Design,structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease

Abstract  

Serine protease activity of the NS3 protein of Dengue virus is an important target of antiviral agents that interfere with the viral polyprotein precursor processing catalyzed by the NS3 protease (NS3pro), which is important for the viral replication and maturation. Recent studies showed that substrate-based peptidomimetics carrying an electrophilic warhead inhibit the NS2B-NS3pro cofactor-protease complex with inhibition constants in the low micromolar concentration range when basic amino acid residues occupy P₁ and P₂ positions of the inhibitor, and an aldehyde warhead is attached to the P₁. We have used computer-assisted combinatorial techniques to design, focus using the NS2B-NS3pro receptor 3D structure, and in silico screen a virtual library of more than 9,200 peptidomimetic analogs targeted around the template inhibitor Bz-Nle-Lys-Arg-Arg-H (Bz—benzoyl) that are composed mainly of unusual amino acid residues in all positions P₁–P₄. The most promising virtual hits were analyzed in terms of computed enzyme-inhibitor interactions and Adsorption, Distribution, Metabolism and Excretion (ADME) related physico-chemical properties. Our study can direct the interest of medicinal chemists working on a next generation of antiviral chemotherapeutics against the Dengue Fever towards the explored subset of the chemical space that is predicted to contain peptide aldehydes with NS3pro inhibition potencies in nanomolar range which display ADME-related properties comparable to the training set inhibitors.     

Binding of low molecular weight inhibitors promotes large conformational changes in the dengue virus NS2B-NS3 protease: fold analysis by pseudocontact shifts

The two-component dengue virus NS2B-NS3 protease (DEN NS2B-NS3pro) is an established drug target, but inhibitor design is hampered by the lack of a crystal structure of the protease in its fully active form. In solution and without inhibitors, the functionally important C-terminal segment of the NS2B cofactor is dissociated from DEN NS3pro ("open state"), necessitating a large structural change to produce the "closed state" thought to underpin activity. We analyzed the fold of DEN NS2B-NS3pro in solution with and without bound inhibitor by nuclear magnetic resonance (NMR) spectroscopy. Multiple paramagnetic lanthanide tags were attached to different sites to generate pseudocontact shifts (PCS). In the face of severe spectral overlap and broadening of many signals by conformational exchange, methods for assignment of (15)N-HSQC cross-peaks included selective mutation, combinatorial isotope labeling, and comparison of experimental PCSs and PCSs back-calculated for a structural model of the closed conformation built by using the structure of the related West Nile virus (WNV) protease as a template. The PCSs show that, in the presence of a positively charged low-molecular weight inhibitor, the enzyme assumes a closed state that is very similar to the closed state previously observed for the WNV protease. Therefore, a model of the protease built on the closed conformation of the WNV protease is a better template for rational drug design than available crystal structures, at least for positively charged inhibitors. To assess the open state, we created a binding site for a Gd(3+) complex and measured paramagnetic relaxation enhancements. The results show that the specific open conformation displayed in the crystal of DEN NS2B-NS3pro is barely populated in solution. The techniques used open an avenue to the fold analysis of proteins that yield poor NMR spectra, as PCSs from multiple sites in combination with model building generate powerful information even from incompletely assigned (15)N-HSQC spectra.     

Hepatitis C virus NS3 protease requires its NS4A cofactor peptide for optimal binding of a boronic acid inhibitor as shown by NMR

NMR spectroscopy was used to characterize the hepatitis C virus (HCV) NS3 protease in a complex with the 24 residue peptide cofactor from NS4A and a boronic acid inhibitor, Ac-Asp-Glu-Val-Val-Pro-boroAlg-OH. Secondary-structure information, NOE constraints between protease and cofactor, and hydrogen-deuterium exchange rates revealed that the cofactor was an integral strand in the N-terminal beta-sheet of the complex as observed in X-ray crystal structures. Based upon chemical-shift perturbations, inhibitor-protein NOEs, and the protonation state of the catalytic histidine, the boronic acid inhibitor was bound in the substrate binding site as a transition state mimic. In the absence of cofactor, the inhibitor had a lower affinity for the protease. Although the inhibitor binds in the same location, differences were observed at the catalytic site of the protease.     

