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1.
Biochemistry ; 63(11): 1434-1444, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38780522

ABSTRACT

The active form of the murine urokinase-type plasminogen activator (muPA) is formed by a 27-residue disordered light chain connecting the amino-terminal fragment (ATF) with the serine protease domain. The two chains are tethered by a disulfide bond between C1CT in the disordered light chain and C122CT in the protease domain. Previous work showed that the presence of the disordered light chain affected the inhibition of the protease domain by antibodies. Here we show that the disordered light chain induced a 3.7-fold increase in kcat of the protease domain of muPA. In addition, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and accelerated molecular dynamics (AMD) were performed to identify the interactions between the disordered light chain and the protease domain. HDX-MS revealed that the light chain is contacting the 110s, the turn between the ß10- and ß11-strand, and the ß7-strand. A reduction in deuterium uptake was also observed in the activation loop, the 140s loop and the 220s loop, which forms the S1-specificty pocket where the substrate binds. These loops are further away from where the light chain seems to be interacting with the protease domain. Our results suggest that the light chain most likely increases the activity of muPA by allosterically favoring conformations in which the specificity pocket is formed. We propose a model by which the allostery would be transmitted through the ß-strands of the ß-barrels to the loops on the other side of the protease domain.


Subject(s)
Urokinase-Type Plasminogen Activator , Animals , Mice , Urokinase-Type Plasminogen Activator/metabolism , Urokinase-Type Plasminogen Activator/chemistry , Allosteric Regulation , Molecular Dynamics Simulation , Hydrogen Deuterium Exchange-Mass Spectrometry , Kinetics
2.
Phytochem Anal ; 35(1): 28-39, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37571866

ABSTRACT

INTRODUCTION: Numerous species of the Euphorbiaceae family, including Euphorbia maculata, Euphorbia humifusa, and Acalypha australis, have been used to manage bleeding disorders. However, few investigations have demonstrated their hemostatic potential, and their procoagulant compounds remain elusive. OBJECTIVE: This study aimed to determine the most active procoagulant extracts from the three species' crude extract (CE) and fractions in order to screen out the active compounds and to analyze their possible mechanisms of action. METHODS: An integrative approach, comprising prothrombin time and activated partial thromboplastin time evaluations and urokinase-type plasminogen activator (uPA) inhibitory assessment, followed by bio-affinity ultrafiltration paired with UPLC/QTOF-MS targeting uPA and docking simulations, was used. RESULTS: The extracts with highest procoagulant activity were the CE for both E. maculata (EMCE) and E. humifusa (EHCE) and the n-butanol fraction (NB) for A. australis (AANB). The most promising ligands, namely, isoquercetin, orientin, rutin, and brevifolin carboxylic acid, were selected from these lead extracts. All of these compounds exhibited pronounced specific binding values to the uPA target and showed tight intercalation with the crucial side chains forming the uPA active pocket, which may explain their mode of action. The activity validation substantiated their hemostatic effectivity in inhibiting uPA as they had better inhibition constant (Ki) values than the reference drug tranexamic acid. CONCLUSION: Collectively, the integrative strategy applied to these three species allowed the elucidation of the mechanisms underlying their therapeutic effects on bleeding disorders, resulting in the fast detection of four potential hemostatic compounds and their mode of action.


Subject(s)
Acalypha , Euphorbia , Euphorbiaceae , Hemostatics , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/metabolism , Euphorbiaceae/chemistry , Ultrafiltration , Chromatography, Liquid , Liquid Chromatography-Mass Spectrometry , Tandem Mass Spectrometry
3.
Proteins ; 92(1): 76-95, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37646459

ABSTRACT

Cell invasion is an important process in cancer progression and recurrence. Invasion and implantation of cancer cells from their original place to other tissues, by disabling vital organs, challenges the treatment of cancer patients. Given the importance of the matter, many molecular treatments have been developed to inhibit cancer cell invasion. Because of their low production cost and ease of production, peptides are valuable therapeutic molecules for inhibiting cancer cell invasion. In recent years, advances in the field of computational biology have facilitated the design of anti-cancer peptides. In our investigation, using computational biology approaches such as evolutionary analysis, residue scanning, protein-peptide interaction analysis, molecular dynamics, and free energy analysis, our team designed a peptide library with about 100 000 candidates based on A6 (acetyl-KPSSPPEE-amino) sequence which is an anti-invasion peptide. During computational studies, two of the designed peptides that give the highest scores and showed the greatest sequence similarity to A6 were entered into the experimental analysis workflow for further analysis. In experimental analysis steps, the anti-metastatic potency and other therapeutic effects of designed peptides were evaluated using MTT assay, RT-qPCR, zymography analysis, and invasion assay. Our study disclosed that the IK1 (acetyl-RPSFPPEE-amino) peptide, like A6, has great potency to inhibit the invasion of cancer cells.


