Irreversible Inhibition of Serine Proteases – Design and In Vivo Activity of Diaryl α-Aminophosphonate Derivatives

Covalent activity-based probes for imaging of serine proteases

Serine proteases are one of the largest mechanistic classes of proteases. They regulate a plethora of biochemical pathways inside and outside the cell. Aberrant serine protease activity leads to a wide variety of human diseases. Reagents to visualize these activities can be used to gain insight into the biological roles of serine proteases. Moreover, they may find future use for the detection of serine proteases as biomarkers. In this review, we discuss small molecule tools to image serine protease activity. Specifically, we outline different covalent activity-based probes and their selectivity against various serine protease targets. We also describe their application in several imaging methods.

Targeted Library of Phosphonic-Type Inhibitors of Human Neutrophil Elastase

Despite many years of research, human neutrophil elastase (HNE) still remains an area of interest for many researchers. This multifunctional representative of neutrophil serine proteases is one of the most destructive enzymes found in the human body which can degrade most of the extracellular matrix. Overexpression or dysregulation of HNE may lead to the development of several inflammatory diseases. Previously, we presented the HNE inhibitor with kinact/KI value over 2,000,000 [M-1s-1]. In order to optimize its structure, over 100 novel tripeptidyl derivatives of α-aminoalkylphosphonate diaryl esters were synthesized, and their activity toward HNE was checked. To confirm the selectivity of the resultant compounds, several of the most active were additionally checked against the two other neutrophil proteases: proteinase 3 and cathepsin G. The developed modifications allowed us to obtain a compound with significantly increased inhibitory activity against human neutrophil elastase with high selectivity toward cathepsin G, but none toward proteinase 3.

Site-Selective Incorporation of a Functional Group into Lys175 in the Vicinity of the Active Site of Chymotrypsin by Using Peptidyl α-Aminoalkylphosphonate Diphenyl Ester-Derivatives

We previously reported that Lys175 in the region of the active site of chymotrypsin (Csin) could be site-selectively modified by using an N-hydroxy succinimide (NHS) ester of the peptidyl derivative containing 1-amino-2-ethylphenylphosphonate diphenyl ester [NHS-Suc-Ala-Ala-PheP(OPh)2]. In this study, the Lys175-selective modification method was expanded to incorporate functional groups into Lys 175 in Csin. Two types of peptidyl phosphonate derivatives with the dansyl group (Dan) as a functional molecule, Dan-β-Ala-[Asp(NHS) or Glu(NHS)]-Ala-Ala-(R)-PheP(OPh)2 (DanD and DanE, respectively), were synthesized, and their action was evaluated when modifying Lys175 in Csin. Ion-exchange chromatography (IEC), fluorescence spectroscopy, and LC-MS/MS were used to analyze the products from the reaction of Csin with DanD or DanE. By IEC and LC-MS/MS, the results showed that DanE reacted with Csin more effectively than DanD to produce the modified Csin (DanMCsin) bearing Dan at Lys175. DanMCsin exhibited an enzymatic activity corresponding to 1/120 of Csin against Suc-Ala-Ala-Phe-pNA. In addition, an effect of Lys175 modification on the access of the proteinaceous Bowman–Birk inhibitor to the active site of DanMCsin was investigated. In conclusion, by using a peptidyl derivative containing 1-amino-2-ethylphenylphosphonate diphenyl ester, we demonstrated that a functional group could be incorporated into Lys175 in Csin.

Cytotoxic Activity of α-Aminophosphonic Derivatives Coming from the Tandem Kabachnik–Fields Reaction and Acylation

Encouraged by the significant cytotoxic activity of simple α-aminophosphonates, a molecular library comprising phosphonoylmethyl- and phosphinoylmethyl-α-aminophosphonates, a tris derivative, and N-acylated species was established. The promising aminophosphonate derivatives were subjected to a comparative structure–activity analysis. We evaluated 12 new aminophosphonate derivatives on tumor cell cultures of different tissue origins (skin, lung, breast, and prostate). Several derivatives showed pronounced, even selective cytostatic effects. According to IC50 values, phosphinoylmethyl-aminophosphonate derivative 2e elicited a significant cytostatic effect on breast adenocarcinoma cells, but it was even more effective against prostatic carcinoma cells. Based on our data, these new compounds exhibited promising antitumor activity on different tumor types, and they might represent a new group of alternative chemotherapeutic agents.

