Plasminogen Kringle Research Articles

Anti-angiogenic activity of a novel angiostatin-like plasminogen fragment produced by a bacterial metalloproteinase

Tumor growth depends on angiogenesis, a process by which new blood vessel are formed from pre-existing normal blood vessels. Proteolytic fragments of plasminogen, containing varying numbers of plasminogen kringle domains, collectively known as angiostatin, are a naturally occurring inhibitor of angiogenesis and inhibit tumor growth. We have developed an “affinity-capture reactor” that enables a single-step method for the production/purification of an angiostatin-like plasminogen fragment from human plasma using an immobilized bacterial metalloproteinase. The resulting fragment, named BL-angiostatin, contains one or two glycosyl chains and the N-terminal PAN module, which are not present in canonical angiostatins tested for cancer treatment. BL-angiostatin inhibited angiogenesis in vitro at 20 nM and the growth of both allograft and human xenograft tumors as well as lung metastasis of primary tumors mice at 0.3–10 mg kg−1. Derivatives of BL angiostatin lacking the PAN module or the terminal sialic acids in the glycosyl chains showed reduced anti-angiogenic activity in vivo, suggesting a role for these functions in activity, possibly via conferring a pharmacokinetic advantage to BL angiostatin compared to recombinant angiostatin lacking both features. These results highlight the potential of BL-angiostatin for therapeutic applications.

Multiple effects of angiostatins in injured cornea

Prolonged inflammation and excessive neovascularization of the cornea due to severe injury can impair optical clarity and lead to vision impairment. Plasminogen kringle (K) fragments, known as angiostatins (AS), play a well-established role as inhibitors of neovascularization by suppressing pro-angiogenic signaling­. However, AS effects in the cornea, beyond inhibiting the angiogenesis, are still unexplored. In this study, we estimate the protective effect of two AS variants (K1-3 and K5) against alkali burn injury induced in rabbit and rat corneas. AS K1-3 in the single doses of 0.075 or 0.75 μg (0.1 or 1.0 μM, respectively) or 0.3 μg of AS K5 (1.0 μM) were applied locally as eye drops daily for 14 days after the injury. A significant regression of corneal vessels in-growth in injured eyes treated with AS was revealed. Western blot analysis of corneal tissue lysates revealed that injury-induced overexpression of protein markers­ of hypoxia (HIF-1α), angiogenesis (VEGF), tissue remodeling and fibrosis (MMP-9), autophagy (beclin-1) and endoplasmic reticulum stress (GRP-78) was significantly reduced under AS treatment. Besides, the level of tight junctions protein ZO-1 was shown to be up-regulated after the treatment of the damaged cornea with AS K1-3. Summarizing, our study uncovered novel biological functions of the kringle-containing plasminogen fragments indicating its beneficial effects during corneal healing in the experimental model of alkali burn. The data obtained can be helpful for the development of novel efficient formulations to manage complications of ocular surface injuries.

Molecular recognition and binding between human plasminogen Kringle 5 and α-chain of human complement component C3b by frontal chromatography and dynamics simulation

The binding and molecular recognition between α-chain of human complement C3b (α-chain of C3b) and human plasminogen Kringle 5 (Kringle 5) were studied and explored by frontal chromatography and dynamics simulation in the combination of bio-specific technologies. The specific interaction between the α-chain of C3b and Kringle 5 was initially confirmed by ligand blot and ELISA (Kd = 4.243×10−6 L/mol). Furthermore, the binding determination conducted via frontal chromatography showed that the presence of a single binding site between them, with the binding constant of 2.98 × 105 L/mol. Then the molecular recognition by dynamics simulation and molecular docking showed that there were 9 and 13 amino acid residues respective in the Kringle 5 and α-chain of C3b directly implicated in the binding and the main stabilizing forces were electrostatic force (-55.99 ± 11.82 kcal/mol) and Van der Waals forces (-42.70 ± 3.45 kcal/mol). Additionally, a loop structure (65–71) in Kringle 5 underwent a conformational change from a random structure to an α-helix and a loop structure (417–425) in α-chain of C3b was closer to the molecular center, both of them were more conducive to the binding between them. Meanwhile, the involvement of the lysine binding site of Kringle 5 played an important role in the binding process. In addition, the erythrocyte-antibody complement rosette assay substantiated that the presence of Kringle 5 hindered the transportation of α-chain of C3b to antigen-antibody complex in a dose-dependent manner. These findings collectively indicated that the α-chain of C3b is very likely a receptor protein for Kringle 5, which provides a methodology for other similar investigations and valuable insights into expansion of the pharmacological effects and potential application of Kringle 5 in immune-related diseases.

