To bind zinc or not to bind zinc: an examination of innovative approaches to improved metalloproteinase inhibition. Biochim Biophys Acta. 2010;1803:72-94. [PMID: 19712708 DOI: 10.1016/j.bbamcr.2009.08.006]

Self-assembled genistein nanoparticles suppress the epithelial-mesenchymal transition in glioblastoma by targeting MMP9

Glioblastoma (GBM) is the most prevalent and aggressive primary malignant brain tumor in adults, known for its poor prognosis and resistance to conventional treatments. The blood-brain barrier (BBB) presents a significant challenge in delivering effective treatments. In this study, we developed a carrier-free, self-assembled nanosystem using genistein (GE), a naturally occurring isoflavone, to enhance therapeutic delivery across the BBB. GE nanoparticles (GE NPs) were synthesized via solvent emulsification evaporation, in uniform spherical particles (∼180 nm), stabilized by hydrogen bonding and π-π interactions. The GE NPs demonstrated optimal physicochemical properties, including stability, high BBB permeability, prolonged circulation time. In vitro studies revealed that GE NPs inhibited GBM cell proliferation, induced apoptosis and suppressed epithelial-mesenchymal transition (EMT) by promoting the degradation of MMP9. In vivo, GE NPs significantly reduced tumor growth and extended survival in an orthotopic GBM mouse model, outperforming temozolomide treatment. Mechanistic analysis indicated that GE NPs inhibited the degradation of the extracellular matrix by targeting the catalytic domain of MMP9, thereby effectively suppressing the EMT of GBM. This research highlights the potential of GE NPs as a novel therapeutic approach for GBM, addressing drug delivery challenges while improving anti-tumor efficacy. Further optimization for enhanced tumor retention and exploration of combination therapies may improve clinical outcomes (Graphical Abstract).

A tailored 4G s-triazine-based dendrimer vehicle for quercetin endowed with MMP-2/9 inhibition and VEGF downregulation for targeting breast cancer progression and liver metastasis

Motivated by our recent research progress on the exploitation of s-triazine dendritic platforms as bioactive carriers for well-known anticancer agents and/or targeting ligands, we set out to synthesize new rationally designed dendrimers endowed with MMP-2/9 inhibition potential for halting both breast and liver cancer progression with reduced off-target side effects. New three and four generation s-triazine based dendrimers were developed to incorporate potential ZBGs (Zinc Binding Groups) and carboxyl terminal groups to facilitate direct conjugation of anti-cancer drugs (quercetin) and/or targeting ligands (lactobionic acid) through a biodegradable ester bond. Compared to free quercetin (QUR), MTT assay revealed that all the quercetin-coupled dendrimers displayed better anticancer potential (IC50 = 12.690-29.316, 4.137-29.090 μM) against MCF-7 and HepG-2 cancer cells, respectively within their safe doses (EC100 = 134.35-78.44 μM). Conjugation of lactobionic acid and PEG boosted the anticancer potency against both treated cells, improved apoptosis and down regulated MMP-9 and VEGF gene expression levels in both treated cancer cells. Generally, the more branched G4 dendrimer conjugates exhibited a superior overall anticancer performance compared to their respective G3 analogues, except for their MMP-9 inhibition where G3 conjugate appeared to be more potent and more selective than its G4 analogue.

Function and inhibition of the DNA repair enzyme SNM1A

SNM1A is an enzyme involved in several important biological pathways. To date, most investigations have focused on its role in repairing interstrand crosslinks, a highly cytotoxic form of DNA damage. SNM1A acts as a 5'-3' exonuclease, displaying an unusual capability to digest DNA past the site of a crosslink lesion. Recently, additional functions of this enzyme in the repair of DNA double-strand breaks and critically shortened telomeres have been uncovered. Furthermore, SNM1A is involved in two cell cycle checkpoints that arrest cell division in response to DNA damage. Inhibition of both DNA repair enzymes and cell cycle checkpoint proteins are effective strategies for cancer treatment, and SNM1A is therefore of significant interest as a potential therapeutic target. As a member of the metallo-β-lactamase superfamily, SNM1A is postulated to contain two metal ions in the active site that catalyse hydrolysis of the phosphodiester backbone of DNA. Substrate-mimic probes based on a nucleoside or oligonucleotide scaffold appended with a metal-binding group have proven effective in vitro. High-throughput screening campaigns have identified potent inhibitors, some of which were successful in sensitising cells to DNA-damaging cancer drugs. This review discusses the biological role, structure, and mechanism of action of SNM1A, and the development of SNM1A inhibitors for cancer therapy.

Multi-target-directed therapeutic strategies for Alzheimer's disease: controlling amyloid-β aggregation, metal ion homeostasis, and enzyme inhibition

Alzheimer's disease (AD) is the most prevalent neurodegenerative dementia, marked by progressive cognitive decline and memory impairment. Despite advances in therapeutic research, single-target-directed treatments often fall short in addressing the complex, multifactorial nature of AD. This arises from various pathological features, including amyloid-β (Aβ) aggregate deposition, metal ion dysregulation, oxidative stress, impaired neurotransmission, neuroinflammation, mitochondrial dysfunction, and neuronal cell death. This review illustrates their interrelationships, with a particular emphasis on the interplay among Aβ, metal ions, and AD-related enzymes, such as β-site amyloid precursor protein cleaving enzyme 1 (BACE1), matrix metalloproteinase 9 (MMP9), lysyl oxidase-like 2 (LOXL2), acetylcholinesterase (AChE), and monoamine oxidase B (MAOB). We further underscore the potential of therapeutic strategies that simultaneously inhibit Aβ aggregation and address other pathogenic mechanisms. These approaches offer a more comprehensive and effective method for combating AD, overcoming the limitations of conventional therapies.

Non-small cell lung cancer sensitisation to platinum chemotherapy via new thiazole-triazole hybrids acting as dual T-type CCB/MMP-9 inhibitors

Cisplatin remains the unchallenged standard therapy for NSCLC. However, it is not completely curative due to drug resistance and oxidative stress-induced toxicity. Drug resistance is linked to overexpression of matrix metalloproteinases (MMPs) and aberrant calcium signalling. We report synthesis of novel thiazole-triazole hybrids as MMP-9 inhibitors with T-type calcium channel blocking and antioxidant effects to sensitise NSCLC to cisplatin and ameliorate its toxicity. MTT and whole cell patch clamp assays revealed that 6d has a balanced profile of cytotoxicity (IC50 = 21 ± 1 nM, SI = 12.14) and T-type calcium channel blocking activity (⁓60% at 10 μM). It exhibited moderate ROS scavenging activity and nanomolar MMP-9 inhibition (IC50 = 90 ± 7 nM) surpassing NNGH with MMP-9 over -2 and MMP-10 over -13 selectivity. Docking and MDs simulated its receptor binding mode. Combination studies confirmed that 6d synergized with cisplatin (CI = 0.69 ± 0.05) lowering its IC50 by 6.89 folds. Overall, the study introduces potential lead adjuvants for NSCLC platinum-based therapy.