Subject(s)
Receptors, Urokinase Plasminogen Activator , Urokinase-Type Plasminogen Activator , Humans , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/pharmacology , Urokinase-Type Plasminogen Activator/therapeutic use , Peptides/pharmacology , Neoplasm Invasiveness
4.
Bioorg Med Chem ; 95: 117499, 2023 11 15.
Article in English | MEDLINE | ID: mdl-37879145

ABSTRACT

The inhibition of human urokinase-type plasminogen activator (huPA), a serine protease that plays an important role in pericellular proteolysis, is a promising strategy to decrease the invasive and metastatic activity of tumour cells. However, the generation of selective small molecule huPA inhibitors has proven to be challenging due to the high structural similarity of huPA to other paralogue serine proteases. Efforts to generate more specific therapies have led to the development of cyclic peptide-based inhibitors with much higher selectivity against huPA. While this latter property is desired, the sparing of the orthologue murine poses difficulties for the testing of the inhibitor in preclinical mouse model. In this work, we have applied a Darwinian evolution-based approach to identify phage-encoded bicyclic peptide inhibitors of huPA with better cross-reactivity towards murine uPA (muPA). The best selected bicyclic peptide (UK132) inhibited huPA and muPA with Ki values of 0.33 and 12.58 µM, respectively. The inhibition appears to be specific for uPA, as UK132 only weakly inhibits a panel of structurally similar serine proteases. Removal or substitution of the second loop with one not evolved in vitro led to monocyclic and bicyclic peptide analogues with lower potency than UK132. Moreover, swapping of 1,3,5-tris-(bromomethyl)-benzene with different small molecules not used in the phage selection, resulted in an 80-fold reduction of potency, revealing the important structural role of the branched cyclization linker. Further substitution of an arginine in UK132 to a lysine resulted in a bicyclic peptide UK140 with enhanced inhibitory potency against both huPA (Ki = 0.20 µM) and murine orthologue (Ki = 2.79 µM). By combining good specificity, nanomolar affinity and a low molecular mass, the bicyclic peptide inhibitor developed in this work may provide a novel human and murine cross-reactive lead for the development of a potent and selective anti-metastatic therapy.


Subject(s)
Peptides , Urokinase-Type Plasminogen Activator , Mice , Humans , Animals , Urokinase-Type Plasminogen Activator/chemistry , Peptides/pharmacology , Peptides/chemistry , Serine Proteases , Peptides, Cyclic/pharmacology , Peptides, Cyclic/chemistry
5.
Cancer Lett ; 559: 216117, 2023 04 10.
Article in English | MEDLINE | ID: mdl-36889376

ABSTRACT

The fibrinolytic system is involved in many physiological functions, among which the important members can interact with each other, either synergistically or antagonistically to participate in the pathogenesis of many diseases. Plasminogen activator inhibitor 1 (PAI-1) acts as a crucial element of the fibrinolytic system and functions in an anti-fibrinolytic manner in the normal coagulation process. It inhibits plasminogen activator, and affects the relationship between cells and extracellular matrix. PAI-1 not only involved in blood diseases, inflammation, obesity and metabolic syndrome but also in tumor pathology. Especially PAI-1 plays a different role in different digestive tumors as an oncogene or cancer suppressor, even a dual role for the same cancer. We term this phenomenon "PAI-1 paradox". PAI-1 is acknowledged to have both uPA-dependent and -independent effects, and its different actions can result in both beneficial and adverse consequences. Therefore, this review will elaborate on PAI-1 structure, the dual value of PAI-1 in different digestive system tumors, gene polymorphisms, the uPA-dependent and -independent mechanisms of regulatory networks, and the drugs targeted by PAI-1 to deepen the comprehensive understanding of PAI-1 in digestive system tumors.


Subject(s)
Digestive System Neoplasms , Gastrointestinal Neoplasms , Humans , Digestive System Neoplasms/genetics , Inflammation , Plasminogen Activator Inhibitor 1/genetics , Plasminogen Activator Inhibitor 1/metabolism , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/genetics , Urokinase-Type Plasminogen Activator/metabolism
6.
Small ; 19(4): e2205260, 2023 01.
Article in English | MEDLINE | ID: mdl-36424174

