Identification and characterization of 3-substituted pyrazolyl esters as alternate substrates for cathepsin B: the confounding effects of DTT and cysteine in biological assays

Crystal structure of 2-[(5-amino-1-tosyl-1H-pyrazol-3-yl)-oxy]-1-(4-meth-oxy-phen-yl)ethan-1-one 1,4-dioxane monosolvate

In the structure of the title compound, C19H19N3O5S·C4H8O2, the two independent dioxane mol-ecules each display inversion symmetry. The pyrazole ring is approximately parallel to the aromatic ring of the oxy-ethanone group and approximately perpendicular to the tolyl ring of the sulfonyl substituent. An extensive system of classical and 'weak' hydrogen bonds connects the residues to form a layer structure parallel to (201), within which dimeric subunits are conspicuous; neighbouring layers are connected by classical hydrogen bonds to dioxanes and by 'weak' hydrogen bonds from Htol-yl donors.

Covalent Antiviral Agents

Nowadays, many viral infections have emerged and are taking a huge toll on human lives globally. Meanwhile, viral resistance to current drugs has drastically increased. Hence, there is a pressing need to design potent broad-spectrum antiviral agents to treat a variety of viral infections and overcome viral resistance. Covalent inhibitors have the potential to achieve both goals owing to their biochemical efficiency, prolonged duration of action, and the capability to inhibit shallow, solvent-exposed substrate-binding domains. In this chapter, we review the structures, activities, and inhibition mechanisms of covalent inhibitors against severe acute respiratory syndrome coronavirus 2, dengue virus, enterovirus, hepatitis C virus, human immunodeficiency virus, and influenza viruses. We also discuss the application of in silico study in covalent inhibitor design.

Crystal structure of ethyl 2-(3-amino-5-oxo-2-tosyl-2,5-di-hydro-1H-pyrazol-1-yl)acetate

In the title compound, C14H17N3O5S, the five-membered ring is essentially planar. The substituents at the nitro-gen atoms subtend a C-N-N-S torsion angle of -95.52 (6)°. The amino group forms an intra-molecular hydrogen bond to a sulfonyl oxygen atom; two inter-molecular hydrogen bonds from the amino group, to the other S=O group and to the oxo substituent, form a layer structure parallel to the ab plane. The structure determination confirms that the title compound is N- rather than O-alkyl-ated.

Design and Synthesis of a New Class of Pyridine-Based N-Sulfonamides Exhibiting Antiviral, Antimicrobial, and Enzyme Inhibition Characteristics

A new strategy for designing and assembling a novel class of functionalized pyridine-based benzothiazole and benzimidazole incorporating sulfonamide moieties was developed. The synthesis was carried out by reacting N-cyanoacetoarylsulfonylhydrazide with various electrophiles such as 2-(benzo[d]thiazol-2-yl)-3,3-bis(alkylthio)acrylonitriles and 2-(benzo[d]imidazol-2-yl)-3,3-bis(methylthio)-acrylonitriles, as well as 2-ethoxyl acrylonitrile derivatives. The synthesized compounds were tested for their antiviral and antimicrobial potency. Two of the synthesized compounds, 15c and 15d, showed more than 50% viral reduction against HSV-1 and CBV4, with significant IC₅₀ and CC₅₀ values. The two potent compounds 15c and 15d have also shown inhibitory activity against Hsp90α protein with IC₅₀ values of 10.24 and 4.48 μg/mL, respectively. A combination of 15c and 15d with acyclovir has led to IC₅₀ values that are lower than that of acyclovir alone. Molecular modeling studies were used to identify the interactions between the 15c and 15d compounds and the active site of Hsp90α enzyme. The antimicrobial investigation of the new compounds has also shown that 8b and 15d exhibited a higher inhibition zone (IZ) than sulfadiazine and gentamicin against Klebsiella pneumonia, whereas 9a showed higher IZ than ampicillin against Staphylococcus aureus. According to the enzyme assay study on dihydrofolate reductase, 9a was shown to be the most potent compound among all examined compounds.