Glycocalyx disruption, endothelial dysfunction and vascular remodeling as underlying mechanisms and treatment targets of chronic venous disease

The glycocalyx is an essential structural and functional component of endothelial cells. Extensive hemodynamic changes cause endothelial glycocalyx disruption and vascular dysfunction, leading to multiple arterial and venous disorders. Chronic venous disease (CVD) is a common disorder of the lower extremities with major health and socio-economic implications, but complex pathophysiology. Genetic aberrations accentuated by environmental factors, behavioral tendencies, and hormonal disturbances promote venous reflux, valve incompetence, and venous blood stasis. Increased venous hydrostatic pressure and changes in shear-stress cause glycocalyx injury, endothelial dysfunction, secretion of adhesion molecules, leukocyte recruitment/activation, and release of cytokines, chemokines, and hypoxia-inducible factor, causing smooth muscle cell switch from contractile to synthetic proliferative phenotype, imbalance in matrix metalloproteinases (MMPs), degradation of collagen and elastin, and venous tissue remodeling, leading to venous dilation and varicose veins. In the advanced stages of CVD, leukocyte infiltration of the vein wall causes progressive inflammation, fibrosis, disruption of junctional proteins, accumulation of tissue metabolites and reactive oxygen and nitrogen species, and iron deposition, leading to skin changes and venous leg ulcer (VLU). CVD management includes compression stockings, venotonics, and surgical intervention. In addition to its antithrombotic and fibrinolytic properties, literature suggests sulodexide benefits in reducing inflammation, promoting VLU healing, improving endothelial function, exhibiting venotonic properties, and inhibiting MMP-9. Understanding the role of glycocalyx, endothelial dysfunction, and vascular remodeling should help delineate the underlying mechanisms and develop improved biomarkers and targeted therapy for CVD and VLU.

Human Keratin Matrices Suppress Matrix Metalloproteinase Activity to Support Wound Healing

Elevated protease activity is a hallmark of non-healing chronic wounds. Though multiple biomaterials exist that are successful in treating wounds, their roles in modulating the enzymatic environment of the wound are only beginning to be elucidated. Because keratin has long been known to be resistant to degradation by most enzymes, we studied a keratin biomaterial, the human keratin matrix (HKM), in the presence of enzymes identified to contribute to wound chronicity: neutrophil-derived elastase (NE), matrix metalloproteinase 1 (MMP-1), and MMP-9. Upon finding the suppression of MMP-9 activity in the presence of HKM without reducing enzyme protein levels, we further studied the ability of HKM to bind metal ions in the wound and showed the reduction of Zn2+ ion concentration in the presence of HKM. Finally, because of the enzyme resistance of keratin and the suppression of wound enzymes, we demonstrated that HKM was durable in the wound environment, and did not degrade in wound healing efficacy when left in place for two weeks compared to one week in a diabetic mouse model of wound non-healing. In this way, we show HKM is a unique and effective biomaterial for the treatment of chronic wounds through the modulation of wound MMP activity.

Synthesis and antiproliferative activity of 2-oxo-3-phenylquinoxaline derivatives and related compounds against colon cancer

We have designed 17 new 2-oxo-3-phenylquinoxalines via the chemoselective Michael reaction of 3-phenylquinoxalin-2(1H)-one with acrylic acid derivatives. The ester, ethyl 3-(2-oxo-3-phenylquinoxalin-1(2H)-yl)propanoate, was reacted with hydroxylamine and hydrazine to produce N-hydroxy-3-(2-oxo-3-phenylquinoxalin-1(2H)-yl)propanamide and hydrazide, respectively. Further modifications were made through reactions with isothiocyanates and azide coupling with amines, yielding thiosemicarbazides and N-alkyl derivatives. Molecular docking studies identified compound 7j as the most potent binder, fitting well into the active site, with the phenyl ring occupying the S1 pocket and the amino acid chain positioned in the S2 pocket. The synthesized compounds (2a, 4, 7a, 7g, 7d, 7h, 7e, 7b, 7c, 7f, and 7j) were evaluated for their anti-cancer activity on colorectal cancer (HCT-116) cells. Compounds 2a and 7j showed significant reductions in cell viability, with IC50 values of 28.85 ± 3.26 μg mL-1 and 26.75 ± 3.50 μg mL-1, respectively. Image analysis of HCT-116 cells treated with 60 μg mL-1 of compound 7j for 48 hours revealed notable morphological changes in both nuclei and cells. The number of cells reduced from 447 in the control to 238 in the treated group, with a corresponding reduction in the area covered by cells from 41.9% to 17.6%. Nuclear disintegration and chromatin fragmentation were observed, confirming apoptosis. These results highlight the potent cytotoxic effect of compound 7j.

Unveiling the bidirectional role of MMP9: A key player in kidney injury

Matrix metalloproteinases (MMPs) are a group of zinc-dependent proteolytic metalloenzymes that are involved in numerous pathological conditions, including nephropathy. MMP9, a member of the MMPs family, is categorized as a constituent of the gelatinase B subgroup, and its involvement in extracellular matrix (ECM) remodeling and renal fibrosis highlights its importance in the development and progression of renal diseases. The exact role of MMP9 in the development of kidney diseases is still controversial. This study investigated the dual role of MMP9 in kidney injury, discussing its implications in the pathogenesis of kidney diseases and investigating the design and mechanism of MMP9 inhibitors based on previous studies. This study provides an effective basis for the development of novel and selective MMP9 inhibitors for treating renal diseases.