ABSTRACT

Thrombotic diseases have a high rate of mortality and disability, and pose a serious threat to global public health. Currently, most thrombolytic drugs especially protein drugs have a short blood-circulation time, resulting in low thrombolytic efficiency. Therefore, a platelet membrane (Pm) cloaked nanotube (NT-RGD/Pm) biomimetic delivery system with enhanced thrombolytic efficiency is designed. Nanotubes (NT) with an excellent clot-penetration properties are used to load a protein thrombolytic drug urokinase (Uk). Platelet-targeting arginine glycine-aspartic peptide (RGD) is grafted onto the surface of the nanotubes (NT-RGD) prior to cloaking. Multiple particle tracking (MPT) technique and confocal laser scanning microscope (CLSM) analysis are applied and the results show that the nanotubes possess a strong penetration and diffusion capacity in thrombus clots. After the Pm cloaking on NT-RGD/Uk, it shows a thrombus microenvironmental responsive release property and the half-life of Uk is six times longer than that of free Uk. Most importantly, NT-RGD-Uk/Pm exhibits a 60% thrombolytic efficiency in the FeCl3 -induced thrombosis mouse model, and it is able to significantly reduce the bleeding side effects of Uk. This Pm-cloaked nanotube system is an effective and promising platform for the controlled and targeted delivery of drugs for the thrombus treatment.


Subject(s)
Thrombosis , Mice , Animals , Thrombosis/drug therapy , Fibrinolysis , Fibrinolytic Agents/pharmacology , Fibrinolytic Agents/therapeutic use , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/pharmacology , Urokinase-Type Plasminogen Activator/therapeutic use , Thrombolytic Therapy , Oligopeptides/therapeutic use
7.
Biophys J ; 121(20): 3940-3949, 2022 10 18.
Article in English | MEDLINE | ID: mdl-36039386

ABSTRACT

Nafamostat mesylate (NM) is a synthetic compound that inhibits various serine proteases produced during the coagulation cascade and inflammation. Previous studies showed that NM was a highly safe drug for the treatment of different cancers, but the precise functions and mechanisms of NM are not clear. In this study, we determined a series of crystal structures of NM and its hydrolysates in complex with a serine protease (urokinase-type plasminogen activator [uPA]). These structures reveal that NM was cleaved by uPA and that a hydrolyzed product (4-guanidinobenzoic acid [GBA]) remained covalently linked to Ser195 of uPA, and the other hydrolyzed product (6-amidino-2-naphthol [6A2N]) released from uPA. Strikingly, in the inactive uPA (uPA-S195A):NM structure, the 6A2N side of intact NM binds to the specific pocket of uPA. Molecular dynamics simulations and end-point binding free-energy calculations show that the conf1 of NM (6A2N as P1 group) in the uPA-S195A:NM complex may be more stable than conf2 of NM (GBA as P1 group). Moreover, in the structure of uPA:NM complex, the imidazole group of His57 flips further away from Ser195 and disrupts the stable canonical catalytic triad conformation. These results not only reveal the inhibitory mechanism of NM as an efficient serine protease inhibitor but also might provide the structural basis for the further development of serine protease inhibitors.


Subject(s)
Serine Proteinase Inhibitors , Urokinase-Type Plasminogen Activator , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/metabolism , Serine Proteinase Inhibitors/pharmacology , Serine Proteinase Inhibitors/chemistry , Serine Proteinase Inhibitors/metabolism , Serine Proteases , Imidazoles
8.
J Mater Chem B ; 9(41): 8659-8666, 2021 10 27.
Article in English | MEDLINE | ID: mdl-34608926

ABSTRACT

It is of great significance to find effective thrombolytic treatments due to the harm caused by thrombosis to human health. Based on the formation mechanism and complex microenvironment of a thrombus, polydopamine nanomotors (PDANMs) modified by the peptide of Arg-Gly-Asp (RGD) and loaded with urokinase (UK) were designed and prepared. A polydopamine (PDA) substrate has a good photothermal conversion effect. Under near-infrared (NIR) light irradiation, it can not only perform photothermal therapy (PTT) on thrombus, but also provide the driving force of PDANMs. Thrombolytic drug UK was loaded in the mesoporous structure of the PDA substrate and can be released at the thrombus site for drug therapy. The modified RGD can target the thrombus site, moreover, benefiting from the guanidine group of L-arginine in the peptide chain, and RGD can interact with reactive oxygen species (ROS) in the thrombus microenvironment to produce nitric oxide (NO). NO not only propelled the movement of nanomotors, but also promoted the growth of vascular endothelial cells to repair damaged blood vessels. The experimental results show that NIR and NO can provide dual driving sources for the nanosystem to achieve continuous and deep penetration of the drug-loaded nanomotors at the thrombus site, while realizing the photothermal and drug synergistic therapy to enhance the therapeutic effect and promote the growth of vascular endothelium cells. This kind of thrombus treatment strategy based on nanomotor drug delivery systems will provide good technical support for the clinical treatment of inferior vena cava thrombus.