Crystal structure of ethyl 2-(5-amino-1-benzene-sulfonyl-3-oxo-2,3-di-hydro-1H-pyrazol-2-yl)acetate

In the title compound, C13H15N3O5S, the two rings face each other in a 'V' form at the S atom, with one N-H⋯O=S and one C-H⋯O=S contact from the pyrazolyl substituents to the sulfonyl group. Two classical hydrogen bonds from the amine group, one of the form N-H⋯O=S and one N-H⋯O=Coxo, link the mol-ecules to form layers parallel to the bc plane.

Therapeutic Efficacy of Nyctanthes arbor-tristis Flowers to Inhibit Proliferation of Acute and Chronic Primary Human Leukemia Cells, with Adipocyte Differentiation and in Silico Analysis of Interactions between Survivin Protein and Selected Secondary Metabolites

Although the antidiabetic efficacy of Nyctanthes arbor-tristis flowers has been reported, antiproliferative and anti-obesity activities are yet to be explored. We examined the anti-obesity and antiproliferative potentials of different fractions (hexane, chloroform, ethyl acetate, methanol) of N. abor-tristis flower extract for the first time using 3T3-L1 cells, primary peripheral blood mononuclear cells (PBMC) isolated from healthy and adult acute myeloid (AML) and chronic lymphocytic leukemia (CLL) patients, recombinant Jurkat T cells, and MCF7 cell lines. The in vitro hypoglycemic activity was evaluated using the inhibition of α-amylase enzyme and glucose uptake by yeast cells. The percentage glucose uptake and α-amylase inhibitory activity increased in a dose-dependent manner in the crude and the tested fractions (hexane and ethyl acetate). Inhibition of the 3T3-L1 cells’ differentiation was observed in the ethyl acetate and chloroform fractions, followed by the hexane fraction. Antiproliferative analyses revealed that Nyctanthes exerted a high specific activity against anti-AML and anti-CLL PBMC cells, especially by the hexane and ethyl acetate fractions. The gas chromatography/mass spectrometry analysis indicated the presence of 1-heptacosanol (hexane fraction), 1-octadecene (hexane and chloroform fractions), and other organic compounds. Molecular docking demonstrated that phenol,2,5-bis(1,1-dimethylethyl) and 4-hydroxypyridine 1-oxide compounds showed specificity toward survivin protein, indicating the feasibility of N. abor-tristis in developing new drug leads against leukemia.

Synthesis, characterization, and antimicrobial evaluation of novel 5-benzoyl-N-substituted amino- and 5-benzoyl-N-sulfonylamino-4-alkylsulfanyl-2-pyridones

The present research describes the synthesis of novel 5-benzoyl-N-substituted-amino- and 5-benzoyl-N-sulfonylamino-4-alkylsulfanyl-2-pyridones 5a–c and 6a–c via the reaction of 2-benzoyl-3,3-bis(alkylthio)acrylonitriles 2a–c with N-cyanoacetohydrazide 3 and cyanoaceto-N-phenylsulfonylhydrazide 4, respectively. Also, the reactivity of the compounds 5a–c toward hydrazine hydrate to give product 1H-pyrazolo[4,3-c]pyridine derivative 7 was studied. In addition, the reactivity of the 2a–c toward 1-cyanoacetyl-4 arylidenesemicarbazides 8a–c afforded 3,5-dihydro[1,2,4]triazolo[1,5-a]pyridine-6-carbonitrile derivatives (12–14)a–c, which reacted with hydrazine hydrate to give 3H-pyrazolo[4,3-c][1,2,4]triazolo[1,5-a]pyridine-6-carbonitrile derivatives 15a–c. The structures of the new products were characterized based on ¹H nuclear magnetic resonance, ¹³C nuclear magnetic resonance, infrared, mass-spectroscopy, and elemental analyses. The products were screened in vitro for their antibacterial and antifungal activity properties.

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.