Interaction of E2 and NS3 synthetic peptides of GB virus C/hepatitis G virus with model lipid membranes

The membrane-interacting properties of two potential epitopes of the GB virus C/Hepatitis G virus, located respectively at the regions (99-118) of the E2 structural protein and (440-460) of the NS3 non-structural protein were studied. Changes in the intrinsic fluorescence of Trp and Tyr residues after the addition of DPPC-LUV revealed that the peptide-membrane interaction was optimal above the gel-liquid crystalline transition temperature of the lipid. Differential scanning calorimetry studies showed that the E2 peptide incorporated into lipid bilayers perturbs the packing of lipids and affects their thermotropic properties. Moreover, the 20-mer structural peptide induced a slow leakage of vesicular contents at 55 degrees C.     

1-Aminocyclopropaneboronic acid: synthesis and incorporation into an inhibitor of hepatitis C virus NS3 protease

The previously unreported alpha,alpha-disubstituted 1-aminoboronate esters have potential utility in peptidomimetic design, particularly against serine protease targets. A concise synthesis of 1-aminocyclopropaneboronate pinanediol ester is reported, and a peptidyl derivative is shown to have modest affinity (K(i) = 1.6 microM) for hepatitis C NS3 protease.     

Synthesis of (1R,2S)-1-amino-2-vinylcyclopropanecarboxylic acid vinyl-ACCA) derivatives: key intermediates for the preparation of inhibitors of the hepatitis C virus NS3 protease

(1R,2S)-1-Amino-2-vinylcyclopropanecarboxylic acid (vinyl-ACCA) is a key building block in the synthesis of potent inhibitors of the hepatitis C virus NS3 protease such as BILN 2061, which was recently shown to dramatically reduce viral load after administration to patients infected with HCV genotype 1. We have developed a scalable process that delivers derivatives of this unusual amino acid in >99% ee. The strategy was based on the dialkylation of a glycine Schiff base using trans-1,4-dibromo-2-butene as an electrophile to produce racemic vinyl-ACCA, which was subsequently resolved using a readily available, inexpensive esterase enzyme (Alcalase 2.4L). Factors that affect diastereoselection in the initial dialkylation steps were examined and the conditions optimized to deliver the desired diastereomer selectively. Product inhibition, which was encountered during the enzymatic resolution step, initially resulted in prolonged cycle times. Enrichment of racemic vinyl-ACCA through a chemical resolution via diastereomeric salt formation or the use of forcing conditions in the enzymatic reaction both led to improvements in throughput and the development of a viable process. The chemistry described herein was scaled up to produce multikilogram quantities of this building block.     

Potent inhibitors of the hepatitis C virus NS3 protease: design and synthesis of macrocyclic substrate-based beta-strand mimics

The virally encoded NS3 protease is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. The design and synthesis of 15-membered ring beta-strand mimics which are capable of inhibiting the interactions between the HCV NS3 protease enzyme and its polyprotein substrate will be described. The binding interactions between a macrocyclic ligand and the enzyme were explored by NMR and molecular dynamics, and a model of the ligand/enzyme complex was developed.     

Design and synthesis of novel fluoro amino acids: synthons for potent macrocyclic HCV NS3 protease inhibitors

The Hepatitis C Virus (HCV) is a major health hazard and its infection is a leading cause of chronic liver disease world wide. In our efforts toward the discovery of a back up to our first clinical candidate, Boceprevir (SCH 503034), we approached the depeptidization of the molecule through macrocyclization. Herein we report the design and synthesis of fluoro amino acids with desired stereochemistry required for the synthesis of macrocyclic inhibitors with fluorine at various positions of the aliphatic chain. Biological activities of representative examples are also reported.     