Subject(s)
Indoles/pharmacology , Nanoparticles/chemistry , Polymers/pharmacology , Thrombosis/drug therapy , Vena Cava, Inferior/drug effects , Animals , Humans , Indoles/chemistry , Indoles/metabolism , Infrared Rays , Mice , Nanoparticles/metabolism , Oligopeptides/chemistry , Particle Size , Photothermal Therapy , Polymers/chemistry , Polymers/metabolism , Thrombosis/pathology , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/metabolism , Vena Cava, Inferior/pathology
9.
ACS Appl Mater Interfaces ; 13(21): 24453-24462, 2021 Jun 02.
Article in English | MEDLINE | ID: mdl-34008940

ABSTRACT

A dual-response (near-infrared, alternating magnetic field) multifunctional nanoplatform was developed based on urokinase plasminogen activators (uPA)-loaded metal-organic-framework (MOF)-derived carbon nanomaterials (referred to uPA@CFs below) for thrombolytic therapy. uPA loaded in mesoporous CFs could be released under the action of near-infrared (NIR)-mediated photothermy to achieve superficial thrombolysis. More importantly, with the assistance of alternating magnetic field (AMF), this system could also precisely heat the thrombosis in the deep tissue area. Quantitative experiments proved that the thrombolytic efficiency of this dual-response system at deep venous thrombosis was nearly 6 times than that of NIR alone. This is the first application that MOF-derived carbon nanomaterials in the field of targeted thrombolysis. To our delight, the MOF-derived carbon nanomaterials (CFs) not only maintained the drug-carrying capacity, but also endowed CFs with reliable magnetic targeting ability. More encouragingly, the CFs also showed extraordinary angiogenic performance, thus opening up the prospect of its clinical application.


Subject(s)
Carbon/chemistry , Metal-Organic Frameworks/chemistry , Nanoparticles/chemistry , Thrombolytic Therapy , Animals , Biocompatible Materials/chemistry , Human Umbilical Vein Endothelial Cells , Humans , Tissue Distribution , Urokinase-Type Plasminogen Activator/chemistry
10.
Prep Biochem Biotechnol ; 51(2): 191-200, 2021.
Article in English | MEDLINE | ID: mdl-32845203

ABSTRACT

Fibrinolytic enzymes have been considered promising for treatment and protection of healthy circulation due its ability to dissolve the fibrin in blood clots. Extractive fermentation is a not explored and efficient downstream process which segregates the desired product simultaneously in a fermentation process fast and economically. Extraction of fibrinolytic enzymes by Bacillus stearothermophilus DPUA 1729 employing conventional aqueous two-phase systems (ATPS) and extractive fermentation with ATPS was evaluated. The results of both systems were compared using a factorial design with PEG molar mass, PEG and salt concentrations as independent variables and extraction parameters as a response. In all conditions evaluated it was observed a similar partitioning of fibrinolytic enzymes through the phases, both in conventional ATPS and extractive fermentation. Salt concentration and interaction among PEG and salt concentration influenced in the partition coefficient. The fibrinolytic activity was determined by hydrolysis of fibrin in plate using the extract of one condition from extractive fermentation. The zone degradation presented a diameter of 7.03 ± 0.94 mm. In conclusion, there was no significant difference among the results obtained using conventional ATPS and extractive fermentation, however, the second one presents more advantages and can integrate production and extraction in one single step, reducing the costs.


Subject(s)
Fermentation , Geobacillus stearothermophilus/metabolism , Peptide Hydrolases/metabolism , Thrombosis/enzymology , Animals , Fibrinolysis , Hydrolysis , Microbial Sensitivity Tests , Polyethylene Glycols , Rats , Rats, Wistar , Software , Soy Foods , Sulfates , Thrombosis/drug therapy , Tissue Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/chemistry , Water
11.
Biochim Biophys Acta Proteins Proteom ; 1869(2): 140562, 2021 02.
Article in English | MEDLINE | ID: mdl-33221341

ABSTRACT

Affinity maturation of U33, a recombinant Fab inhibitor of uPA, was used to improve the affinity and the inhibitory effect compared to the parental Fab. Arginine scanning of the six CDR loops of U33 was done to identify initial binding determinants since uPA prefers arginine in its primary substrate binding pocket. Two CDR loops were selected to create an engineered affinity maturation library of U33 that was diversified around ArgL91 (CDR L3) and ArgH52 (CDR H2). Biopanning of the randomized U33 library under stringent conditions resulted in eight Fabs with improved binding properties. One of the most potent inhibitors, AB2, exhibited a 13-fold decrease in IC50 when compared to U33 largely due to a decrease in its off rate. To identify contributions of interfacial residues that might undergo structural rearrangement upon interface formation we used X-ray footprinting and mass spectrometry (XFMS). Four residues showed a pronounced decrease in solvent accessibility, and their clustering suggests that AB2 targets the active site and also engages residues in an adjacent pocket unique to human uPA. The 2.9 Å resolution crystal structure of AB2-bound to uPA shows a binding mode in which the CDR L1 loop inserts into the active site cleft and acts as a determinant of inhibition. The selectivity determinant of this binding mode is unlike previously identified inhibitory Fabs against uPA related serine proteases, MTSP-1, HGFA and FXIa. CDRs H2 and L3 loops aid in interface formation and provide critical salt-bridges to remodel loops surrounding the active site of uPA providing specificity and further evidence that antibodies can be potent and selective inhibitors of proteolytic enzymes.