BIOMEDICAL APPLICATION OF K5 PLASMINOGEN FRAGMENT

Aim. Plasminogen kringle 5 is an endogenous angiogenic inhibitor. The purpose of the present review was to highlight the potential biomedical application of kringle 5 in the regulation of angiogenesis and tumor growth. Methods. Angiogenesis is a complex process that involves endothelial cell proliferation, migration, basement membrane degradation, and neovessel organization. Since the uncontrolled growth of new blood vessels causes the progression of many common diseases, first of all, oncological diseases, autoimmune disorders, neovascular damage of the eye, the use of angiostatins can be a promising pharmacotherapeutic approach to the prevention and adjuvant therapy of these pathological conditions. The advantages of angiostatins application are their non-toxicity even at high doses, non-immunogenicity, lack of tolerance of target cells to their action. Angiostatins comprise a group of kringle-containing proteolytically-derived fragments of plasminogen/plasmin, which act as potent inhibitory mediators of endothelial proliferation and migration. Among all known angiostatin species, isolated K5 plasminogen fragment was shown to display the most potent inhibitory activity against proliferation of endothelial cells via triggering multiple signaling pathways, which lead to cell death and resulting angiogenesis suppression. Results. Current literature data suggest that in addition to expressed and highly specific cytotoxicity in relation to endotheliocytes and some types of tumor cells, the kringle domain 5 of human plasminogen has other advantages as an antiangiogenic and antitumor regulator, including its specific inhibitory activity, which affects only activated, proliferating endothelial cells, and therefore is non-toxic to other types of normal cells. As an endogenous protein, which is formed in the human organism, K5 does not provoke an immune response. K5 as a small polypeptide molecule with a stable structure can be obtained as a recombinant protein in E. coli cells, and can also be used in pharmacokinetic systems of targeted delivery and sustained release. Conclusions. The prospect of successful use of K5 as a therapeutic agent to manage pathological processes associated with dysregulation of angiogenesis makes it necessary to develop and improve methods of its production and to further test its plausible pleiotropic biological activities.

Screening, characterization and specific binding mechanism of aptamers against human plasminogen Kringle 5

Plasminogen Kringle 5 is one of the most potent cytokines identified to inhibit the proliferation and migration of vascular endothelial cells. Herein, six aptamer candidates that specifically bind to Kringle 5 were generated by the systematic evolution of ligands by exponential enrichment (SELEX). After 10 rounds of screening against Kringle 5, a highly enriched ssDNA pool was sequenced and the representative aptamers were subjected to binding assays to evaluate their affinity and specificity. The preferred aptamer KG-4, which demonstrated a low dissociation constant (Kd) of ∼ 432 nM and excellent selectivity for Kringle 5. A conserved “motif” of eight bases located at the stem-loop intersection, common to the aptamer, was further confirmed as the recognition element for binding with Kringle 5. The bulge formed by the motif and depression on the lysine binding site of Kringle 5 were both located at the binding interface, and the “induced fit” between their structures played a central role in the recognition process. Kringle 5 interacts KG-4 primarily through enthalpy-driven van der Waals forces and hydrogen bond. The key nucleotides A34 and C35 at motif on KG-4 and the positively charged amino acids in the loop 1 and loop 4 regions on Kringle 5 play a major role in the interaction. Furthermore, KG-4 dose-dependently reduced the proliferation inhibition of vascular endothelial cells by Kringle 5 and had a blocking effect on the function of Kringle 5 in inhibiting migration and promoting apoptosis of vascular endothelial cells in vitro. This study put a new light on protein-aptamer binding mechanism and may provide insight into the treatment of ischemic diseases by target depletion of Kringle 5.