True symmetry or pseudosymmetry: 5-amino-1-(4-methylphenylsulfonyl)-4-pyrazolin-3-one and a comparison with its 1-phenylsulfonyl analogue

The title compound, C(10)H(11)N(3)O(3)S, (I), crystallizes as the NH tautomer. The two rings subtend an interplanar angle of 72.54 (4)°. An intramolecular hydrogen bond is formed from the NH(2) group to a sulfonyl O atom. The molecular packing involves layers of molecules parallel to the bc plane at x ≃ 0, 1 etc., with two classical linear hydrogen bonds (amino-sulfonyl and pyrazoline-carbonyl N-H...O) and a further interaction (amino-sulfonyl N-H...O) completing a three-centre system with the intramolecular contact. The analogous phenyl derivative, (II) [Elgemeie, Hanfy, Hopf & Jones (1998). Acta Cryst. C54, 136-138], crystallizes with essentially the same unit cell and packing pattern, but with two independent molecules that differ significantly in the orientation of the phenyl groups. The space group is P2(1)/c for (I) but P2(1) for (II), which is thus a pseudosymmetric counterpart of (I).

Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors

Cathepsin B has been found being responsible for many human diseases. Inhibitors of cathepsin B, a ubiquitous lysosomal cysteine protease, have been developed as a promising treatment for human diseases resulting from malfunction and over-expression of this enzyme. Through a high throughput screening assay, a set of compounds were found able to inhibit the enzymatic activity of cathepsin B. The binding structures of these active compounds were modeled through docking simulation. Three-dimensional (3D) quantitative structure-activity relationship (QSAR) models were constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on the docked structures of the compounds. Strong correlations were obtained for both CoMFA and CoMSIA models with cross-validated correlation coefficients (q²) of 0.605 and 0.605 and the regression correlation coefficients (r²) of 0.999 and 0.997, respectively. The robustness of these models was further validated using leave-one-out (LOO) method and training-test set method. The activities of eight (8) randomly selected compounds were predicted using models built from training set of compounds with prediction errors of less than 1 unit for most compounds in CoMFA and CoMSIA models. Structural features for compounds with improved activity are suggested based on the analysis of the CoMFA and CoMSIA contour maps and the property map of the protein ligand binding site. These results may help to provide better understanding of the structure-activity relationship of cathepsin B inhibitors and to facilitate lead optimization and novel inhibitor design. The multi-conformation method to build 3D QSAR is very effective approach to obtain satisfactory models with high correlation with experimental results and high prediction power for unknown compounds.

QSAR models for predicting cathepsin B inhibition by small molecules--continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules

Cathepsin B is a potential target for the development of drugs to treat several important human diseases. A number of inhibitors targeting this protein have been developed in the past several years. Recently, a group of small molecules were identified to have inhibitory activity against cathepsin B through high throughput screening (HTS) tests. In this study, traditional continuous and binary QSAR models were built to classify the biological activities of previously identified compounds and to distinguish active compounds from inactive compounds for drug development based on the calculated molecular and physicochemical properties. Strong correlations were obtained for the continuous QSAR models with regression correlation coefficients (r²) and cross-validated correlation coefficients (q²) of 0.77 and 0.61 for all compounds, and 0.82 and 0.68 for the compound set excluding 3 outliers, respectively. The models were further validated through the leave-one-out (LOO) method and the training-test set method. The binary models demonstrated a strong level of predictability in distinguishing the active compounds from inactive compounds with accuracies of 0.89 and 0.94 for active and inactive compounds, respectively, in non-cross-validated models. Similar results were obtained for the cross-validated models. Collectively, these results demonstrate the models’ ability to discriminate between active and inactive compounds, suggesting that the models may be used to pre-screen compounds to facilitate compound optimization and to design novel inhibitors for drug development.

Structure-activity relationship and improved hydrolytic stability of pyrazole derivatives that are allosteric inhibitors of West Nile Virus NS2B-NS3 proteinase

West Nile Virus (WNV) is a potentially deadly mosquito-borne flavivirus which has spread rapidly throughout the world. Currently there is no effective vaccine against flaviviral infections. We previously reported the identification of pyrazole ester derivatives as allosteric inhibitors of WNV NS2B-NS3 proteinase. These compounds degrade rapidly in pH 8 buffer with a half life of 1-2h. We now report the design, synthesis and in vitro evaluation of pyrazole derivatives that are inhibitors of WNV NS2B-NS3 proteinase with greatly improved stability in the assay medium.