Subject(s)
Recombinant Proteins/ultrastructure , Serine Proteases/chemistry , Serine Proteinase Inhibitors/chemistry , Urokinase-Type Plasminogen Activator/chemistry , Amino Acid Sequence/genetics , Humans , Quinuclidines/chemistry , Quinuclidines/pharmacology , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Serine Endopeptidases/chemistry , Serine Endopeptidases/ultrastructure , Serine Proteases/genetics , Serine Proteinase Inhibitors/pharmacology , Urokinase-Type Plasminogen Activator/antagonists & inhibitors , Urokinase-Type Plasminogen Activator/genetics
12.
Int J Mol Sci ; 21(19)2020 Oct 01.
Article in English | MEDLINE | ID: mdl-33019770

ABSTRACT

Ly-6/uPAR or three-finger proteins (TFPs) contain a disulfide-stabilized ß-structural core and three protruding loops (fingers). In mammals, TFPs have been found in epithelium and the nervous, endocrine, reproductive, and immune systems. Here, using heteronuclear NMR, we determined the three-dimensional (3D) structure and backbone dynamics of the epithelial secreted protein SLURP-1 and soluble domains of GPI-anchored TFPs from the brain (Lynx2, Lypd6, Lypd6b) acting on nicotinic acetylcholine receptors (nAChRs). Results were compared with the data about human TFPs Lynx1 and SLURP-2 and snake α-neurotoxins WTX and NTII. Two different topologies of the ß-structure were revealed: one large antiparallel ß-sheet in Lypd6 and Lypd6b, and two ß-sheets in other proteins. α-Helical segments were found in the loops I/III of Lynx2, Lypd6, and Lypd6b. Differences in the surface distribution of charged and hydrophobic groups indicated significant differences in a mode of TFPs/nAChR interactions. TFPs showed significant conformational plasticity: the loops were highly mobile at picosecond-nanosecond timescale, while the ß-structural regions demonstrated microsecond-millisecond motions. SLURP-1 had the largest plasticity and characterized by the unordered loops II/III and cis-trans isomerization of the Tyr39-Pro40 bond. In conclusion, plasticity could be an important feature of TFPs adapting their structures for optimal interaction with the different conformational states of nAChRs.


Subject(s)
Adaptor Proteins, Signal Transducing/chemistry , Antigens, Ly/chemistry , GPI-Linked Proteins/chemistry , Neuropeptides/chemistry , Receptors, Nicotinic/chemistry , Urokinase-Type Plasminogen Activator/chemistry , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Amino Acid Sequence , Antigens, Ly/genetics , Antigens, Ly/metabolism , Binding Sites , Cloning, Molecular , Elapid Venoms/chemistry , Elapid Venoms/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , GPI-Linked Proteins/genetics , GPI-Linked Proteins/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Humans , Hydrophobic and Hydrophilic Interactions , Models, Molecular , Neuropeptides/genetics , Neuropeptides/metabolism , Nuclear Magnetic Resonance, Biomolecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , Receptors, Nicotinic/genetics , Receptors, Nicotinic/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Urokinase-Type Plasminogen Activator/genetics , Urokinase-Type Plasminogen Activator/metabolism
13.
J Mol Graph Model ; 100: 107710, 2020 11.
Article in English | MEDLINE | ID: mdl-32829149

ABSTRACT

The emergence of SARS-CoV-2 has prompted a worldwide health emergency. There is an urgent need for therapeutics, both through the repurposing of approved drugs and the development of new treatments. In addition to the viral drug targets, a number of human drug targets have been suggested. In theory, targeting human proteins should provide an advantage over targeting viral proteins in terms of drug resistance, which is commonly a problem in treating RNA viruses. This paper focuses on the human protein TMPRSS2, which supports coronavirus life cycles by cleaving viral spike proteins. The three-dimensional structure of TMPRSS2 is not known and so we have generated models of the TMPRSS2 in the apo state as well as in complex with a peptide substrate and putative inhibitors to aid future work. Importantly, many related human proteases have 80% or higher identity with TMPRSS2 in the S1-S1' subsites, with plasminogen and urokinase-type plasminogen activator (uPA) having 95% identity. We highlight 376 approved, investigational or experimental drugs targeting S1A serine proteases that may also inhibit TMPRSS2. Whilst the presence of a relatively uncommon lysine residue in the S2/S3 subsites means that some serine protease inhibitors will not inhibit TMPRSS2, this residue is likely to provide a handle for selective targeting in a focused drug discovery project. We discuss how experimental drugs targeting related serine proteases might be repurposed as TMPRSS2 inhibitors to treat coronaviruses.