Investigation of binding mechanism for human plasminogen Kringle 5 with its potential receptor vWA1 domain in Cochlin by bio-specific technologies and molecular dynamic simulation

Given the significant clinical potential of human plasminogen Kringle 5 on tumours, it is crucial to seek its receptors for a thorough comprehension of its physiological functions and mechanism. Eleven candidates have been screened out in our previous works. In the present work, we further inquired whether the candidate, von Willebrand factor type A domain 1 in coagulation factor C homology protein (abbr. vWA1), was a potential receptor of Kringle 5, and investigated their binding mechanism by bio-specific experiments, frontal affinity analysis (FA), and molecular dynamic simulation (MDS). After the potential was validated by bio-specific experiments, the FA results stated that vWA1 exhibited a strong interaction towards Kringle 5 in the proportion of 1:1 with the binding constant of 4.18 × 104 L/mol. The MDS results showed that the binding was mainly driven by electrostatic and Van der Waals forces and occurred spontaneously, during which vWA1 and Kringle 5 mutually fit each other by conformational changing into more flexible and suitable structures including fluctuations for five loops and partial transformation into a random coil for α6-helix in vWA1. Moreover, lysine binding site Leu71-Tyr74 was speculated responsible for Kringle 5 in binding and Tyr72 to be the key amino acid residue. In short, this work not only confirmed vWA1 as a potential Kringle 5 receptor but also provided valuable information on the detailed binding, facilitating the application development of Kringle 5 in regulating immune or inhibiting tumour migration through vWA1.

Abstract 530: Identification Of The Specific Residue In Apolipoprotein(a) Responsible For Mediating Covalent Attachment Of Oxidized Phospholipids

Oxidized phospholipids (oxPL) are highly inflammatory molecules that are linked to atherogenesis. Previously, Lp(a) was identified as the major carrier of oxPL in human plasma, with the majority of the oxPL being covalently associated to its apolipoprotein(a) (apo(a)) component. Earlier work by our group identified the Kringle (K) IV 10 domain of apo(a) as the site of oxPL binding; additionally, mutation of the strong lysine binding site (sLBS) in this domain eliminated oxPL addition. However, the specific residue(s) in apo(a) that bind oxPL remain elusive. In this study, we used site-directed mutagenesis of KIV 10 to identify the key residue of apo(a) involved in covalent attachment of oxPL and induction of inflammatory responses in vitro . Specifically, two residues in KIV 10 capable of binding oxPL by a Michael addition reaction (His 31 and 33) were identified as the probable sites of attachment. We mutagenized the residues to aspartic acid (Asp) and asparagine (Asn), respectively, based on the presence of these residues at these positions in plasminogen kringles. Six-kringle (6K) apo(a) variants harbouring these mutations were expressed in human embryonic kidney 293 cells and purified using lysine-Sepharose chromatography. Covalent oxPL modification of each apo(a) variant was assessed by E06 immunoblotting. Wild-type (WT) 6K and 6KHis31Asp were detected by E06 whereas 6KHis33Asn and 6KAsp56Ala (the LBS mutant) were not. Next, THP-1 macrophages were treated for 4 hours with 300 nmol/L of WT 6K apo(a), 6KHis33Asn, or 6KAsp56Ala. Expression of mRNA encoding the pro-inflammatory cytokine IL-8 by THP-1 cells was measured with quantitative real-time PCR. Relative to control, WT 6K apo(a) treatment of THP-1 cells significantly increased expression of IL8 (2.32-fold; p<0.001). Treatment of THP-1 cells with 6KHis33Asn or 6KAsp56Ala apo(a) did not significantly affect IL8 expression. We have thus identified the site of covalent attachment of oxPL to apo(a) as His33 in KIV 10 and we demonstrate that apo(a)-induced inflammatory responses in macrophages are abolished when oxPL binding is prevented through mutation of this residue. These findings provide avenues for development of therapeutics to potentially mitigate Lp(a)-mediated atherogenesis.

Abstract 410: Lipoprotein(a) And Apolipoprotein(a) Inhibit Lysis Of Human Thrombi Formed From Whole Blood Under Conditions Of Flow