Design, synthesis and biological evaluation of novel antipyrine based α-aminophosphonates as anti-Alzheimer and anti-inflammatory agent

Herein, a series of novel antipyrine based α-aminophosphonates derivatives were synthesized and characterized. The synthesized derivatives were subjected for in vitro cholinesterase inhibition, enzyme kinetic studies, protein denaturation assay, proteinase inhibitory assay and cell viability assay. For cholinesterase inhibition, the results inferred that the test compounds possess better AChE activity (0.46 to 6.67 µM) than BuChE (2.395 to 12.47 µM). Compound 4j inhibited both AChE and BuChE (IC₅₀ = 0.475 ± 0.12 µM and 2.95 ± 0.16 µM, respectively), implying that it serves as a dual AChE/BuChE inhibitor. Also, kinetic studies revealed that compound 4j exhibits mixed-type inhibition against both AChE and BuChE, with K_i values of 3.003 µM and 5.750 µM, respectively. Further, protein denaturation and proteinase inhibitory assays were used to test in vitro anti-inflammatory potential. It was found that compound 4o exhibited highest activity against protein denaturation (IC₅₀ = 42.64 ± 0.19 µM) and proteinase inhibition (IC₅₀ = 37.57 ± 0.19 µM) when compared to diclofenac. In addition, cell viability assay revealed that active compounds possess no cytotoxicity against N2a cell and RAW 264.7 macrophages. Finally, molecular docking experiments for AChE, BuChE, and COX-2 were conducted to better understand the binding modes of active compounds.Communicated by Ramaswamy H. Sarma.

Progress and Development of Carbazole Scaffold Based as Potential Anti- Alzheimer Agents Using MTDL Approach

Abstract:

Alzheimer’s is a neurodegenerative disease (NDs) found in old age people with associated most common symptom dementia. MTDLs (Multi-Target Direct Ligand strategy) is based on a combination of two or more bioactive pharmacophores into a single molecule and this phenomenon has received a great attention in the new era of modern drug discovery and emerging as a choice to treat this complex Alzheimer’s disease (AD). In last fifteen years, many research groups designed, and synthesized new carbazole integrated molecules linked with other bioactive pharmacophores like thiazoles, carvedilol, α- naphthylaminopropan-2-ol, tacrine, ferulic acid, piperazine, coumarin, chalcones, stilbene, benzyl piperidine, adamantane, quinoline, phthalocyanines, α-amino phosphonate, thiosemicarbazones, hydrazones, etc. derivatives using MTDLs approach to confront AD. The present review entails the scientific data on carbazole hybrids as potential Anti-Alzheimer activities from 2007 to 2021 that have shown potential anti-Alzheimer activities through multiple target pathways thereby promising hope for new drug development to confront AD.

Theoretical exploration on structures, bonding aspects and molecular docking of α-aminophosphonate ligated copper complexes against SARS-CoV-2 proteases

Recent years have witnessed a growing interest in the biological activity of metal complexes of α-aminophosphonates. Here for the first time, a detailed DFT study on five α-aminophosphonate ligated mononuclear/dinuclear CuII complexes is reported using the dispersion corrected density functional (B3LYP-D2) method. The electronic structures spin densities, FMO analysis, energetic description of spin states, and theoretical reactivity behaviour using molecular electrostatic potential (MEP) maps of all five species are reported. All possible spin states of the dinuclear species were computed and their ground state S values were determined along with the computation of their magnetic coupling constants. NBO analysis was also performed to provide details on stabilization energies. A molecular docking study was performed for the five complexes against two SARS-CoV-2 coronavirus protein targets (PDB ID: 6LU7 and 7T9K). The docking results indicated that the mononuclear species had a higher binding affinity for the targets compared to the dinuclear species. Among the species investigated, species I showed the highest binding affinity with the SARS-CoV-2 Omicron protease. NPA charge analysis showed that the heteroatoms of model species III had a more nucleophilic nature. A comparative study was performed to observe any variations and/or correlations in properties among all species.