Biological significance and pathophysiological role of Matrix Metalloproteinases in the Central Nervous System

Matrix Metalloproteinases (MMPs), which are endopeptidase reliant on zinc, are low in embryonic tissues but increases in response to a variety of physiological stimulus and pathological stresses. Neuro-glial cells, endothelial cells, fibroblasts, and leucocytes secrete MMPs, which cleave extracellular matrix proteins in a time-dependent manner. MMPs affect synaptic plasticity and the development of short-term memory by controlling the size, shape, and excitatory synapses' function through the lateral diffusion of receptors. In addition, MMPs influence the Extracellular Matrix proteins in the Peri-Neuronal Net at the Neuro-glial interface, which aids in the establishment of long-term memory. Through modulating neuronal, and glial cells migration, differentiation, Neurogenesis, and survival, MMPs impact brain development in mammals. In adult brains, MMPs play a beneficial role in physiological plasticity, which includes learning, memory consolidation, social interaction, and complex behaviors, by proteolytically altering a wide variety of factors, including growth factors, cytokines, receptors, DNA repair enzymes, and matrix proteins. Additionally, stress, depression, addiction, hepatic encephalopathy, and stroke may all have negative effects on MMPs. In addition to their role in glioblastoma development, MMPs influence neurological diseases such as epilepsy, schizophrenia, autism spectrum disorder, brain damage, pain, neurodegeneration, and Alzheimer's and Parkinson's. To help shed light on the potential of MMPs as a therapeutic target for neurodegenerative diseases, this review summarizes their regulation, mode of action, and participation in brain physiological plasticity and pathological damage. Finally, by employing different MMP-based nanotools and inhibitors, MMPs may also be utilized to map the anatomical and functional connectome of the brain, analyze its secretome, and treat neurodegenerative illnesses.

Biphenylsulfonamides as effective MMP-2 inhibitors with promising antileukemic efficacy: Synthesis, in vitro biological evaluation, molecular docking, and MD simulation analysis

Overexpression of matrix metalloproteinase-2 (MMP-2) possesses a correlation with leukemia especially chronic myeloid leukemia (CML). However, no such MMP-2 inhibitor has come out in the market to date for treating leukemia. In this study, synthesis, biological evaluation, and molecular modeling studies of a set of biphenylsulfonamide derivatives as promising MMP-2 inhibitors were performed, focusing on their potential applications as antileukemic therapeutics. Compounds DH-18 and DH-19 exerted the most effective MMP-2 inhibition (IC50 of 139.45 nM and 115.16 nM, respectively) with potent antileukemic efficacy against the CML cell line K562 (IC50 of 0.338 µM and 0.398 µM, respectively). The lead molecules DH-18 and DH-19 reduced the MMP-2 expression by 21.3% and 17.8%, respectively with effective apoptotic induction (45.4% and 39.8%, respectively) in the K562 cell line. Moreover, both these compounds significantly arrested different phases of the cell cycle. Again, both these molecules depicted promising antiangiogenic efficacy in the ACHN cell line. Nevertheless, the molecular docking and molecular dynamics (MD) simulation studies revealed that DH-18 formed strong bidentate chelation with the catalytic Zn2+ ion through the hydroxamate zinc binding group (ZBG). Apart from that, the MD simulation study also disclosed stable binding interactions of DH-18 and MMP-2 along with crucial interactions with active site amino acid residues namely His120, Glu121, His124, His130, Pro140, and Tyr142. In a nutshell, this study highlighted the importance of biphenylsulfonamide-based novel and promising MMP-2 inhibitors to open up a new avenue for potential therapy against CML.

Machine learning and biological evaluation-based identification of a potential MMP-9 inhibitor, effective against ovarian cancer cells SKOV3

MMP-9, also known as gelatinase B, is a zinc-metalloproteinase family protein that plays a key role in the degradation of the extracellular matrix (ECM). The normal function of MMP-9 includes the breakdown of ECM, a process that aids in normal physiological processes such as embryonic development, angiogenesis, etc. Interruptions in these processes due to the over-expression or downregulation of MMP-9 are reported to cause some pathological conditions like neurodegenerative diseases and cancer. In the present study, an integrated approach for ML-based virtual screening of the Maybridge library was carried out and their biological activity was tested in an attempt to identify novel small molecule scaffolds that can inhibit the activity of MMP-9. The top hits were identified and selected for target-based activity against MMP-9 protein using the kit (Biovision K844). Further, MTT assay was performed in various cancer cell lines such as breast (MCF-7, MDA-MB-231), colorectal (HCT119, DL-D-1), cervical (HeLa), lung (A549) and ovarian cancer (SKOV3). Interestingly, one compound viz., RJF02215 exhibited anti-cancer activity selectively in SKOV3. Wound healing assay and colony formation assay performed on SKOV3 cell line in the presence of RJF02215 confirmed that the compound had a significant inhibitory effect on this cell line. Thus, we have identified a novel molecule that can inhibit MMP-9 activity in vitro and inhibits the proliferation of SKOV3 cells. Novel molecules based on the structure of RJF02215 may become a good value addition for the treatment of ovarian cancer by exhibiting selective MMP-9 activity.Communicated by Ramaswamy H. Sarma.

Intracellular Zn2+ promotes extracellular matrix remodeling in dexamethasone-treated trabecular meshwork

Given the widespread application of glucocorticoids in ophthalmology, the associated elevation of intraocular pressure (IOP) has long been a vexing concern for clinicians, yet the underlying mechanisms remain inconclusive. Much of the discussion focuses on the extracellular matrix (ECM) of trabecular meshwork (TM). It is widely agreed that glucocorticoids impact the expression of matrix metalloproteinases (MMPs), leading to ECM deposition. Since Zn2+ is vital for MMPs, we explored its role in ECM alterations induced by dexamethasone (DEX). Our study revealed that in human TM cells treated with DEX, the level of intracellular Zn2+ significantly decreased, accompanied by impaired extracellular Zn2+ uptake. This correlated with changes in several Zrt-, Irt-related proteins (ZIPs) and metallothionein. ZIP8 knockdown impaired extracellular Zn2+ uptake, but Zn2+ chelation did not affect ZIP8 expression. Resembling DEX's effects, chelation of Zn2+ decreased MMP2 expression, increased the deposition of ECM proteins, and induced structural disarray of ECM. Conversely, supplementation of exogenous Zn2+ in DEX-treated cells ameliorated these outcomes. Notably, dietary zinc supplementation in mice significantly reduced DEX-induced IOP elevation and collagen content in TM, thereby rescuing the visual function of the mice. These findings underscore zinc's pivotal role in ECM regulation, providing a novel perspective on the pathogenesis of glaucoma.NEW & NOTEWORTHY Our study explores zinc's pivotal role in mitigating extracellular matrix dysregulation in the trabecular meshwork and glucocorticoid-induced ocular hypertension. We found that in human trabecular meshwork cells treated with dexamethasone, intracellular Zn2+ significantly decreased, accompanied by impaired extracellular Zn2+ uptake. Zinc supplementation rescues visual function by modulating extracellular matrix proteins and lowering intraocular pressure, offering a direction for further exploration in glaucoma management.