The apolipoprotein(a) (apo(a)) component of Lp(a) is homologous to the proenzyme plasminogen, containing domains which are highly similar to plasminogen kringle (K) 4, followed by sequences that closely resemble the K5 and protease domains of plasminogen. Due to key amino acid substitutions/deletions, the protease (P) domain of apo(a) is catalytically inactive. It has been hypothesized that by competing for binding to fibrin, apo(a) can inhibit plasminogen activation and hence fibrinolysis, thereby leading to a prothrombotic role for Lp(a) in the vasculature. Although previous studies have shown inhibition by apo(a), but not Lp(a), of fibrinolysis in an ex vivo clot lysis assay, the ability of Lp(a) to inhibit lysis of clots formed from whole blood under conditions of flow that more closely resemble arterial thrombi in vivo has not been assessed. In the current study, whole blood was collected from a human donor with low Lp(a) levels, recalcified, and rotated in a Chandler loop device at 30 rpm for 90 minutes. Blood in the closed loops was supplemented with fluorescently labelled fibrinogen, and 0 or 250 nmol/L of purified plasma-derived Lp(a), 17-kringle (17K) recombinant apo(a) or a 17KΔP apo(a) variant lacking the protease-like domain. Interestingly, this protease-like domain has been shown to mediate lysine-dependent binding of apo(a) to plasminogen. Resultant thrombi were exposed to tPA and clot lysis was measured as release of fluorescent fibrinogen over time in a fluorescent plate reader. The addition of 250 nmol/L Lp(a) significantly decreased clot lysis by up to 15% compared to control (p<0.05). On the other hand, 250 nmol/L 17K apo(a) markedly reduced clot lysis by up to 48% relative to control (p<0.01). 17KΔP apo(a), however, did not affect clot lysis in this system. Our findings show that Lp(a) impedes lysis of human clots formed from whole blood under flow conditions, albeit with a much lower potency than 17K apo(a). Interestingly, our results indicate that the antifibrinolytic effect of apo(a) is dependent on the presence of the inactive protease domain, revealing the importance of the apo(a)-plasminogen interaction. These findings suggest that markedly elevated plasma Lp(a) levels might predispose thrombotic events in vivo .

Structural Characterization of Haemophilus influenzae Enolase and Its Interaction with Human Plasminogen by In Silico and In Vitro Assays.

Haemophilus influenzae is the causal agent of invasive pediatric diseases, such as meningitis, epiglottitis, pneumonia, septic arthritis, pericarditis, cellulitis, and bacteremia (serotype b). Non-typeable H. influenzae (NTHi) strains are associated with localized infections, such as otitis media, conjunctivitis, sinusitis, bronchitis, and pneumonia, and can cause invasive diseases, such as as meningitis and sepsis in immunocompromised hosts. Enolase is a multifunctional protein and can act as a receptor for plasminogen, promoting its activation to plasmin, which leads to the degradation of components of the extracellular matrix, favoring host tissue invasion. In this study, using molecular docking, three important residues involved in plasminogen interaction through the plasminogen-binding motif (251EFYNKENGMYE262) were identified in non-typeable H. influenzae enolase (NTHiENO). Interaction with the human plasminogen kringle domains is conformationally stable due to the formation of four hydrogen bonds corresponding to enoTYR253-plgGLU1 (K2), enoTYR253-plgGLY310 (K3), and enoLYS255-plgARG471/enoGLU251-plgLYS468 (K5). On the other hand, in vitro assays, such as ELISA and far-western blot, showed that NTHiENO is a plasminogen-binding protein. The inhibition of this interaction using polyclonal anti-NTHiENO antibodies was significant. With these results, we can propose that NTHiENO–plasminogen interaction could be one of the mechanisms used by H. influenzae to adhere to and invade host cells.

Combined oncolytic adenovirus carrying MnSOD and mK5 genes both regulated by survivin promoter has a synergistic inhibitory effect on gastric cancer.

Gastric cancer (GC) is one of the major causes of cancer-related mortality. The use of oncolytic virus for cancer gene-virotherapy is a new approach for the treatment of human cancers. In this study, a novel Survivin promoter-driven recombinant oncolytic adenovirus carrying mK5 or MnSOD gene was constructed, which was modified after deletion of the E1B gene. Human plasminogen Kringle 5 mutant (mK5) and manganese superoxide dismutase (MnSOD) are both potential tumor suppressor genes. By constructing Ad-Surp-mK5 and Ad-Surp-MnSOD oncolytic adenoviruses, we hypothesized that the combination of the two viruses would enhance the therapeutic efficacy of GC as compared to the one virus alone. The results of the in vitro experiments revealed that the combination of adenovirus carrying mK5 and MnSOD gene exhibited stronger cytotoxicity to GC cell lines as compared to the virus alone. Additionally, the virus could selectively kill cancer cells and human somatic cells. Cell staining, flow cytometry, and western blot analysis showed that the combination of two adenoviruses containing therapeutic genes could promote the apoptosis of cancer cells. In vivo experiments further verified that Ad-Surp-mK5 in combination with Ad-Surp-MnSOD exhibited a significant inhibitory effect on the growth of GC tumor xenograft as compared to the virus alone, and no significant difference was observed in the bodyweight of treatment and the normal mice. In conclusion, the combination of our two newly constructed recombinant oncolytic adenoviruses containing mK5 or MnSOD therapeutic genes could significantly inhibit gastric cancer growth by inducing apoptosis, suggestive of its potential for GC therapy.