Improved 2-nitrobenzenesulfenyl method: optimization of the protocol and improved enrichment for labeled peptides

We have developed the NBS (2-nitrobenzenesulfenyl) method, a quantitative proteome analysis method utilizing stable isotope labeling followed by mass spectrometry. The potential of this method was reported previously, and the procedure has now been further optimized. Here, we describe a procedure utilizing urea or guanidine hydrochloride as a protein denaturant, in conjunction with an improved chromatographic enrichment method for the NBS-labeled peptides using a phenyl resin column. By using this new protocol, both sample loss throughout the protocol and the elution of unwanted unlabeled peptides can be minimized, improving the efficiency of the analysis significantly.     

Olefin ring-closing metathesis as a powerful tool in drug discovery and development – potent macrocyclic inhibitors of the hepatitis C virus NS3 protease

Peptidomimetic inhibitors of the hepatitis C NS3 protease often exhibit poor biopharmaceutical properties. Structure modification of a substrate-based tripeptide into a β-strand 15-membered ring scaffold provided a new class of peptidomimetics that are significantly superior as drug candidates to their acyclic precursors. Tripeptide dienes composed of three unnatural amino acid residues with numerous chiral centers were efficiently converted to macrocyclic peptides, in high diastereomeric purity, using ring-closing metathesis (RCM). The conformation of the acyclic diene and the protocol for the RCM reaction were investigated and optimized extensively in order to achieve an efficient synthesis of potential therapeutic agents for the treatment of hepatitis C infections. These studies provided the fist small molecule (BILN 2061) that was clinically validated for the treatment of hepatitis C infection in man and opened the door to a plethora of new pre-clinical pharmaceutical agents that can be made in multi kilogram quantities using RCM chemistry.     

Microplate assay for determination of cathepsin D activity based on quantification of a specific and stable peptide released from hemoglobin: VV-hemorphin-7

Cathepsins are key enzymes in mediating turnover of cytosolic proteins. In the context of cancer progression, those most actively studied include cathepsins D and B which have been implicated in processes such as growth and metastasis of many types of cancer. For more than 10 years, their roles as tumor marker and prognostic indicators have been studied, especially in breast cancer. Most of the studies relating the role of cathepsin D in cancer used immunological detection methods to determine the level of enzyme but do not reflect enzyme activity. Moreover, one of the problems in understanding cathepsin D clinical studies is that immunoassays may employ antibodies against the different form of the antigen. As an alternative, this work describes an indirect method to assess the active form of cathepsin D based on ELISA quantification of a specific and stable product of hemoglobin hydrolysis: VV-hemorphin-7. The procedure described here allows a low detection limit (ca. 5×10⁻⁹ M) and thus can represent an original approach to evaluate cathepsin D activity in biological samples.     

alpha-Ketocarbonyl peptides: a general approach to reactive resin-bound intermediates in the synthesis of peptide isosteres for protease inhibitor screening on solid support.

alpha-Ketocarbonyl peptides were generated from peptide precursors on solid support via a metal-ion-catalyzed transamination. The reaction proceeded to completion within 2 h with glyoxylate as electrophile and copper(II) ions as catalyst in an aqueous acetate buffer at pH 5.5-6.0. The variety of naturally occurring alpha-amino acid substrates gave rise to a diverse set of differentially functionalized ketones. The highly reactive terminal ketocarbonyls were prone to aldol-type dimerization and could be transferred into stable moieties by oxime formation, reduction to the alcohol, or reductive amination, respectively. The alpha-ketocarbonyl peptides were efficient in nucleophilic addition of C-nucleophiles such as phosphono-ylides and allylsilanes.     

A precolumn derivatization high-performance liquid chromatographic method with improved sensitivity and specificity for the determination of astragaloside IV in Radix Astragali

A reversed-phase high-performance liquid chromatographic method is developed for the determination of astragaloside (AGS) IV, which is known as the active constituent of Radix Astragali. The method uses precolumn derivatization with benzoyl chloride to form the benzoyl ester of AGS IV quantitatively and is carried out with a wide-ranging concentration (0.004-0.080 mg/mL) of the derivatized AGS IV. The eluent consists of 90% methanol, 4% tetrahydrofuran, 6% water, and 0.2% triethylamine, with vitamin D3 added as the internal standard.     

