ray ◽  
Enzyme Active Site ◽  
Conformational Ensembles ◽  
X Ray Crystallography ◽  
General Base

How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme’s reaction cycle. To examine positioning and motions and test catalytic proposals, we collected “room temperature” X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Ensemble analyses indicated limited change through KSI’s reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI’s general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure–function relationships, providing the basis for a new era of “ensemble–function” interrogation of enzymes.

scholarly journals Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles

2019 ◽  
Author(s):  
Filip Yabukarski ◽  
Justin T Biel ◽  
Margaux M Pinney ◽  
Tzanko Doukov ◽  
Alexander S Powers ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Enzyme Design ◽  
Reaction Cycle ◽  
New Era ◽  
X Ray ◽  
Enzyme Active Site ◽  
Conformational Ensembles ◽  
X Ray Crystallography ◽  
General Base

AbstractHow enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme’s reaction cycle. To examine positioning and motions and test catalytic proposals, we collected “room temperature” X-ray crystallography data for P. putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Ensemble analyses indicated limited change through KSI’s reaction cycle. Active site positioning was on the 1-1.5 Å scale, and was not exceptional compared to non-catalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI’s general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active site motions. Most generally, this ensemble perspective extends traditional structure–function relationships, providing the basis for a new era of “ensemble–function” interrogation of enzymes.

scholarly journals Binding of Phosphate and pyrophosphate ions at the active site of human angiogenin as revealed by X-ray crystallography

2001 ◽  
Vol 10 (8) ◽  
pp. 1669-1676 ◽  
Author(s):  
Demetres D. Leonidas ◽  
Gayatri B. Chavali ◽  
Anwar M. Jardine ◽  
Songlin Li ◽  
Robert Shapiro ◽  
...  
Keyword(s):  
Active Site ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Mechanism of IPPase shown by high resolution Neutron and X-ray crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1211-C1211
Author(s):  
Joseph Ng ◽  
Ronny Hughes ◽  
Michelle Morris ◽  
Leighton Coates ◽  
Matthew Blakeley ◽  
...  
Keyword(s):  
High Resolution ◽  
Active Site ◽  
Inorganic Pyrophosphatase ◽  
Inorganic Pyrophosphate ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cellular Processes ◽  
Crystallographic Structures ◽  
Hydrolysis Of ◽  
Low Energy Conformations

Soluble inorganic pyrophosphatase (IPPase) catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to form orthophosphate (Pi). The action of this enzyme shifts the overall equilibrium in favor of synthesis during a number of ATP-dependent cellular processes such as in the polymerization of nucleic acids, production of coenzymes and proteins and sulfate assimilation pathways. Two Neutron crystallographic (2.10-2.50Å) and five high-resolution X-ray (0.99Å-1.92Å) structures of the archaeal IPPase from Thermococcus thioreducens have been determined under both cryo and room temperatures. The structures determined include the recombinant IPPase bound to Mg+2, Ca+2, Br-, SO2-2 or PO4-2 involving those with non-hydrolyzed and hydrolyzed pyrophosphate complexes. All the crystallographic structures provide snapshots of the active site corresponding to different stages of the hydrolysis of inorganic pyrophosphate. As a result, a structure-based model of IPPase catalysis is devised showing the enzyme's low-energy conformations, hydration states, movements and nucleophile generation within the active site.

Introduction

1986 ◽  
Vol 317 (1540) ◽  
pp. 293-294 ◽  
Keyword(s):  
Direct Method ◽  
Hydrolytic Enzyme ◽  
Hydrolytic Enzymes ◽  
Three Dimensional ◽  
X Ray ◽  
Enzyme Active Site ◽  
X Ray Crystallography ◽  
Protein Molecules ◽  
Biological Catalysis ◽  
The 1960S

Our understanding of the function of protein molecules was revolutionized in the 1960s by the use of X-ray crystallography to give a three-dimensional picture of their structures at atomic resolution. The structure of myoglobin was rapidly followed by the structure of several hydrolytic enzymes such as lysozyme, carboxypeptidase, ribonuclease, chymotrypsin, and subtilisin; and, not long after, by the much more complicated structure of haemoglobin, composed of four myoglobin-like molecules interacting with each other. The first hydrolytic enzyme structures showed us how enzymes perform biological catalysis by immobilizing their substrates at the enzyme active site, and gave us definite ideas about the specific functions of different parts of the protein molecules. These ideas had to be treated as hypotheses, because there was no direct method to check them. A few particular points could be proved by cunning but tedious experiments.

scholarly journals Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography

2010 ◽  
Vol 19 (12) ◽  
pp. 2430-2439 ◽  
Author(s):  
Louise J. Gourlay ◽  
Silvia Sommaruga ◽  
Marco Nardini ◽  
Paola Sperandeo ◽  
Gianni Dehò ◽  
...  
Keyword(s):  
Active Site ◽  
X Ray ◽  
E Coli ◽  
X Ray Crystallography

scholarly journals Mechanism-based inactivator of isocitrate lyases 1 and 2 fromMycobacterium tuberculosis

2017 ◽  
Vol 114 (29) ◽  
pp. 7617-7622 ◽  
Author(s):  
Truc V. Pham ◽  
Andrew S. Murkin ◽  
Margaret M. Moynihan ◽  
Lawrence Harris ◽  
Peter C. Tyler ◽  
...  
Keyword(s):  
Active Site ◽  
High Efficiency ◽  
Isocitrate Lyase ◽  
Partition Ratio ◽  
Kinetic Properties ◽  
Ionization Mass ◽  
X Ray ◽  
X Ray Crystallography ◽  
Covalent Adduct ◽  
Reversible Covalent

Isocitrate lyase (ICL, types 1 and 2) is the first enzyme of the glyoxylate shunt, an essential pathway forMycobacterium tuberculosis(Mtb) during the persistent phase of human TB infection. Here, we report 2-vinyl-d-isocitrate (2-VIC) as a mechanism-based inactivator ofMtbICL1 and ICL2. The enzyme-catalyzed retro-aldol cleavage of 2-VIC unmasks a Michael substrate, 2-vinylglyoxylate, which then forms a slowly reversible, covalent adduct with the thiolate form of active-site Cys191. 2-VIC displayed kinetic properties consistent with covalent, mechanism-based inactivation of ICL1 and ICL2 with high efficiency (partition ratio, <1). Analysis of a complex of ICL1:2-VIC by electrospray ionization mass spectrometry and X-ray crystallography confirmed the formation of the predicted covalentS-homopyruvoyl adduct of the active-site Cys191.

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