Molecular recognition and interaction between human plasminogen Kringle 5 and voltage-dependent anion channel-1 by biological specificity technologies and molecular dynamic simulation

Voltage-dependent anion channel-l (VDAC-1) can bind with plasminogen Kringle 5 as the cell surface receptor and induce cell apoptosis, but the detailed information of binding is not clear yet. Thus, the mutual recognition and binding were investigated here utilizing frontal affinity chromatography, surface plasma resonance, mutation analysis combining molecular dynamics simulation. The results showed that Kringle 5 binds with VDAC-1 in equimolar driven mainly by electrostatic force, with 15 amino acid residues participating in Kringle 5 and 21 in VDAC-1. The observed conformational changes indicated the automatic structure regulation providing these two proteins suitable conformations and spatial surroundings for the tighter and stabler binding. Moreover, Glu29 in Kringle 5 was speculated as the key residue maintaining the largest energy contribution. Therefore, this work provided precise information for the recognition and binding of Kringle 5 with VDAC-1 that is valuable for the corresponding treatment of tumours or other angiogenic diseases.

Autophagy: Instructions from the extracellular matrix

In recent years, extensive research has uncovered crucial regulatory roles for the extracellular matrix (ECM) in regulating autophagy. Autophagy is a ubiquitous and highly conserved catabolic process that allows the selective removal and recycling of cytosolic components via lysosomal or vacuolar degradation. Due to its pivotal role in cellular homeostasis, the impairment of autophagy is involved in the pathophysiology of numerous diseases, comprising infectious diseases, immune and neurodegenerative disorders, renal and hepatic diseases, intervertebral and cartilage disorders, as well as fibrosis and cancer. Several ECM-derived proteoglycans and proteins, including decorin, biglycan, endorepellin, endostatin, collagen VI, and plasminogen kringle 5, have been identified as strong inducers of autophagy. In contrast, laminin α2, perlecan, and lumican exert opposite function by suppressing autophagy. Importantly, by direct interaction with various receptors, which interplay with their co-receptors and adhesion molecules, the ECM is able to direct autophagy in a molecular and cell context-specific manner. Thus, vast pharmacological potential resides in translating this knowledge into the development of ECM-derived therapeutics selectively regulating autophagy.

Glucose‐regulated protein (GRP78) is an important cell surface receptor for viral invasion, cancers, and neurological disorders

The 78 kDa glucose-regulated protein (GRP78) is an endoplasmic reticulum (ER)-resident molecular chaperone. GRP78 is a member of the 70 kDa heat shock family of proteins involved in correcting and clearing misfolded proteins in the ER. In response to cellular stress, GRP78 escapes from the ER and moves to the plasma membrane where it (a) functions as a receptor for many ligands, and (b) behaves as an autoantigen for autoantibodies that contribute to human disease and cancer. Cell surface GRP78 (csGRP78) associates with the major histocompatibility complex class I (MHC-I), and is the port of entry for several viruses, including the predictive binding of the novel SARS-CoV-2. Furthermore, csGRP78 is found in association with partners as diverse as the teratocarcinoma-derived growth factor 1 (Cripto), the melanocortin-4 receptor (MC4R) and the DnaJ-like protein MTJ-1. CsGRP78 also serves as a receptor for a large variety of ligands including activated α2 -macroglobulin (α2 M*), plasminogen kringle 5 (K5), microplasminogen, the voltage-dependent anion channel (VDAC), tissue factor (TF), and the prostate apoptosis response-4 protein (Par-4). In this review, we discuss the mechanisms involved in the translocation of GRP78 from the ER to the cell surface, and the role of secreted GRP78 and its autoantibodies in cancer and neurological disorders.

