Identification of covalent active site inhibitors of dengue virus protease.

Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described.

Lyso-myristoyl phosphatidylcholine micelles sustain the activity of Dengue non-structural (NS) protein 3 protease domain fused with the full-length NS2B.

Dengue virus (DENV), a member of the flavivirus genus, affects 50-100 million people in tropical and sub-tropical regions. The DENV protease domain is located at the N-terminus of the NS3 protease and requires for its enzymatic activity a hydrophilic segment of the NS2B that acts as a cofactor. The protease is an important antiviral drug target because it plays a crucial role in virus replication by cleaving the genome-coded polypeptide into mature functional proteins. Currently, there are no drugs to inhibit DENV protease activity. Most structural and functional studies have been conducted using protein constructs containing the NS3 protease domain connected to a soluble segment of the NS2B membrane protein via a nine-residue linker. For in vitro structural and functional studies, it would be useful to produce a natural form of the DENV protease containing the NS3 protease domain and the full-length NS2B protein. Herein, we describe the expression and purification of a natural form of DENV protease (NS2BFL-NS3pro) containing the full-length NS2B protein and the protease domain of NS3 (NS3pro). The protease was expressed and purified in detergent micelles necessary for its folding. Our results show that this purified protein was active in detergent micelles such as lyso-myristoyl phosphatidylcholine (LMPC). These findings should facilitate further structural and functional studies of the protease and will facilitate drug discovery targeting DENV.

NMR analysis of a novel enzymatically active unlinked dengue NS2B-NS3 protease complex.

The dengue virus (DENV) is a mosquito-borne pathogen responsible for an estimated 100 million human infections annually. The viral genome encodes a two-component trypsin-like protease that contains the cofactor region from the nonstructural protein NS2B and the protease domain from NS3 (NS3pro). The NS2B-NS3pro complex plays a crucial role in viral maturation and has been identified as a potential drug target. Using a DENV protease construct containing NS2B covalently linked to NS3pro via a Gly4-Ser-Gly4 linker ("linked protease"), previous x-ray crystal structures show that the C-terminal fragment of NS2B is remote from NS3pro and exists in an open state in the absence of an inhibitor; however, in the presence of an inhibitor, NS2B complexes with NS3pro to form a closed state. This linked enzyme produced NMR spectra with severe signal overlap and line broadening. To obtain a protease construct with a resolved NMR spectrum, we expressed and purified an unlinked protease complex containing a 50-residue segment of the NS2B cofactor region and NS3pro without the glycine linker using a coexpression system. This unlinked protease complex was catalytically active at neutral pH in the absence of glycerol and produced dispersed cross-peaks in a (1)H-(15)N heteronuclear single quantum correlation spectrum that enabled us to conduct backbone assignments using conventional techniques. In addition, titration with an active-site peptide aldehyde inhibitor and paramagnetic relaxation enhancement studies demonstrated that the unlinked DENV protease exists predominantly in a closed conformation in solution. This protease complex can serve as a useful tool for drug discovery against DENV.

West Nile virus protease activity in detergent solutions and application for affinity tag removal.

Affinity tags are typically used to facilitate membrane protein purification. A protease needs to remain active in the presence of detergent to remove a fusion tag from a recombinant membrane protein. Our results show that the West Nile virus (WNV) protease activity was not affected while in the presence of a wide range of detergents. In a detergent solution, the WNV protease can remove the fusion tag from a recombinant protein containing KCNE3 and a WNV protease site. Therefore, the WNV protease may be useful as an alternative enzyme to remove affinity tags in protein purifications.

¹H, ¹³C and ¹5N chemical shift assignments for an intracellular proteinase inhibitor of Bacillus subtilis.

Intracellular proteinases (ISPs) are the main component of the bacilli degradome and a distinctive class in different bacilli. An intracellular proteinase inhibitor of the bacteria Bacillus subtillis was shown to regulate the activity of ISP-1. To study the structure of this inhibitor, we report the resonance assignment for this protein with 119 amino acid. The data will allow us to perform structural study on this inhibitor to understand its mechanism for ISP-1 inhibition.

Exploring the binding of peptidic West Nile virus NS2B-NS3 protease inhibitors by NMR.

West Nile virus (WNV) NS2B-NS3 protease is an important drug target since it is an essential protein for the replication of the virus. In order to determine the minimum pharmacophore for protease inhibition, a series of dipeptide aldehydes were synthesized. The 50% inhibitory concentration (IC(50)) measurements revealed that a simple acetyl-KR-aldehyde was only threefold less active than 4-phenyl-phenylacetyl-KKR-aldehyde (1) (Stoermer et al., 2008) that was used as the reference compound. The ligand efficiency of 0.40 kcal/mol/HA (HA=heavy atom) for acetyl-KR-aldehyde is much improved compared to the reference compound 1 (0.23 kcal/mol/HA). The binding of the inhibitors was examined using (1)H-(15)N-HSQC experiments and differential chemical shifts were used to map the ligand binding sites. The biophysical studies show that the conformational mobility of WNV protease has a major impact on the design of novel inhibitors, since the protein conformation changes profoundly depending on the structure of the bound ligand.

West Nile Virus (WNV) protease and membrane interactions revealed by NMR spectroscopy.