X-ray Structure Determination of Naphthalen-2-yl 1-(Benzamido(diethoxyphosphoryl)methyl)-1H-1,2,3-triazole-4-carboxylate

We have previously published on a new triazolic phosphonic α-amino ester in position 4 on the triazole ring of a naphthalene ester. The aim of the present paper was to describe its crystallographic study by XRD. The crystal structure of naphthalen-2-yl 1-(benzamido(diethoxyphosphoryl)methyl)-1H-1,2,3-triazole-4-carboxylate was determined by single-crystal X-ray diffraction. This compound crystallizes in the monoclinic system, space group P21/c. The naphthalene system is almost planar and makes dihedral angles of 67.1(2)° and 63.9(2)° with the triazole ring and the phenyl cycle, respectively. The phosphorus atom is surrounded by three oxygen atoms and one carbon atom building a distorted tetrahedron. It is also noted, that one of the two ethyl groups is disordered. In the crystal, the molecules are connected through C-H…O and N-H…O hydrogen bonds to build dimers that are linked together by C-H…O hydrogen bonds, in addition to C-H…π interactions. The presence of an intramolecular hydrogen bond contributes to the stability of the molecular conformation by completing the S(5) cycle.

Synthesis, in silico studies and antibacterial assessment of α-amino phosphonates derivatives

The widespread of multi-resistant strains due to the lack of specific treatment and the propagation of infectious diseases requires all resources to remedy this scourge. This study is therefore aimed to assess the antibacterial activity of four synthetic α-Aminophosphonate 4(a-d). Methods: Firstly, α-Aminophosphonate has been synthesized and characterized, then molecular docking of these compounds 4(a-d) into the active binding site of Escherichia coli MurB enzyme (PDB Id: 1MBT) was performed to gain a comprehensive understanding of their biological activity. These compounds have been subjected to in vitro antibacterial screening against three multi-resistant strains E. coli, S. aureus, and L. monocytogenes. These compounds showed crucial antibacterial behavior against all studied strains. Thus, their docking estimation supported the in vitro results and showed that the 4c derivative has considerable binding energy towards the active site of Escherichia coli MurB. These findings provide critical information for the exploration of α-amino phosphonates as novel antibacterial agents.

Enantioselective Reductive Cyanation and Phosphonylation of Secondary Amides by Iridium and Chiral Thiourea Sequential Catalysis

The combination of transition-metal catalysis and organocatalysis increasingly offers chemists opportunities to realize diverse unprecedented chemical transformations. By combining iridium with chiral thiourea catalysis, direct enantioselective reductive cyanation and phosphonylation of secondary amides have been accomplished for the first time for the synthesis of enantioenriched chiral α-aminonitriles and α-aminophosphonates. The protocol is highly efficient and enantioselective, providing a novel route to the synthesis of optically active α-functionalized amines from the simple, readily available feedstocks. In addition, the reactions are scalable and the thiourea catalyst can be recycled and reused.

Activity-Based Probes to Utilize the Proteolytic Activity of Cathepsin G in Biological Samples

Neutrophils, migrating to the site of infection, are able to release serine proteases after being activated. These serine proteases comprise cathepsin G (CatG), neutrophil elastase protease 3 (PR3), and neutrophil serine protease 4 (NSP4). A disadvantage of the uncontrolled proteolytic activity of proteases is the outcome of various human diseases, including cardiovascular diseases, thrombosis, and autoimmune diseases. Activity-based probes (ABPs) are used to determine the proteolytic activity of proteases, containing a set of three essential elements: Warhead, recognition sequence, and the reporter tag for detection of the covalent enzyme activity–based probe complex. Here, we summarize the latest findings of ABP-mediated detection of proteases in both locations intracellularly and on the cell surface of cells, thereby focusing on CatG. Particularly, application of ABPs in regular flow cytometry, imaging flow cytometry, and mass cytometry by time-of-flight (CyTOF) approaches is advantageous when distinguishing between immune cell subsets. ABPs can be included in a vast panel of markers to detect proteolytic activity and determine whether proteases are properly regulated during medication. The use of ABPs as a detection tool opens the possibility to interfere with uncontrolled proteolytic activity of proteases by employing protease inhibitors.