A functional outside-in signaling network of proteoglycans and matrix molecules regulating autophagy

Proteoglycans and selected extracellular matrix constituents are emerging as intrinsic and critical regulators of evolutionarily conversed, intracellular catabolic pathways. Often, these secreted molecules evoke sustained autophagy in a variety of cell types, tissues, and model systems. The unique properties of proteoglycans have ushered in a paradigmatic shift to broaden our understanding of matrix-mediated signaling cascades. The dynamic cellular pathway controlling autophagy is now linked to an equally dynamic and fluid signaling network embedded in a complex meshwork of matrix molecules. A rapidly emerging field of research encompasses multiple matrix-derived candidates, representing a menagerie of soluble matrix constituents including decorin, biglycan, endorepellin, endostatin, collagen VI and plasminogen kringle 5. These matrix constituents are pro-autophagic and simultaneously anti-angiogenic. In contrast, perlecan, laminin α2 chain, and lumican have anti-autophagic functions. Mechanistically, each matrix constituent linked to intracellular catabolic events engages a specific cell surface receptor that often converges on a common core of the autophagic machinery including AMPK, Peg3 and Beclin 1. We consider this matrix-evoked autophagy as non-canonical given that it occurs in an allosteric manner and is independent of nutrient availability or prevailing bioenergetics control. We propose that matrix-regulated autophagy is an important outside-in signaling mechanism for proper tissue homeostasis that could be therapeutically leveraged to combat a variety of diseases.

High resolution structure of human apolipoprotein (a) kringle IV type 2: beyond the lysine binding site

Lipoprotein (a) [Lp(a)] is characterized by an LDL-like composition in terms of lipids and apoB100, and by one copy of a unique glycoprotein, apo(a). The apo(a) structure is mainly based on the repetition of tandem kringle domains with high homology to plasminogen kringles 4 and 5. Among them, kringle IV type 2 (KIV-2) is present in a highly variable number of genetically encoded repeats, whose length is inversely related to Lp(a) plasma concentration and cardiovascular risk. Despite it being the major component of apo(a), the actual function of KIV-2 is still unclear. Here, we describe the first high-resolution crystallographic structure of this domain. It shows a general fold very similar to other KIV domains with high and intermediate affinity for the lysine analog, ε-aminocaproic acid. Interestingly, KIV-2 presents a lysine binding site (LBS) with a unique shape and charge distribution. KIV-2 affinity for predicted small molecule binders was found to be negligible in surface plasmon resonance experiments; and with the LBS being nonfunctional, we propose to rename it "pseudo-LBS". Further investigation of the protein by computational small-molecule docking allowed us to identify a possible heparin-binding site away from the LBS, which was confirmed by specific reverse charge mutations abolishing heparin binding. This study opens new possibilities to define the pathogenesis of Lp(a)-related diseases and to facilitate the design of specific therapeutic drugs.

Research progress of tumor angiogenesis inhibitors

Angiogenesis is one of the most important pathological characteristics in the development of tumor growth. Hence, antiangiogenesis is a hot topic in the field of cancer research. The current strategy for antiangiogenesis therapy of tumors is restoration of the angiogenic balance via either blockage of proangiogenic factors or application of angiogenic inhibitors. Endogenous angiogenic inhibitors show more promising prospects compared with proangiogenic factor antagonists. However, the underlying mechanisms of angiogenic inhibitors remain to be thoroughly elucidated. There are two types of endogenous angiogenic inhibitors. The first are hydrolyzed fragments of precursor proteins, such as plasminogen kringle 5 (K5), angiostatin/kringle 1–4, and endostatin, and the other are secreted proteins, such as pigment epithelium-derived factor (PEDF), kallikrein-binding protein (KBP/kallistatin), and antithrombin. Here we summarized research progress on the biological functions underlying mechanisms of tumor angiogenesis and application prospects of K5, PEDF, and KBP, so as to provide insights into the antiangiogenic therapies of tumor in the future.

Identification of the binding site for plasminogen kringle 5 in the ?-chain of fibrin(ogen) D-fragment

Identification of the binding site for plasminogen kringle 5 in the ?-chain of fibrin(ogen) D-fragment

Combining Monte Carlo and Molecular Dynamics Simulations for Enhanced Binding Free Energy Estimation through Markov State Models.