Subject(s)
Antiviral Agents/chemistry , Betacoronavirus/chemistry , Protease Inhibitors/chemistry , Serine Endopeptidases/chemistry , Small Molecule Libraries/chemistry , Amino Acid Sequence , Betacoronavirus/enzymology , COVID-19 , Catalytic Domain , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Drug Repositioning , Host-Pathogen Interactions , Humans , Ligands , Molecular Dynamics Simulation , Pandemics , Plasminogen/antagonists & inhibitors , Plasminogen/chemistry , Plasminogen/metabolism , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , SARS-CoV-2 , Sequence Alignment , Serine Endopeptidases/metabolism , Structural Homology, Protein , Structure-Activity Relationship , Thermodynamics , Urokinase-Type Plasminogen Activator/antagonists & inhibitors , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/metabolism
14.
Angew Chem Int Ed Engl ; 59(24): 9398-9402, 2020 06 08.
Article in English | MEDLINE | ID: mdl-32176815

ABSTRACT

Secondary structures tend to be recognizable because they have repeating structural motifs, but mimicry of these does not have to follow such well-defined patterns. Bioinformatics studies to match side-chain orientations of a novel hydantoin triazole chemotype (1) to protein-protein interfaces revealed it tends to align well across parallel and antiparallel sheets, like rungs on a ladder. One set of these overlays was observed for the protein-protein interaction uPA⋅uPAR. Consequently, chemotype 1 was made with appropriate side-chains to mimic uPA at this interface. Biophysical assays indicate these compounds did in fact bind uPAR, and elicit cellular responses that affected invasion, migration, and wound healing.


Subject(s)
Biomimetic Materials/chemistry , Proteins/chemistry , Biomimetic Materials/pharmacology , Protein Structure, Secondary , Triazoles/chemistry , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/metabolism
15.
Biosci Biotechnol Biochem ; 84(6): 1153-1159, 2020 Jun.
Article in English | MEDLINE | ID: mdl-32019421

ABSTRACT

Peptidic inhibitors of proteases are attracting increasing interest not only as drug candidates but also for studying the function and regulation mechanisms of these enzymes. Previously, we screened out a cyclic peptide inhibitor of human uPA [Formula: see text] and found that Ala substitution of P2 residue turns upain-1 to a substrate. To further investigate the effect of P2 residue on the peptide behavior transformation, we constructed upain-1-W3F, which has Phe replacement in the P2 position. We determined KD and Ki of upain-1-W3F and found that upain-1-W3F might still exist as an inhibitor. Furthermore, the high-resolution crystal structure of upain-1-W3F·uPA reveals that upain-1-W3F indeed stays as an intact inhibitor bind to uPA. We thus propose that the P2 residue plays a nonnegligible role in the conversion of upain-1 to a substrate. These results also proposed a strategy to optimize the pharmacological properties of peptide-based drug candidates by hydrophobicity and steric hindrance.Abbreviations : uPA: urokinase-type plasminogen activator; SPD: serine protease domain; S1 pocket: specific substrate-binding pocket.


Subject(s)
Peptides, Cyclic/chemistry , Saccharomycetales/genetics , Saccharomycetales/metabolism , Serine Proteinase Inhibitors/chemistry , Urokinase-Type Plasminogen Activator/chemistry , Catalytic Domain , Crystallography, X-Ray , Humans , Hydrogen Bonding , Hydrolysis , Protein Binding , Protein Structure, Secondary
16.
ACS Appl Mater Interfaces ; 12(3): 3445-3452, 2020 Jan 22.
Article in English | MEDLINE | ID: mdl-31922399

ABSTRACT

For effective treatment of ischemic cerebral thrombosis, it is of great significance to find a facile way in assessing the early damage of blood-brain barrier (BBB) after ischemic stroke during thrombolysis by integrating thrombolytic agents with fluorescent materials. Herein, a novel type of protein-carbon dot  nanohybrids is reported by the incorporation of carbon dots on thrombolytic agents through covalent linkage. Both in vitro and ex vivo fluorescence imaging measurements have demonstrated remarkable imaging effects in the brain of transient middle cerebral artery occlusion mice. Besides, the outstanding thrombolytic capacity of the nanohybrids was determined by in vitro thrombolysis tests. As one of the few reports of the construction of thrombolytic agents and fluorescent nanomaterials, the nanohybrids retain thrombolysis ability and fluorescent traceability simultaneously. It may provide a promising indicator for early BBB damage and thrombolytic agent distribution to estimate the possibility of symptomatic intracranial hemorrhage after thrombolysis and supply tissue window evidence for clinical thrombolytic agent application.