Newly discovered clouting interplay between matrix metalloproteinases structures and novel quaternary Ammonium K21: computational and in-vivo testing

AIMS AND OBJECTIVES

To analyze anti-MMP mode of action of Quaternary Ammonium Silane (QAS, codenamed as k21) by binding onto specific MMP site using computational molecular simulation and Anti-Sortase A (SrtA) mode of action by binding onto specific site using computational molecular simulation.

MATERIALS AND METHODS

In silico Molecular Dynamics (MD) was used to determine the interactions of K21 inside the pocket of the targeted protein (crystal structure of fibroblast collagenase-1 complexed to a diphenyl-ether sulphone based hydroxamic acid; PDB ID: 966C; Crystal structure of MMP-2 active site mutant in complex with APP-derived decapeptide inhibitor. MD simulations were accomplished with the Desmond package in Schrödinger Drug Discovery Suite. Blood samples (~ 0.5 mL) collected into K2EDTA were immediately transferred for further processing using the Litron MicroFlow® PLUS micronucleus analysis kit for mouse blood according to the manufacturer's instructions. Bacterial Reverse Mutation Test of K21 Molecule was performed to evaluate K21 and any possible metabolites for their potential to induce point mutations in amino acid-requiring strains of Escherichia coli (E. coli) (WP2 uvrA (tryptophan-deficient)).

RESULTS

Molecular Simulation depicted that K21 has a specific pocket binding on various MMPs and SrtA surfaces producing a classical clouting effect. K21 did not induce micronuclei, which are the result of chromosomal damage or damage to the mitotic apparatus, in the peripheral blood reticulocytes of male and female CD-1 mice when administered by oral gavage up to the maximum recommended dose of 2000 mg/kg. The test item, K21, was not mutagenic to Salmonella typhimurium (S. typhimurium) strains TA98, TA100, TA1535 and TA1537 and E. coli strain WP2 uvrA in the absence and presence of metabolic activation when tested up to the limit of cytotoxicity or solubility under the conditions of the test.

CONCLUSION

K21 could serve as a potent protease inhibitor maintaining the physical and biochemical properties of dental structures.

Chemosensitization of non-small cell lung cancer to sorafenib via non-hydroxamate s-triazinedione-based MMP-9/10 inhibitors

Non-small cell lung cancer (NSCLC) continues to be a leading cause of cancer death. Its fatality is associated with angiogenesis and metastasis. While VEGFR inhibitors are expected to be the central pillar for halting lung cancer, several clinical reports declared their subpar activities as monotherapy. These results directed combination studies of VEGFR inhibitors, especially sorafenib (Nexavar®), with various chemotherapeutic agents. Matrix metalloproteinase (MMP) inhibitors are seldom utilized in such combinations despite the expected complementary therapeutic outcome. This could be attributed to the clinical unsuitability of MMP inhibitors from the hydroxamate family. Herein, we report new non-hydroxamate s-triazinedione-based inhibitors of MMP-9 (6b; IC50 = 0.112 μM), and MMP-10 (6e; IC50 = 0.076 μM) surpassing the hydroxamate inhibitor NNGH for chemosensitization of NSCLC to sorafenib. MMPs inhibition profiling of the hits revealed MMP-9 over -2 and MMP-10 over -13 selectivity. 6b and 6e were potent (IC50 = 0.139 and 0.136 µM), safe (SI up to 6.77) and superior to sorafenib (IC50 = 0.506 µM, SI = 6.27) against A549 cells. When combined with sorafenib, the studied MMP inhibitors enhanced its cytotoxic efficacy up to 26 folds as confirmed by CI and DRI values for 6b (CI = 0.160 and DRI = 22.175) and 6e (CI = 0.096 and DRI = 29.060). 6b and 6e exerted anti-invasive activities in A549 cells as single agents (22.66 and 39.67 %) and in sorafenib combinations (29.96 and 91.83 %) compared to untreated control. Both compounds downregulated VEGF in A549 cells by approximately 70 % when combined with sorafenib, highlighting enhanced anti-angiogenic activities. Collectively, combinations of 6b and 6e with sorafenib demonstrated synergistic NSCLC cytotoxicity with pronounced anti-invasive and anti-angiogenic activities introducing a promising start point for preclinical studies.

Discovery of Novel Metalloenzyme Inhibitors Based on Property Characterization: Strategy and Application for HDAC1 Inhibitors

Metalloenzymes are ubiquitously present in the human body and are relevant to a variety of diseases. However, the development of metalloenzyme inhibitors is limited by low specificity and poor drug-likeness associated with metal-binding fragments (MBFs). A generalized drug discovery strategy was established, which is characterized by the property characterization of zinc-dependent metalloenzyme inhibitors (ZnMIs). Fifteen potential Zn2+-binding fragments (ZnBFs) were identified, and a customized pharmacophore feature was defined based on these ZnBFs. The customized feature was set as a required feature and applied to a search for novel inhibitors for histone deacetylase 1 (HDAC1). Ten potential HDAC1 inhibitors were recognized, and one of them (compound 9) was a known potent HDAC1 inhibitor. The results demonstrated the effectiveness of our strategy to identify novel inhibitors for zinc-dependent metalloenzymes.

The Leptospermum scoparium (Mānuka)-Specific Nectar and Honey Compound 3,6,7-Trimethyllumazine (LepteridineTM) That Inhibits Matrix Metalloproteinase 9 (MMP-9) Activity

3,6,7-trimethyllumazine (Lepteridine™) is a newly discovered natural pteridine derivative unique to Mānuka (Leptospermum scoparium) nectar and honey, with no previously reported biological activity. Pteridine derivative-based medicines, such as methotrexate, are used to treat auto-immune and inflammatory diseases, and Mānuka honey reportedly possesses anti-inflammatory properties and is used topically as a wound dressing. MMP-9 is a potential candidate protein target as it is upregulated in recalcitrant wounds and intestinal inflammation. Using gelatin zymography, 40 μg/mL LepteridineTM inhibited the gelatinase activities of both pro- (22%, p < 0.0001) and activated (59%, p < 0.01) MMP-9 forms. By comparison, LepteridineTM exerted modest (~10%) inhibition against a chromogenic peptide substrate and no effect against a fluorogenic peptide substrate. These findings suggest that LepteridineTM may not interact within the catalytic domain of MMP-9 and exerts a negligible effect on the active site hydrolysis of small soluble peptide substrates. Instead, the findings implicate fibronectin II domain interactions by LepteridineTM which impair gelatinase activity, possibly through perturbed tethering of MMP-9 to the gelatin matrix. Molecular modelling analyses were equivocal over interactions at the S1' pocket versus the fibronectin II domain, while molecular dynamic calculations indicated rapid exchange kinetics. No significant degradation of synthetic or natural LepteridineTM in Mānuka honey occurred during simulated gastrointestinal digestion. MMP-9 regulates skin and gastrointestinal inflammatory responses and extracellular matrix remodelling. These results potentially implicate LepteridineTM bioactivity in Mānuka honey's reported beneficial effects on wound healing via topical application and anti-inflammatory actions in gastrointestinal disorder models via oral consumption.