Phosphonic Analogs of Alanine as Acylpeptide Hydrolase Inhibitors

Acylpeptide hydrolase is a serine protease, which, together with prolyl oligopeptidase, dipeptidyl peptidase IV and oligopeptidase B, belongs to the prolyl oligopeptidase family. Its primary function is associated with the removal of N-acetylated amino acid residues from proteins and peptides. Although the N-acylation occurs in 50-90 % of eukaryotic proteins, the precise functions of this modification remains unclear. Recent findings have indicated that acylpeptide hydrolase participates in various events including oxidized proteins degradation, amyloid β-peptide cleavage, and response to DNA damage. Considering the protein degradation cycle cross-talk between acylpeptide hydrolase and proteasome, inhibition of the first enzyme resulted in down-regulation of the ubiquitin-proteasome system and induction of cancer cell apoptosis. Acylpeptide hydrolase has been proposed as an interesting target for the development of new potential anticancer agents. Here, we present the synthesis of simple derivatives of (1-aminoethyl)phosphonic acid diaryl esters, phosphonic analogs of alanine diversified at the N-terminus and ester rings, as inhibitors of acylpeptide hydrolase and discuss the ability of the title compounds to induce apoptosis of U937 and MV-4-11 tumor cell lines.

Synthesis of carbazole based α-aminophosphonate derivatives: design, molecular docking and in vitro cholinesterase activity

A series of novel carbazole based α-aminophosphonate derivatives were synthesized under solvent-free condition, characterized and evaluated for their cholinesterase inhibition, enzyme kinetic inhibition, in-vitro cell viability using N2a cells, neuroprotective studies against H₂O₂-induced stress using N2a cells and antioxidant studies using DPPH radical activity. Test compounds displayed better AChE activity (0.475 to 7.781 µM) than BuChE (3.306 to 21.32 µM). Compound 4j was most potent derivative against AChE as well as BuChE with IC₅₀=0.475 ± 0.12 µM and IC₅₀=3.306 ± 0.21 µM respectively. Kinetic inhibition studies indicate that compound 4j exhibits mixed type inhibition against both enzymes which was supported by molecular docking studies. Cell viability studies showed that compounds did not induce any cytotoxic effect against N2a cells using MTT assay. Also, compound 4j, 4 s and 4r were subjected to H₂O₂-induced stress using N2a cells and were found to be protective in nature. ADME predictions were carried out to understand the pharmacokinetics behaviour.Communicated by Ramaswamy H. Sarma.

Efficient one-pot, three-component procedure to prepare new α-aminophosphonate and phosphonic acid acyclic nucleosides

An efficient one-pot three-component Kabachnik-Fields reaction of aldehydes (acyclic nucleosides), amines (or amino acid), and triethyl phosphite proceeded for the synthesis of aminophosphonates using natural phosphate coated with iodine (I₂@NP) as a catalyst. The novel α-aminophosphonate and phosphonic acid acyclic nucleosides were tested for their anti-HCV and anti-HIV activities. The molecular docking showed that the non-activity of these compounds could be due to the absence of hydrophobic pharmacophores.

Design, synthesis and evaluation of new chromone-derived aminophosphonates as potential acetylcholinesterase inhibitor

A series of novel N-substituted α-aminophosphonates-bearing chromone moiety were synthesized and evaluated for acetylcholinesterase (AChE), butyrylcholinesterase (BuChE) activities and antioxidant properties. Porcine pancreatic lipase was employed as a catalyst. Inhibitory activity against AChE ranged between 0.103 and 5.781 µM, whereas for BuChE, activities ranged between 8.619 and 18.789 µM. The results show that among the various synthesized compounds, strongest AChE inhibition was found for the compound containing aliphatic amine analogs, while in case of BuChE, aromatic amines showed better activity as compared to aliphatic amines. Compound 4j was found to be the most potent inhibitor of AChE with an IC₅₀ value of 0.103 ± 0.24 μM and inhibited AChE through mixed-type inhibition. Compound 4j was twofolds more potent than tacrine, 35-folds potent than galantamine and 50-folds potent than rivastigmine. Also, docking study revealed that compound 4j binds to both the peripheral anionic site and catalytic anionic site of AChE and BuChE. The antioxidant activities of synthesized compounds were performed against 2,2-diphenyl-1-picrylhydrazyl and hydrogen peroxide scavenging. DNA nicking activity of selected compounds also suggested that the compounds do not harm plasmid DNA pBR322. Compound 4j also showed significant DNA damage protection activity. Novel N-substituted α-aminophosphonates bearing chromone moiety were synthesized and evaluated for anti-acetylcholinesterase, anti-butyrylcholinesterase, antioxidant and DNA damage activities.