Subject(s)
Blood-Brain Barrier/drug effects , Carbon/chemistry , Fibrinolytic Agents/administration & dosage , Nanostructures/chemistry , Stroke/drug therapy , Theranostic Nanomedicine/methods , Urokinase-Type Plasminogen Activator/administration & dosage , Animals , Fibrinolytic Agents/chemistry , Humans , Male , Mice , Mice, Inbred BALB C , Stroke/diagnostic imaging , Theranostic Nanomedicine/instrumentation , Urokinase-Type Plasminogen Activator/chemistry
17.
Phys Chem Chem Phys ; 22(6): 3570-3583, 2020 Feb 14.
Article in English | MEDLINE | ID: mdl-31995079

ABSTRACT

Despite being recognized as a therapeutic target in the processes of cancer cell proliferation and metastasis for over 50 years, the interaction of the urokinase plasminogen activator uPA with its receptor uPAR still needs an improved understanding. High resolution crystallographic data (PDB ) of the uPA-uPAR binding geometry was used to perform quantum biochemistry computations within the density functional theory (DFT) framework. A divide to conquer methodology considering a mixed homogeneous/inhomogeneous dielectric model and explicitly taking water molecules into account was employed to obtain a large set of uPA-uPAR residue-residue interaction energies. In order of importance, not only were Phe25 > Tyr24 > Trp30 > Ile28 shown to be the most relevant uPA residues binding it to uPAR, but the residues Lys98 > His87 > Gln40 > Asn22 > Lys23 > Val20 also had significant interaction energies, which helps to explain published experimental mutational data. Furthermore, the results obtained with the uPA-uPAR in/homogeneous dielectric function show that a high dielectric constant value ε = 40 is adequate to take into account the electrostatic environment at the interface between the proteins, while using a smaller value of ε (<10) leads to an overestimation of the uPA-uPAR binding energy. Hot spots of the uPA-uPAR binding domain were identified and a quantum biochemistry description of the uPAR blockers uPA21-30 and cyclo21,29uPA21-29[(S21C;H29C)] was performed, demonstrating that cyclization improves the stability of mimetic peptides without compromising their binding energies to uPAR.


Subject(s)
Receptors, Urokinase Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/chemistry , Amino Acid Sequence , Amino Acids/chemistry , Density Functional Theory , Peptides, Cyclic/chemistry , Protein Binding , Protein Conformation , Static Electricity , Structure-Activity Relationship , Thermodynamics
18.
Ann Clin Lab Sci ; 49(6): 710-721, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31882421

ABSTRACT

The SLURP1 (secreted LY6/urokinase type plasminogen activator receptor related protein-1) belongs to the gene family of urokinase, a type of plasminogen activator receptor (uPAR). Mutations in the SLURP1 have been reported to cause serious genetic problems of skin, Mal De Meleda, and malignancies. With the advancement of computational tools, it became possible to predict the potential impact of gene variants on the structure and function of protein. Therefore, in present study, we aimed to perform in-silico analyses of the disease causing SLURP1 mutations using online tools. In-total, 21 variants occurring in coding and non-coding regions of SLURP1 were found from public databases. In curated data, we have found 57.14% (12/21) missense, 23.81% (5/21) splice site, 9.52% (2/21) nonsense, 4.76% (1/21) deletion, and 4.76% (1/21) frameshift mutations. Moreover, heterogeneity in genotypes and phenotypes, along with 7 hotspot points in SLURP1 has been noted. In-silico analyses of the subjected variants have depicted a range of pathogenicity by combinatorial predictions of different tools from being lowly to highly pathogenic. Thus, the present study paves a platform to link computational analyses of mutations for important regulatory genes that can be undertaken for their phenotypes and their correlation with the disease status in case control studies.


Subject(s)
Antigens, Ly/genetics , Keratoderma, Palmoplantar/genetics , Mutation , Urokinase-Type Plasminogen Activator/genetics , Amino Acid Substitution , Animals , Antigens, Ly/chemistry , Antigens, Ly/metabolism , Humans , Melanoma/genetics , Mutation Rate , Mutation, Missense , RNA Splice Sites , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/metabolism
19.
Cell Death Dis ; 10(10): 775, 2019 10 10.
Article in English | MEDLINE | ID: mdl-31601791