We present a multistep protocol, combining Monte Carlo and molecular dynamics simulations, for the estimation of absolute binding free energies, one of the most significant challenges in computer-aided drug design. The protocol is based on an initial short enhanced Monte Carlo simulation, followed by clustering of the ligand positions, which serve to identify the most relevant states of the unbinding process. From these states, extensive molecular dynamics simulations are run to estimate an equilibrium probability distribution obtained with Markov State Models, which is subsequently used to estimate the binding free energy. We tested the procedure on two different protein systems, the Plasminogen kringle domain 1 and Urokinase, each with multiple ligands, for an aggregated molecular dynamics length of 760 μs. Our results indicate that the initial sampling of the unbinding events largely facilitates the convergence of the subsequent molecular dynamics exploration. Moreover, the protocol is capable to properly rank the set of ligands examined, albeit with a significant computational cost for the, more realistic, Urokinase complexes. Overall, this work demonstrates the usefulness of combining enhanced sampling methods with regular simulation techniques as a way to obtain more reliable binding affinity estimates.

Identification and analyses of inhibitors targeting apolipoprotein(a) kringle domains KIV-7, KIV-10, and KV provide insight into kringle domain function

Increased plasma concentrations of lipoprotein(a) (Lp(a)) are associated with an increased risk for cardiovascular disease. Lp(a) is composed of apolipoprotein(a) (apo(a)) covalently bound to apolipoprotein B of low-density lipoprotein (LDL). Many of apo(a)'s potential pathological properties, such as inhibition of plasmin generation, have been attributed to its main structural domains, the kringles, and have been proposed to be mediated by their lysine-binding sites. However, available small-molecule inhibitors, such as lysine analogs, bind unselectively to kringle domains and are therefore unsuitable for functional characterization of specific kringle domains. Here, we discovered small molecules that specifically bind to the apo(a) kringle domains KIV-7, KIV-10, and KV. Chemical synthesis yielded compound AZ-05, which bound to KIV-10 with a Kd of 0.8 μm and exhibited more than 100-fold selectivity for KIV-10, compared with the other kringle domains tested, including plasminogen kringle 1. To better understand and further improve ligand selectivity, we determined the crystal structures of KIV-7, KIV-10, and KV in complex with small-molecule ligands at 1.6-2.1 Å resolutions. Furthermore, we used these small molecules as chemical probes to characterize the roles of the different apo(a) kringle domains in in vitro assays. These assays revealed the assembly of Lp(a) from apo(a) and LDL, as well as potential pathophysiological mechanisms of Lp(a), including (i) binding to fibrin, (ii) stimulation of smooth-muscle cell proliferation, and (iii) stimulation of LDL uptake into differentiated monocytes. Our results indicate that a small-molecule inhibitor targeting the lysine-binding site of KIV-10 can combat the pathophysiological effects of Lp(a).

Kringles of substrate plasminogen provide a 'catalytic switch' in plasminogen to plasmin turnover by Streptokinase.

To understand the role of substrate plasminogen kringles in its differential catalytic processing by the streptokinase - human plasmin (SK-HPN) activator enzyme, Fluorescence Resonance Energy Transfer (FRET) model was generated between the donor labeled activator enzyme and the acceptor labeled substrate plasminogen (for both kringle rich Lys plasminogen - LysPG, and kringle less microplasminogen - µPG as substrates). Different steps of plasminogen to plasmin catalysis i.e. substrate plasminogen docking to scissile peptide bond cleavage, chemical transformation into proteolytically active product, and the decoupling of the nascent product from the SK-HPN activator enzyme were segregated selectively using (1) FRET signal as a proximity sensor to score the interactions between the substrate and the activator during the cycle of catalysis, (2) active site titration studies and (3) kinetics of peptide bond cleavage in the substrate. Remarkably, active site titration studies and the kinetics of peptide bond cleavage have shown that post docking chemical transformation of the substrate into the product is independent of kringles adjacent to the catalytic domain (CD). Stopped-flow based rapid mixing experiments for kringle rich and kringle less substrate plasminogen derivatives under substrate saturating and single cycle turnover conditions have shown that the presence of kringle domains adjacent to the CD in the macromolecular substrate contributes by selectively speeding up the final step, namely the product release/expulsion step of catalysis by the streptokinase-plasmin(ogen) activator enzyme.