Cobalt Catalyzed C-P Bond Formation by Cross-Coupling of Boronic Acids with P(O)H Compounds in Presence of Zinc

In our current work, we have reported the first cobalt-catalyzed cross-coupling of arylboronic acid with alkyl/aryl phosphites under mild conditions. The reaction was carried out in the presence of zinc powder as an additive and ter-pyridine as a ligand. The use of non-precious cobalt salt makes the protocol advantageous, as it is inexpensive and more abundant than the previously used methods where precious metal salts (Pd and Pt) were used. The reaction has a wide substrate scope and the products were obtained in good yields.

Peptide and Pseudopeptide Bond Synthesis in Phosphorus Dipeptide Analogs

Peptide analogs modified with a phosphorus-based moiety (phosphonate, phosphonamidate, or phosphinate) have emerged as invaluable tools in fundamental and medicinal, mechanistic, and inhibitory studies of proteolytic enzymes and other catalytic proteins that process the amino acids and peptides. The first stages of the chemical synthesis of these compounds frequently involve formation of peptide or pseudopeptide bond between a suitably protected α-amino acid and an α-aminoalkyl phosphorus derivative. These preparative protocols are distinct from conventional solution and solid-phase peptide syntheses that have become routine and automatized. In the following chapter, we describe in details the methods and techniques utilized to perform this nonstandard coupling and to obtain P-terminal dipeptidyl phosphonates and pseudodipeptides containing the internal phosphonamidate or phosphinate linkages. Methods of products' purification, the deprotection conditions, and stability issues are also presented and discussed.

Two decades of recent advances of Ugi reactions: synthetic and pharmaceutical applications

Multicomponent reactions (MCRs) are powerful synthetic tools in which more than two starting materials couple with each other to form multi-functionalized compounds in a one-pot process, the so-called “tandem”, “domino” or “cascade” reaction, or utilizing an additional step without changing the solvent, the so-called a sequential-addition procedure, to limit the number of synthetic steps, while increasing the complexity and the molecular diversity, which are highly step-economical reactions. The Ugi reaction, one of the most common multicomponent reactions, has recently fascinated chemists with the high diversity brought by its four- or three-component-based isonitrile. The Ugi reaction has been introduced in organic synthesis as a novel, efficient and useful tool for the preparation of libraries of multifunctional peptides, natural products, and heterocyclic compounds with stereochemistry control. In this review, we highlight the recent advances of the Ugi reaction in the last two decades from 2000–2019, mainly in the synthesis of linear or cyclic peptides, heterocyclic compounds with versatile ring sizes, and natural products, as well as the enantioselective Ugi reactions. Meanwhile, the applications of these compounds in pharmaceutical trials are also discussed.

We highlight the recent advances of the Ugi reaction in the last two decades from 2000–2019, mainly in the synthesis of linear or cyclic peptides, heterocyclic compounds with versatile ring sizes, and natural products, as well as the enantioselective Ugi reactions.

Synthesis, structural studies and biological properties of some phosphono-perfluorophenylalanine derivatives formed by SNAr reactions

Several novel phosphono-perfluorophenylalanine derivatives, as mimetics of phenylalanine, were synthesized by subjecting diethyl (2-(perfluorophenyl)-1-(phenylamino)ethyl)-phosphonate to S_NAr reactions with different types of nucleophiles such as thiols, amines and phenols. The structure of the products was confirmed using spectroscopic and spectrometric techniques. For two compounds X-ray single crystal diffraction analysis and DFT investigations were performed providing information in regard to the preferable conformation, hydrogen bonds and other interactions. The antiproliferative potency of some of the new phosphono-perfluorophenylalanine derivatives obtained as well as representatives of previously synthesized perfluorophenyl phosphonate analogues of phenylalanine was studied on selected glioma cell lines. Preliminary evaluation of the compounds drug likeness was examined with respect to Lipinski's and Veber's rules, and showed that they meet the criteria perfectly. MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide) assay results demonstrated that the compounds exhibit moderate activity against the glioblastoma multiforme cell lines (T98G and U-118 MG). Moreover most of the studied S_NAr reaction products displayed significantly higher inhibitory activity against both cancer cell lines than the parent diethyl (2-(perfluorophenyl)-1-(phenylamino)ethyl)phosphonate.