ABSTRACT

Uterine angiogenesis and vascular remodeling play critical roles in determing the normal menstrual cycle and successful pregnancy. Poor uterine angiogenesis usually results in pregnancy failure. Protein O-fucosyltransferase 1 (poFUT1) is the key enzyme responsible for O-fucosylated glycan biosynthesis on glycoproteins. However, the dynamic expression and regulation of poFUT1 on the uterine angiogenesis and vascular remodeling remain unknown. Here, we showed that the enlargement of the vascular lumen in the secretory phase was greater than that in the proliferative phase of the uterine endometrium during menstrual cycle; whereas there was a narrower vessel lumen and fewer blood vessels in the decidua from miscarriage patients than in that from healthy pregnancy women. Additionally, the expression of poFUT1 was increased in the uterine endometrium during the secretory phase compared with that in the proliferation phase, and its expression was decreased in the uterus of miscarriage patients compared with that of the healthy pregnancy women. Using hESCs and a mouse model, we demonstrated that poFUT1 increased the O-fucosylation on uPA, and activated of the RhoA signaling pathway, thus facilitating uterine angiogenesis and vascular remodeling. We also provide evidence that poFUT1 promotes hESCs angiogenesis by the decreased stemness of hESCs. These findings reveal a new insight into the uterine angiogenesis and vascular remodeling. The study suggests that poFUT1 could be seen as a novel potential diagnostic and therapeutic target for miscarriage.


Subject(s)
Abortion, Spontaneous/enzymology , Endometrium/blood supply , Endometrium/enzymology , Glucosyltransferases/metabolism , Neovascularization, Pathologic/enzymology , Urokinase-Type Plasminogen Activator/metabolism , Abortion, Spontaneous/metabolism , Animals , Endometrium/cytology , Endometrium/metabolism , Female , Fucosyltransferases/genetics , Fucosyltransferases/metabolism , Glucosyltransferases/genetics , Human Umbilical Vein Endothelial Cells , Humans , Male , Mice , Neovascularization, Pathologic/metabolism , Neovascularization, Physiologic/genetics , Pregnancy , Signal Transduction/physiology , Stromal Cells/enzymology , Stromal Cells/metabolism , Urokinase-Type Plasminogen Activator/chemistry , Vascular Remodeling/genetics , Vascular Remodeling/physiology , rhoA GTP-Binding Protein/metabolism
20.
ACS Appl Mater Interfaces ; 11(42): 38417-38428, 2019 Oct 23.
Article in English | MEDLINE | ID: mdl-31556584

ABSTRACT

Triple negative breast cancer (TNBC) is insensitive to either chemotherapy or endocrine therapy because of the powerful DNA reparation and the negative expression of surface antigens, which urgently claims for an effective approach to improve the prognosis. Herein, DNA repair blocker BRCA1 small interfering RNA (siRNA) was introduced with cisplatin (Pt) into the elaborately designed pH-sensitive shell-core platform to enhance the chemotherapeutic treatment effect by silencing the DNA repair related gene. In this platform, BRCA1 siRNA and Pt prodrug (Pro-Pt) were separately encapsulated in the porous outer shell and hydrophobic inner core with extremely high encapsulation efficiency and stability effectively preventing them from degradation during circulation. Suitable size and urokinase plasminogen activator analogues (uPA) with high affinity for the uPA receptor (uPAR) realized an excellent dual passive and active tumor targeting ability. Moreover, the exposed PEG hydrophilic chain prevented the nanoparticles (NPs) from precipitating by serum protein or inactivating by nuclease in the blood cycle. Most importantly, the degradable CaP (calcium ions and phosphate ions) shell with smart pH sensitivity would dissipate from NPs in the lysosomes to burst the lysosome membranes so as to guarantee the lysosomal escape and the sequential release of the siRNA and Pro-Pt where the BRCA1 siRNA blocked the DNA repairing pathway followed by reducing Pro-Pt to Pt for irreversible DNA damage. Hence, the uPA-SP@CaP NPs provided a promising strategy for high-efficiency treatment of TNBC along with bringing new hope for more patients.


Subject(s)
BRCA1 Protein/metabolism , DNA Damage/drug effects , Nanoparticles/chemistry , Prodrugs/pharmacology , RNA, Small Interfering/metabolism , Animals , BRCA1 Protein/antagonists & inhibitors , BRCA1 Protein/genetics , Calcium/chemistry , Cell Line, Tumor , Cisplatin/chemistry , Cisplatin/pharmacology , Female , Humans , Hydrogen-Ion Concentration , Hydrophobic and Hydrophilic Interactions , Mice , Mice, Inbred BALB C , Phosphates/chemistry , Porosity , Prodrugs/chemistry , Prodrugs/therapeutic use , RNA, Small Interfering/chemistry , Receptors, Urokinase Plasminogen Activator/genetics , Receptors, Urokinase Plasminogen Activator/metabolism , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/metabolism , Triple Negative Breast Neoplasms/pathology , Urokinase-Type Plasminogen Activator/chemistry , Urokinase-Type Plasminogen Activator/metabolism
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