The identification, characterization and optimization of small molecule probes of cysteine proteases: experiences of the Penn Center for Molecular Discovery with cathepsin B and cathepsin L

During the pilot phase of the NIH Molecular Library Screening Network, the Penn Center for Molecular Discovery focused on a series of projects aimed at high throughput screening and the development of probes of a variety of protease targets. This review provides our medicinal chemistry experience with two such targets--cathepsin B and cathepsin L. We describe our approach for hit validation, characterization and triage that led to a critical understanding of the nature of hits from the cathepsin B project. In addition, we detail our experience at hit identification and optimization that led to the development of a novel thiocarbazate probe of cathepsin L.

Evaluation of an orthogonal pooling strategy for rapid high-throughput screening of proteases

Orthogonal pooling was evaluated as a strategy for the rapid screening of multiple cysteine and serine proteases against large compound libraries. To validate the method the human cysteine protease cathepsin B was screened against a library of 64,000 individual compounds and also against the same library mixed 10 compounds per well. The orthogonal pooling method used resulted in each compound being present in two wells, mixed with a different set of nine other compounds in each location. Thus hits were identified based on activity in both locations, avoiding the need for retesting of each component of active mixtures. Hits were tested in dose-response both in the dithiothreitol (DTT)-containing buffer used in the primary HTS and in buffer containing cysteine in place of DTT to rule out artifacts due to oxidative inactivation of the enzyme. Comparison of the confirmed actives from single-compound and mixture screening showed that mixture screening identified all of the actives from single-compound HTS. Based on these results the orthogonal pooling strategy has been used successfully to rapidly screen several cysteine and serine proteases.

Design, synthesis, and evaluation of inhibitors of cathepsin L: Exploiting a unique thiocarbazate chemotype

Recently, we identified a thiocarbazate that exhibits potent inhibitory activity against human cathepsin L. Since this structure represents a novel chemotype with potential for activity against the entire cysteine protease family, we designed, synthesized, and assayed a series of analogs to probe the mechanism of action, as well as the structural requirements for cathepsin L activity. Molecular docking studies using coordinates of a papain-inhibitor complex as a model for cathepsin L provided useful insights.

HTS identifies novel and specific uncompetitive inhibitors of the two-component NS2B-NS3 proteinase of West Nile virus

West Nile virus (WNV), a member of the Flavividae family, is a mosquito-borne, emerging pathogen. In addition to WNV, the family includes dengue, yellow fever, and Japanese encephalitis viruses, which affect millions of individuals worldwide. Because countermeasures are currently unavailable, flaviviral therapy is urgently required. The flaviviral two-component nonstructural NS2B-NS3 proteinase (protease [pro]) is essential for viral life cycle and, consequently, is a promising drug target. We report here the results of the miniaturization of an NS2B-NS3pro activity assay, followed by high-throughput screening of the National Institutes of Health's 65,000 compound library and identification of novel, uncompetitive inhibitors of WNV NS2B-NS3pro that appear to interfere with the productive interactions of the NS2B cofactor with the NS3pro domain. We anticipate that following structure optimization, the identified probes could form the foundation for the design of novel and specific therapeutics for WNV infection. We also provide the structural basis for additional species-selective allosteric inhibitors of flaviviruses.

Identification and synthesis of a unique thiocarbazate cathepsin L inhibitor

Library samples containing 2,5-disubstituted oxadiazoles were identified as potent hits in a high throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR) directed at discovering inhibitors of cathepsin L. However, when synthesized in pure form, the putative actives were found to be devoid of biological activity. Analyses by LC-MS of original library samples indicated the presence of a number of impurities, in addition to the oxadiazoles. Synthesis and bioassay of the probable impurities led to the identification of a thiocarbazate that likely originated via ring opening of the oxadiazole. Previously unknown, thiocarbazates (-)-11 and (-)-12 were independently synthesized as single enantiomers and found to inhibit cathepsin L in the low nanomolar range.