Design, synthesis and biological evaluation of novel α-aminophosphonate oxadiazoles via optimized iron triflate catalyzed reaction as apoptotic inducers

α-aminophosphonate oxadiazoles (5a-m) were prepared in high yields by reacting of 1,3,4-oxadiazole acetohydrazide (3) with appropriate aldehydes and diethyl phosphite under Kabachnik-Fields conditions using Iron triflate as a catalyst. The reaction conditions were optimized using D-optimal experimental design. Possible reaction mechanisms were considered, and structures of the new products were based upon compatible elementary and spectroscopic evidence. In vitro antitumor activities of these compounds were evaluated against human cancer cell lines of colon (HCT116), breast (MCF7) and liver (HepG2) and compared with anticancer drug, Doxorubicin, employing standard MTT assay. Compounds 5i and 5l demonstrated good antiproliferative activities against HCT116 tumor cells comparable to doxorubicin with low cytotoxicity towards normal fetal colon cell (FHC). Additionally, their capacity to activate apoptosis cascade was studied in HCT116 cell line by investigating the activation of proteolytic caspases cascade, the levels of Cytochrome C, Bax and Bcl-2. Active caspase-3 level was enhanced by 6-8-folds in HCT116 cell line when stimulated with compounds 5i and 5l compared to the control. The level of Caspases 8 & 9 was also increased signifying that intrinsic and extrinsic pathways are both activated. They also induced Bax and down regulated Bcl-2 protein level in addition to over-expressing Cytochrome C level in HCT116 cell line. Also, HCT116 cell cycle was mainly arrested at the Pre-G1 and G2/M phases when treated with compounds 5i and 5l.

Recent Developments in Peptidyl Diaryl Phoshonates as Inhibitors and Activity-Based Probes for Serine Proteases

This review presents current achievements in peptidyl diaryl phosphonates as covalent, specific mechanism-based inhibitors of serine proteases. Along three decades diaryl phosphonates have emerged as invaluable tools in fundamental and applicative studies involving these hydrolases. Such an impact has been promoted by advantageous features that characterize the phosphonate compounds and their use. First, the synthesis is versatile and allows comprehensive structural modification and diversification. Accordingly, reactivity and specificity of these bioactive molecules can be easily controlled by appropriate adjustments of the side chains and the leaving groups. Secondly, the phosphonates target exclusively serine proteases and leave other oxygen and sulfur nucleophiles intact. Synthetic accessibility, lack of toxicity, and promising pharmacokinetic properties make them good drug candidates. In consequence, the utility of peptidyl diaryl phosphonates continuously increases and involves novel enzymatic targets and innovative aspects of application. For example, conjugation of the structures of specific inhibitors with reporter groups has become a convenient approach to construct activity-based molecular probes capable of monitoring location and distribution of serine proteases.

Chemoselective Synthesis of α-Amino-α-cyanophosphonates by Reductive Gem-Cyanation-Phosphonylation of Secondary Amides

A novel approach to α-amino-α-cyanophosphonates has been developed. The method features a Tf₂O-mediated reductive geminal cyanation/phosphonylation of secondary amides. Mild reaction conditions, high bond-forming efficiency, inexpensive readily available starting materials, and good to excellent yields with wide functional group compatibility constitute the main advantages of this method. The protocol can be run on a gram scale.

Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors

The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.

Phosphonate inhibitors of West Nile virus NS2B/NS3 protease

West Nile virus (WNV) is a member of the flavivirus genus belonging to the Flaviviridae family. The viral serine protease NS2B/NS3 has been considered an attractive target for the development of anti-WNV agents. Although several NS2B/NS3 protease inhibitors have been described so far, most of them are reversible inhibitors. Herein, we present a series of α-aminoalkylphosphonate diphenyl esters and their peptidyl derivatives as potent inhibitors of the NS2B/NS3 protease. The most potent inhibitor identified was Cbz-Lys-Arg-(4-GuPhe)^P(OPh)₂ displaying K_i and k₂/K_i values of 0.4 µM and 28 265 M⁻¹s⁻¹, respectively, with no significant inhibition of trypsin, cathepsin G, and HAT protease.

A BODIPY-Tagged Phosphono Peptide as Activity-Based Probe for Human Leukocyte Elastase

Human leukocyte elastase plays a crucial role in a variety of inflammatory disorders and represents an important subject of biomedical studies. The chemotype of peptidic phosphonates was employed for the design of a new activity-based probe for human leukocyte elastase. Its structure combines the phosphonate warhead with an adequate peptide portion and a BODIPY fluorophore with a clickable ethinylphenyl moiety at meso position. The probe 6 was assembled by copper-catalyzed alkyne-azide 1,3-dipolar cycloaddition. It was characterized as an active site-directed elastase inhibitor exhibiting a second-order rate constant of inactivation of 88400 M^-1s^-1. The suitability of 6 as a fluorescent probe for human leukocyte elastase was demonstrated by in-gel fluorescence analysis. Labeling experiments and inhibition data toward a panel of related proteases underlined the selectivity of the probe for the targeted leukocyte elastase.