Matrix metalloproteinases and tissue inhibitors in multiple myeloma: promote or inhibit?

Matrix metalloproteinases (MMPs) and tissue inhibitor of metalloproteinases (TIMPs) play a vital role in the pathogenesis of multiple myeloma (MM), especially for tumor invasion and osteolytic osteopathy. By breaking down extracellular matrix (ECM) components and releasing the proteins composing the ECM and growth factors, as well as their receptors, MMPs affect tissue integrity and promote cancer cell invasion and metastasis. A vital pathophysiological characteristic of MM is the progress of osteolytic lesions, which are brought on by interactions between myeloma cells and the bone marrow microenvironment. MMPs, certainly, are one of the fundamental causes of myeloma bone disease due to their ability to degrade various types of collagens. TIMPs, as important regulators of MMP hydrolysis or activation, also participate in the occurrence and evolution of MM and the formation of bone disease. This review focuses on the role of MMP-1, MMP-2, MMP-7, MMP-9, MMP-13, MMP-14, and MMP-15 and the four types of TIMPs in the invasion of myeloma cells, angiogenesis, osteolytic osteopathy, to offer some novel perspectives on the clinical diagnostics and therapeutics of MM.

Removal of extracellular human amyloid beta aggregates by extracellular proteases in C. elegans

The amyloid beta (Aβ) plaques found in Alzheimer's disease (AD) patients' brains contain collagens and are embedded extracellularly. Several collagens have been proposed to influence Aβ aggregate formation, yet their role in clearance is unknown. To investigate the potential role of collagens in forming and clearance of extracellular aggregates in vivo, we created a transgenic Caenorhabditis elegans strain that expresses and secretes human Aβ1-42. This secreted Aβ forms aggregates in two distinct places within the extracellular matrix. In a screen for extracellular human Aβ aggregation regulators, we identified different collagens to ameliorate or potentiate Aβ aggregation. We show that a disintegrin and metalloprotease a disintegrin and metalloprotease 2 (ADM-2), an ortholog of ADAM9, reduces the load of extracellular Aβ aggregates. ADM-2 is required and sufficient to remove the extracellular Aβ aggregates. Thus, we provide in vivo evidence of collagens essential for aggregate formation and metalloprotease participating in extracellular Aβ aggregate removal.

Network pharmacology reveals the potential of Dolastatin 16 as a diabetic wound healing agent

Dolastatin 16, a marine cyclic depsipeptide, was initially isolated from the sea hare Dolabella Auricularia by Pettit et al. Due to the lack of information regarding its bioactivity, target identification becomes an indispensable strategy for revealing the potential targets and mechanisms of action of Dolastatin 16. Network pharmacology was utilized to identify targets associated with the disease, gene ontology, and KEGG pathways. The results highlighted Matrix Metalloproteinase-9 (MMP9) as a potential target of Dolastatin 16 through network pharmacology analysis. This target was found to be primarily involved in the TNF signaling pathway and in foot ulceration-associated diabetic polyneuropathy. Furthermore, the binding mode and dynamic behavior of the complex were investigated through molecular docking and molecular dynamics studies. In the docking study, a native ligand (a hydroxamate inhibitor) and (R)-ND-336 were employed as ligand controls, demonstrating binding energy values of - 6.6 and - 8.9 kcal/mol, respectively. The Dolastatin 16 complex exhibited a strong affinity for MMP9, with a binding energy value of - 9.7 kcal/mol, indicating its high potential as an inhibitor. Molecular dynamics also confirmed the stability of the MMP9-Dolastatin complex throughout the simulation process. Dolastatin 16 has the potential to act as an MMP9 inhibitor, offering promise for accelerating the wound healing process in diabetic foot conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00161-5.

Antimicrobial FiteBac® K21 promotes antimicrobial Potency and wound healing

Objectives

Successful root canal therapy is dependent on the efficacy of complete instrumentation and adequate use of chemical irrigant to eliminate the biofilm from dentin surface. The aim of the study was to examine antibiofilm and antimicrobial effectiveness of newly formulated Quaternary ammonium silane (QAS/also codenamed K21; against Fusobacterium nucleatum (F. nucleatum) and Enterococcus faecalis (E. faecalis) biofilm on radicular dentin with evaluation of the anti-inflammatory consequence in vivo.

Methods

Fourier Transform Infrared Spectroscopy (FTIR) was performed after complete hydrolysis of K21 solution. Human teeth were inoculated with biofilms for 7-days followed by treatment with various irrigants. The irrigant groups were Sodium hypochlorite [NaOCl (6%)], Chlorhexidine [CHX (2%)], K21 (0.5%), K21 (1%) and Saline. Scanning electron microscopy (SEM) was performed for biofilm and resin-dentin penetration. Transmission Electron Microscopy (TEM) of biofilms was done to evaluate application of K21. For in vivo evaluation, Albino wistar rats were injected subcutaneously and sections were stained with haematoxylin/eosin. Macrophage, M1/M2 expression were evaluated along with molecular simulation. Raman measurements were done on dried biofilms.

Results

FTIR K21 specimens demonstrated presence of ethanol/silanol groups. Raman band at 1359 cm-1 resemble to -CH2- wagging displaying 29Si atoms in Nuclear Magnetic Resonance (NMR). 0.5%K21 showed cells exhibiting folded membranes. SEM showed staggering amount of resin tags with 0.5% K21 group. TEM showed membrane disruption in K21-groups. K21 groups were initially irritant, which subsided completely afterwards showing increased CD68. K21 and MMP/collagen complex was thermodynamically favourable.

Conclusion

K21 root canal irrigant was able to penetrate bacterial wall and can serve as a potential irrigant for therapeutic benefits. Expression of M2 polarized subsets showed K21 can serve in resolving inflammation and potentiate tissue repair.