Synthesis and resolution of diethyl (1S,2S)-1-amino-2-vinylcyclopropane-1-phosphonate for HCV NS3 protease inhibitors

We herein describe an efficient synthesis of optically active diethyl 1-amino-2-vinylcyclopropane-1-phosphonate (analogous to 1-amino-2-vinylcyclopropane-1-carboxylate). The racemic phosphonate diethyl ester was obtained from an imine derived from aminomethylphosphonate diester and trans-1,4-dibromo-2-butene. Crystallizations of the dibenzoyl-l-tartaric acid salt allowed for separation of enantiomers. The enantiomerically pure material was used to synthesize an extremely potent tripeptide phosphonate inhibitor of HCV NS3 protease. X-ray crystal structure of the inhibitor bound to the HCV NS3 protease confirmed the absolute stereochemistry of the title compound.     

(2R)- and (2S)-3-fluoroalanine and their N-methyl derivatives: synthesis and incorporation in peptide scaffolds

A convergent synthetic methodology has been developed to access both (2S)- and (2R)-3-fluoroalanine and their corresponding N-methyl analogues, in optically pure form, through a common oxazolidinone intermediate that can be obtained from L- or D-serine. In addition, a procedure for incorporation of these unnatural amino acids in peptide scaffolds is also disclosed herein that minimizes the occurrence of beta-elimination during amide bond formation. [reaction: see text]     

High-performance liquid chromatographic determination of 2',3'-didehydro-3'-deoxythymidine, a new anti-human immunodeficiency virus agent, in human plasma and urine.

Sensitive and selective high-performance liquid chromatographic techniques have been developed for the determination of 2'-3'-didehydro-3'-deoxythymidine, d4T (BMY-27857), in human plasma and urine. The methods had linear standard curves over the concentration ranges 0.025-25.0 and 0.5-100 micrograms/ml for the plasma and urine matrices, respectively. Both methods used solid-phase extraction for isolating d4T and the internal standard, thymidine oxetane, from the biological matrix. In addition, the analytical column, mobile phase, instrumentation and chromatographic conditions used for both methods were identical. The ultraviolet absorbance of the column effluent was monitored at 266 nm. Results of analysis of quality control samples indicated that the intra-assay precision values, as measured by percent relative standard deviation, were within 12 and 3%, and accuracy samples deviated less than 10 and 5% from nominal values for the plasma and urine assays, respectively.     

Photocatalytical reduction of disulphide bonds in peptides on Ag-loaded nano-TiO2 for subsequent derivatization and determination

We reported an alternative strategy to reduce disulphide bonds in peptides with Ag-nanoparticle loaded nano-TiO(2) (Ag/TiO(2)) under UV irradiation. The feasibility of this strategy was adequately demonstrated using the model peptides oxidized glutathione, vasopressin and insulin, which contain various disulphide bonds, as well as by its application to the determination of Cd-induced phytochelatins in Phaeodactylum tricornutum.     

Rational Design and Controlled Synthesis of V-Doped Ni3S2/NixPy Heterostructured Nanosheets for the Hydrogen Evolution Reaction

Rational construction of high-efficiency and low-cost catalysts is one of the most promising ways to produce hydrogen but remains a huge challenge. Herein, interface engineering and heteroatom doping were used to synthesize V-doped sulfide/phosphide heterostructures on nickel foam (V-Ni₃S₂/Ni_xP_y/NF) by phosphating treatment at low temperature. The incorporation of V can adjust the electronic structure of Ni₃S₂, expose more active sites, and protect the 3D structure of Ni foam from damage. Meanwhile, the heterogeneous interface formed between Ni₃S₂ and Ni_xP_y can provide abundant active sites and accelerate electron transfer. As a result, the V-Ni₃S₂/Ni_xP_y/NF nanosheet catalyst exhibits outstanding activity in the hydrogen evolution reaction (HER) with an extremely low overpotential of 90 mV at a current density of 10 mA cm⁻² and stable durability in alkaline solution, which exceeds those most of the previously reported Ni-based materials. This work shows that rational design by interfacial engineering and metal-atom incorporation has a significant influence for efficient hydrogen evolution.