Exploiting the S4-S5 Specificity of Human Neutrophil Proteinase 3 to Improve the Potency of Peptidyl Di(chlorophenyl)-phosphonate Ester Inhibitors: A Kinetic and Molecular Modeling Analysis

The neutrophilic serine protease proteinase 3 (PR3) is involved in inflammation and immune response and thus appears as a therapeutic target for a variety of infectious and inflammatory diseases. Here we combined kinetic and molecular docking studies to increase the potency of peptidyl-diphenyl phosphonate PR3 inhibitors. Occupancy of the S1 subsite of PR3 by a nVal residue and of the S4-S5 subsites by a biotinylated Val residue as obtained in biotin-VYDnV^P(O-C₆H₄-4-Cl)₂ enhanced the second-order inhibition constant k_obs/[I] toward PR3 by more than 10 times ( k_obs/[I] = 73000 ± 5000 M^-1 s^-1) as compared to the best phosphonate PR3 inhibitor previously reported. This inhibitor shows no significant inhibitory activity toward human neutrophil elastase and resists proteolytic degradation in sputa from cystic fibrosis patients. It also inhibits macaque PR3 but not the PR3 from rodents and can thus be used for in vivo assays in a primate model of inflammation.

Toolbox of Fluorescent Probes for Parallel Imaging Reveals Uneven Location of Serine Proteases in Neutrophils

Neutrophils, the front line defenders against infection, express four serine proteases (NSPs) that play roles in the control of cell-signaling pathways and defense against pathogens and whose imbalance leads to pathological conditions. Dissecting the roles of individual NSPs in humans is problematic because neutrophils are end-stage cells with a short half-life and minimal ongoing protein synthesis. To gain insight into the regulation of NSP activity we have generated a small-molecule chemical toolbox consisting of activity-based probes with different fluorophore-detecting groups with minimal wavelength overlap and highly selective natural and unnatural amino acid recognition sequences. The key feature of these activity-based probes is the ability to use them for simultaneous observation and detection of all four individual NSPs by fluorescence microscopy, a feature never achieved in previous studies. Using these probes we demonstrate uneven distribution of NSPs in neutrophil azurophil granules, such that they seem to be mutually excluded from each other, suggesting the existence of unknown granule-targeting mechanisms.

Inhibitors and Antibody Fragments as Potential Anti-Inflammatory Therapeutics Targeting Neutrophil Proteinase 3 in Human Disease

Proteinase 3 (PR3) has received great scientific attention after its identification as the essential antigenic target of antineutrophil cytoplasm antibodies in Wegener's granulomatosis (now called granulomatosis with polyangiitis). Despite many structural and functional similarities between neutrophil elastase (NE) and PR3 during biosynthesis, storage, and extracellular release, unique properties and pathobiological functions have emerged from detailed studies in recent years. The development of highly sensitive substrates and inhibitors of human PR3 and the creation of PR3-selective single knockout mice led to the identification of nonredundant roles of PR3 in cell death induction via procaspase-3 activation in cell cultures and in mouse models. According to a study in knockout mice, PR3 shortens the lifespan of infiltrating neutrophils in tissues and accelerates the clearance of aged neutrophils in mice. Membrane exposure of active human PR3 on apoptotic neutrophils reprograms the response of macrophages to phagocytosed neutrophils, triggers secretion of proinflammatory cytokines, and undermines immune silencing and tissue regeneration. PR3-induced disruption of the anti-inflammatory effect of efferocytosis may be relevant for not only granulomatosis with polyangiitis but also for other autoimmune diseases with high neutrophil turnover. Inhibition of membrane-bound PR3 by endogenous inhibitors such as the α-1-protease inhibitor is comparatively weaker than that of NE, suggesting that the adverse effects of unopposed PR3 activity resurface earlier than those of NE in individuals with α-1-protease inhibitor deficiency. Effective coverage of PR3 by anti-inflammatory tools and simultaneous inhibition of both PR3 and NE should be most promising in the future.