Novel Matrix Metalloproteinase-9 (MMP-9) Inhibitors in Cancer Treatment

Matrix metalloproteinases (MMPs) belong to a family of zinc-dependent proteolytic metalloenzymes. MMP-9, a member of the gelatinase B family, is characterized as one of the most intricate MMPs. The crucial involvement of MMP-9 in extracellular matrix (ECM) remodeling underscores its significant correlation with each stage of cancer pathogenesis and progression. The design and synthesis of MMP-9 inhibitors is a potentially attractive research area. Unfortunately, to date, there is no effective MMP-9 inhibitor that passes the clinical trials and is approved by the FDA. This review primarily focuses on exploring the diverse strategies employed in the design and advancement of MMP-9 inhibitors, along with their anticancer effects and selectivity. To illuminate the essential structural characteristics necessary for the future design of novel MMP-9 inhibitors, the current narrative review highlights several recently discovered MMP-9 inhibitors exhibiting notable selectivity and potency.

Two-Step Validation Approach for Tools To Study the DNA Repair Enzyme SNM1A

We report a two-step validation approach to evaluate the suitability of metal-binding groups for targeting DNA damage-repair metalloenzymes using model enzyme SNM1A. A fragment-based screening approach was first used to identify metal-binding fragments suitable for targeting the enzyme. Effective fragments were then incorporated into oligonucleotides using the copper-catalysed azide-alkyne cycloaddition reaction. These modified oligonucleotides were recognised by SNM1A at >1000-fold lower concentrations than their fragment counterparts. The exonuclease SNM1A is a key enzyme involved in the repair of interstrand crosslinks, a highly cytotoxic form of DNA damage. However, SNM1A and other enzymes of this class are poorly understood, as there is a lack of tools available to facilitate their study. Our novel approach of incorporating functional fragments into oligonucleotides is broadly applicable to generating modified oligonucleotide structures with high affinity for DNA damage-repair enzymes.

Protein Ca2+-Sites Prone to Sr2+ Substitution: Implications for Strontium Therapy

Strontium (Sr), an alkali metal with properties similar to calcium, in the form of soluble salts is used to treat osteoporosis. Despite the information accumulated on the role of Sr²⁺ as a Ca²⁺ mimetic in biology and medicine, there is no systematic study of how the outcome of the competition between the two dications depends on the physicochemical properties of (i) the metal ions, (ii) the first- and second-shell ligands, and (iii) the protein matrix. Specifically, the key features of a Ca²⁺-binding protein that enable Sr²⁺ to displace Ca²⁺ remain unclear. To address this, we studied the competition between Ca²⁺ and Sr²⁺ in protein Ca²⁺-binding sites using density functional theory combined with the polarizable continuum model. Our findings indicate that Ca²⁺-sites with multiple strong charge-donating protein ligands, including one or more bidentately bound Asp^-/Glu^- that are relatively buried and rigid are protected against Sr²⁺ attack. On the other hand, Ca²⁺-sites crowded with multiple protein ligands may be prone to Sr²⁺ displacement if they are solvent-exposed and flexible enough so that an extra backbone ligand from the outer shell can bind to Sr²⁺. In addition, solvent-exposed Ca²⁺ sites with only a few weak charge-donating ligands that can rearrange to fit the strontium's coordination requirements are susceptible to Sr²⁺ displacement. We provide the physical basis of these results and discuss potential novel protein targets of therapeutic Sr²⁺.

Influence of N-arylsulfonamido d-valine N-substituents on the selectivity and potency of matrix metalloproteinase inhibitors

To develop matrix metalloproteinase inhibitors (MMPIs) for both therapy and medicinal imaging by fluorescence-based techniques or positron-emission tomography (PET), a small library of eighteen N-substituted N-arylsulfonamido d-valines were synthesized and their potency to inhibit two gelatinases (MMP-2, and MMP-9), two collagenases (MMP-8, and MMP-13) and macrophage elastase (MMP-12) was determined in a Structure-Activity-Relation study with ({4-[3-(5-methylthiophen-2-yl)-1,2,4-oxadiazol-5-yl]phenyl}sulfonyl)-d-valine (1) as a lead. All compounds were shown to be more potent MMP-2/-9 inhibitors (nanomolar range) compared to other tested MMPs. This is a remarkable result considering that a carboxylic acid group is the zinc binding moiety. The compound with a terminal fluoropropyltriazole group at the furan ring (P1' substituent) was only four times less potent in inhibiting MMP-2 activity than the lead compound 1, making this compound a promising probe for PET application (after using a prosthetic group approach to introduce fluorine-18). Compounds with a TEG spacer and a terminal azide or even a fluorescein moiety at the sulfonylamide N atom (P2' substituent) were almost as active as the lead structure 1, making the latter derivative a suitable fluorescence imaging tool.

Bacterial Zinc Metalloenzyme Inhibitors: Recent Advances and Future Perspectives

Human deaths caused by Gram-negative bacteria keep rising due to the multidrug resistance (MDR) phenomenon. Therefore, it is a priority to develop novel antibiotics with different mechanisms of action. Several bacterial zinc metalloenzymes are becoming attractive targets since they do not show any similarities with the human endogenous zinc-metalloproteinases. In the last decades, there has been an increasing interest from both industry and academia in developing new inhibitors against those enzymes involved in lipid A biosynthesis, and bacteria nutrition and sporulation, e.g., UDP-[3-O-(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase (LpxC), thermolysin (TLN), and pseudolysin (PLN). Nevertheless, targeting these bacterial enzymes is harder than expected and the lack of good clinical candidates suggests that more effort is needed. This review gives an overview of bacterial zinc metalloenzyme inhibitors that have been synthesized so far, highlighting the structural features essential for inhibitory activity and the structure-activity relationships. Our discussion may stimulate and help further studies on bacterial zinc metalloenzyme inhibitors as possible novel antibacterial drugs.

Lactate regulates cell cycle by remodelling the anaphase promoting complex

Lactate is abundant in rapidly dividing cells owing to the requirement for elevated glucose catabolism to support proliferation1-6. However, it is not known whether accumulated lactate affects the proliferative state. Here we use a systematic approach to determine lactate-dependent regulation of proteins across the human proteome. From these data, we identify a mechanism of cell cycle regulation whereby accumulated lactate remodels the anaphase promoting complex (APC/C). Remodelling of APC/C in this way is caused by direct inhibition of the SUMO protease SENP1 by lactate. We find that accumulated lactate binds and inhibits SENP1 by forming a complex with zinc in the SENP1 active site. SENP1 inhibition by lactate stabilizes SUMOylation of two residues on APC4, which drives UBE2C binding to APC/C. This direct regulation of APC/C by lactate stimulates timed degradation of cell cycle proteins, and efficient mitotic exit in proliferative human cells. This mechanism is initiated upon mitotic entry when lactate abundance reaches its apex. In this way, accumulation of lactate communicates the consequences of a nutrient-replete growth phase to stimulate timed opening of APC/C, cell division and proliferation. Conversely, persistent accumulation of lactate drives aberrant APC/C remodelling and can overcome anti-mitotic pharmacology via mitotic slippage. In sum, we define a biochemical mechanism through which lactate directly regulates protein function to control the cell cycle and proliferation.