West Nile Virus (WNV) protease is a two-component protease, important for the maturation of virus by cleaving the viral ploypeptide into functional proteins. WNV protease contains a Nonstructural (NS) protein 3 possessing the protease active sites and is regulated by a cofactor region containing approximately 40 amino acids from an integral membrane protein, NS2B. Although NS2B was demonstrated to be important for the location of the protease on the membrane, there was no direct evidence to show the interaction between protease (NS3) and membrane. Herein, we investigated the interaction between WNV protease and dodecylphosphocoline (DPC) micelles using NMR spectroscopy. The results showed that amino acids (31-33) from NS3 were important for the interaction with detergent micelles, which was similar to the finding in the study of protease from Dengue virus. This region may serve as an anchoring site to stabilized NS3 protease domain on the membrane.

Expression and purification of the p75 neurotrophin receptor transmembrane domain using a ketosteroid isomerase tag.

BACKGROUND: Receptors with a single transmembrane (TM) domain are essential for the signal transduction across the cell membrane. NMR spectroscopy is a powerful tool to study structure of the single TM domain. The expression and purification of a TM domain in Escherichia coli (E.coli) is challenging due to its small molecular weight. Although ketosteroid isomerase (KSI) is a commonly used affinity tag for expression and purification of short peptides, KSI tag needs to be removed with the toxic reagent cyanogen bromide (CNBr). RESULT: The purification of the TM domain of p75 neurotrophin receptor using a KSI tag with the introduction of a thrombin cleavage site is described herein. The recombinant fusion protein was refolded into micelles and was cleaved with thrombin. Studies showed that purified protein could be used for structural study using NMR spectroscopy. CONCLUSIONS: These results provide another strategy for obtaining a single TM domain for structural studies without using toxic chemical digestion or acid to remove the fusion tag. The purified TM domain of p75 neurotrophin receptor will be useful for structural studies.

Expression, purification, and initial structural characterization of nonstructural protein 2B, an integral membrane protein of Dengue-2 virus, in detergent micelles.

Dengue virus causes serious diseases affecting people in tropical and sub-tropical regions. The nonstructural (NS) protein 2B is an integral membrane protein and important for the regulation of viral protease NS3, which is significant for virus replication. The NS2B-NS3 complex is an important drug target for treating dengue fever. However, little is known about the structure of NS2B in its entirety. Herein, we describe the expression and purification of this integral membrane protein from cell membrane and inclusion bodies of Escherichia coli cells. The initial nuclear magnetic resonance (NMR) and circular dichroism (CD) results indicate that the purified protein adopts alpha-helical structures in LMPG and TDPC micelles.

An NMR study of the N-terminal domain of wild-type hERG and a T65P trafficking deficient hERG mutant.

The human Ether-à-go-go Related Gene (hERG) potassium channel plays an important role in the heart by controlling the rapid delayed rectifier current. The N-terminal 135 residues (NTD) contain a Per-Arnt-Sim (PAS) domain and an N-terminal amphipathic helix. NMR relaxation analysis and H/D exchange experiments on the NTD demonstrated that the amphipathic helix is rigid and solvent accessible. An NTD containing a T65P mutation, which causes a hERG channel trafficking deficiency, was purified from E.coli. The mutant protein did not aggregate in gel filtration analysis and the amide cross peaks of its residues disappeared in an HSQC spectrum indicating the possibility of structural changes. A carbon chemical shift comparison of the residues with cross peaks in the HSQC spectrum showed no clear difference between the purified wild-type protein and the purified mutant. There were multiple conformations observed for the T65P mutant protein at high temperatures from HSQC experiments and a thermal stability assay showed that the T65P mutation reduced the thermal stability of NTD. This instability may affect protein folding or structural dynamics of other regions.

NMR structural study of the intracellular loop 3 of the serotonin 5-HT(1A) receptor and its interaction with calmodulin.

The serotonin (5-HT(1A)) receptor, a G-protein-coupled receptor (GPCR), plays important roles in serotonergic signaling in the central nervous system. The third intracellular loop (ICL3) of the 5-HT(1A) receptor has been shown to be important for the regulation of this receptor through interactions with proteins such as G-proteins and calmodulin. In this study, the ICL3 of 5-HT(1A) receptor was expressed in E. coli and purified. Gel filtration and mass spectrometry were used to confirm the molecular weight of the purified ICL3. Secondary structure analysis using circular dichroism (CD) demonstrated the presence of α-helical structures. Backbone assignment of ICL3 was achieved using three-dimensional experiments. A chemical shift index and Talos+ analysis showed that residues E326 to R339 form α-helical structure. Residues G256 to S269 of ICL3 were shown to be a novel region that has a molecular interaction with calmodulin in titration assays. Peptide derived from the ICL3 containing residues from G256 to S269 also showed molecular interaction with calmodulin.

NMR solution structure of the N-terminal domain of hERG and its interaction with the S4-S5 linker.

The human Ether-à-go-go Related Gene (hERG) potassium channel mediates the rapid delayed rectifier current (IKr) in the cardiac action potential. Mutations in the 135 amino acid residue N-terminal domain (NTD) cause channel dysfunction or mis-translocation. To study the structure of NTD, it was overexpressed and purified from Escherichia coli cells using affinity purification and gel filtration chromatography. The purified protein behaved as a monomer under purification conditions. Far- and near-UV, circular dichroism (CD) and solution nuclear magnetic resonance (NMR) studies showed that the purified protein was well-folded. The solution structure of NTD was obtained and the N-terminal residues 13-23 forming an amphipathic helix which may be important for the protein-protein or protein-membrane interactions. NMR titration experiment also demonstrated that residues from 88 to 94 in NTD are important for the molecular interaction with the peptide derived from the S4-S5 linker.