Utilizing genetic code expansion to modify N-TIMP2 specificity towards MMP-2, MMP-9, and MMP-14

Matrix metalloproteinases (MMPs) regulate the degradation of extracellular matrix (ECM) components in biological processes. MMP activity is controlled by natural tissue inhibitors of metalloproteinases (TIMPs) that non-selectively inhibit the function of multiple MMPs via interaction with the MMPs' Zn2+-containing catalytic pocket. Recent studies suggest that TIMPs engineered to confer MMP specificity could be exploited for therapeutic purposes, but obtaining specific TIMP-2 inhibitors has proved to be challenging. Here, in an effort to improve MMP specificity, we incorporated the metal-binding non-canonical amino acids (NCAAs), 3,4-dihydroxyphenylalanine (L-DOPA) and (8-hydroxyquinolin-3-yl)alanine (HqAla), into the MMP-inhibitory N-terminal domain of TIMP2 (N-TIMP2) at selected positions that interact with the catalytic Zn2+ ion (S2, S69, A70, L100) or with a structural Ca2+ ion (Y36). Evaluation of the inhibitory potency of the NCAA-containing variants towards MMP-2, MMP-9 and MMP-14 in vitro revealed that most showed a significant loss of inhibitory activity towards MMP-14, but not towards MMP-2 and MMP-9, resulting in increased specificity towards the latter proteases. Substitutions at S69 conferred the best improvement in selectivity for both L-DOPA and HqAla variants. Molecular modeling provided an indication of how MMP-2 and MMP-9 are better able to accommodate the bulky NCAA substituents at the intermolecular interface with N-TIMP2. The models also showed that, rather than coordinating to Zn2+, the NCAA side chains formed stabilizing polar interactions at the intermolecular interface with MMP-2 and MMP-9. Our findings illustrate how incorporation of NCAAs can be used to probe-and possibly exploit-differential tolerance for substitution within closely related protein-protein complexes as a means to improve specificity.

Insight into the development of versatile dentin bonding agents to increase the durability of the bonding interface

Despite the huge improvements made in adhesive technology over the past 50 years, there are still some unresolved issues regarding the durability of the adhesive interface. A complete sealing of the interface between the resin and the dentin substrate remains difficult to achieve, and it is doubtful whether an optimal interdiffusion of the adhesive system within the demineralized collagen framework can be produced in a complete and homogeneous way. In fact, it is suggested that hydrolytic degradation, combined with the action of dentin matrix enzymes, destabilizes the tooth-adhesive bond and disrupts the unprotected collagen fibrils. While a sufficient resin-dentin adhesion is usually achieved immediately, bonding efficiency declines over time. Thus, here, a review will be carried out through a bibliographic survey of scientific articles published in the last few years to present strategies that have been proposed to improve and/or develop new adhesive systems that can help prevent degradation at the adhesive interface. It will specially focus on new clinical techniques or new materials with characteristics that contribute to increasing the durability of adhesive restorations and avoiding the recurrent replacement restorative cycle and the consequent increase in damage to the tooth.

Matrix Metalloproteinases in Cardioembolic Stroke: From Background to Complications

Matrix metalloproteinases (MMPs) are endopeptidases participating in physiological processes of the brain, maintaining the blood-brain barrier integrity and playing a critical role in cerebral ischemia. In the acute phase of stroke activity, the expression of MMPs increase and is associated with adverse effects, but in the post-stroke phase, MMPs contribute to the process of healing by remodeling tissue lesions. The imbalance between MMPs and their inhibitors results in excessive fibrosis associated with the enhanced risk of atrial fibrillation (AF), which is the main cause of cardioembolic strokes. MMPs activity disturbances were observed in the development of hypertension, diabetes, heart failure and vascular disease enclosed in CHA₂DS₂VASc score, the scale commonly used to evaluate the risk of thromboembolic complications risk in AF patients. MMPs involved in hemorrhagic complications of stroke and activated by reperfusion therapy may also worsen the stroke outcome. In the present review, we briefly summarize the role of MMPs in the ischemic stroke with particular consideration of the cardioembolic stroke and its complications. Moreover, we discuss the genetic background, regulation pathways, clinical risk factors and impact of MMPs on the clinical outcome.

Utilizing genetic code expansion to modify N-TIMP2 specificity towards MMP-2, MMP-9, and MMP-14

Matrix metalloproteinases (MMPs) regulate the degradation of extracellular matrix (ECM) components in biological processes. MMP activity is controlled by natural tissue inhibitors of metalloproteinases (TIMPs) that non-selectively inhibit the function of multiple MMPs via interaction with the MMPs' Zn ²⁺ -containing catalytic pocket. Recent studies suggest that TIMPs engineered to confer MMP specificity could be exploited for therapeutic purposes, but obtaining specific TIMP-2 inhibitors has proved to be challenging. Here, in an effort to improve MMP specificity, we incorporated the metal-binding non-canonical amino acids (NCAAs), 3,4-dihydroxyphenylalanine (L-DOPA) and (8-hydroxyquinolin-3-yl)alanine (HqAla), into the MMP-inhibitory N-terminal domain of TIMP2 (N-TIMP2) at selected positions that interact with the catalytic Zn ²⁺ ion (S2, S69, A70, L100) or with a structural Ca ²⁺ ion (Y36). Evaluation of the inhibitory potency of the NCAA-containing variants towards MMP-2, MMP-9 and MMP-14 in vitro revealed that most showed a significant loss of inhibitory activity towards MMP-14, but not towards MMP-2 and MMP-9, resulting in increased specificity towards the latter proteases. Substitutions at S69 conferred the best improvement in selectivity for both L-DOPA and HqAla variants. Molecular modeling revealed how MMP-2 and MMP-9 are better able to accommodate the bulky NCAA substituents at the intermolecular interface with N-TIMP2. The models also showed that, rather than coordinating to Zn ²⁺ , the NCAA side chains formed stabilizing polar interactions at the intermolecular interface with MMP-2 and MMP-9. The findings illustrate how incorporation of NCAAs can be used to probe and exploit differential tolerance for substitution within closely related protein-protein complexes to achieve improved specificity.

Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold

Matrix metalloproteinase-2 (MMP2) is a zinc-dependent endopeptidase and a promising target for various diseases, including cancer and fibrosis. Herein, we report the discovery of a novel MMP2-selective inhibitor with high chemical stability and slow tight-binding features. Based on the degradation mechanism of our small-molecule-peptide hybrid 1, the tripeptide linker {5-aminopentanoic acid [Ape(5)]-Glu-Asp} of 1 was replaced by a shorter linker (γ-D-Glu). Phenylbenzamide was suitable for the new generation of MMP2 inhibitors as an S1' pocket-binding group. The introduction of (4S)-aminoproline dramatically increased the chemical stability while maintaining high subtype selectivity because of its interaction with Glu130. TP0597850 (18) exhibited high stability over a wide range of pH values as well as potent MMP2 inhibition (K_i = 0.034 nM) and ≥2000-fold selectivity determined using the inhibition constants. A kinetic analysis revealed that it possesses slow tight-binding nature with a long MMP2 dissociative half-life (t_1/2 = 265 min).

Insights into the immunomodulatory regulation of matrix metalloproteinase at the maternal-fetal interface during early pregnancy and pregnancy-related diseases

Trophoblast immune cell interactions are central events in the immune microenvironment at the maternal-fetal interface. Their abnormalities are potential causes of various pregnancy complications, including pre-eclampsia and recurrent spontaneous abortion. Matrix metalloproteinase (MMP) is highly homologous, zinc(II)-containing metalloproteinase involved in altered uterine hemodynamics, closely associated with uterine vascular remodeling. However, the interactions between MMP and the immune microenvironment remain unclear. Here we discuss the key roles and potential interplay of MMP with the immune microenvironment in the embryo implantation process and pregnancy-related diseases, which may contribute to understanding the establishment and maintenance of normal pregnancy and providing new therapeutic strategies. Recent studies have shown that several tissue inhibitors of metalloproteinases (TIMPs) effectively prevent invasive vascular disease by modulating the activity of MMP. We summarize the main findings of these studies and suggest the possibility of TIMPs as emerging biomarkers and potential therapeutic targets for a range of complications induced by abnormalities in the immune microenvironment at the maternal-fetal interface. MMP and TIMPs are promising targets for developing new immunotherapies to treat pregnancy-related diseases caused by immune imbalance.

Salvianolic Acid B Strikes Back: New Evidence in the Modulation of Expression and Activity of Matrix Metalloproteinase 9 in MDA-MB-231 Human Breast Cancer Cells

Salvianolic acid B (SalB) is a bioactive compound from Salviae miltiorrhizae, one of the most important traditional herbal medicines widely used in several countries for the treatment of cardiovascular diseases. The aim of this study was to evaluate the in vitro effect of SalB on the expression and the activity of matrix metalloproteinase 9 (MMP-9), a zinc-dependent proteolytic enzyme, in human MDA-MB-231 breast cancer cells. This cellular model is characterized by a marked invasive phenotype, supported by a high constitutive expression of MMPs, especially gelatinases. SalB was first of all evaluated by in silico approaches primarily aimed at predicting the main pharmacokinetic parameters. The most favorable interaction between the natural compound and MMP-9 was instead tested by molecular docking analysis that was subsequently verified by an enzymatic inhibition assay. MDA-MB-231 cells were treated with SalB 5 µM and 50 µM for 24 h and 48 h. The conditioned media obtained from treated cells were then analyzed by gelatin zymography and reverse zymography to, respectively, evaluate the MMP-9 activity and the presence of TIMP-1. The expression of the enzyme was then evaluated by Western blot on conditioned media and by analysis of transcripts through reverse transcriptase-polymerase chain reaction (RT-PCR). The in silico approach showed the ability of SalB to interact with the catalytic zinc ion of the enzyme, with a plausible competitive mode of action. The analysis of conditioned culture media showed a reduction in MMP-9 activity and the concomitant decrease in the enzyme concentration, partially confirmed by analysis of transcripts. SalB showed the ability to modulate the function of MMP-9 in MDA-MB-231 cells. To our knowledge, this is the first time in which the role of SalB on MMP-9 in a highly invasive cellular model is investigated. The obtained results impose further and more specific evaluations in order to obtain a better understanding of the biochemical mechanisms that regulate the interaction between this natural compound and the MMP-9.

Recent Update on Applications of Quaternary Ammonium Silane as an Antibacterial Biomaterial: A Novel Drug Delivery Approach in Dentistry

Quaternary ammonium silane [(QAS), codename – k21] is a novel biomaterial developed by sol-gel process having broad spectrum antimicrobial activities with low cytotoxicity. It has been used in various concentrations with maximum antimicrobial efficacy and biocompatibility. The antimicrobial mechanism is displayed via contact killing, causing conformational changes within the bacterial cell membrane, inhibiting Sortase-A enzyme, and causing cell disturbances due to osmotic changes. The compound can attach to S1' pockets on matrix metalloproteinases (MMPs), leading to massive MMP enzyme inhibition, making it one of the most potent protease inhibitors. Quaternary ammonium silane has been synthesized and used in dentistry to eliminate the biofilm from dental tissues. QAS has been tested for its antibacterial activity as a cavity disinfectant, endodontic irrigant, restorative and root canal medication, and a nanocarrier for drug delivery approaches. The review is first of its kind that aims to discuss applications of QAS as a novel antibacterial biomaterial for dental applications along with discussions on its cytotoxic effects and future prospects in dentistry.

Selective Inhibitors of Medium-Size S1' Pocket Matrix Metalloproteinases: A Stepping Stone of Future Drug Discovery

Among various matrix metalloproteinases (MMPs), MMPs having medium-size S1' pockets are established as promising biomolecular targets for executing crucial roles in cancer, cardiovascular diseases, and neurodegenerative diseases. However, no such MMP inhibitors (MMPIs) are available to date as drug candidates despite a lot of continuous research work for more than three decades. Due to a high degree of structural resemblance among these MMPs, designing selective MMPIs is quite challenging. However, the variability and uniqueness of the S1' pockets of these MMPs make them promising targets for designing selective MMPIs. In this perspective, the overall structural aspects of medium-size S1' pocket MMPs including the unique binding patterns of enzyme-inhibitor interactions have been discussed in detail to acquire knowledge regarding selective inhibitor designing. This overall knowledge will surely be a curtain raiser for the designing of selective MMPIs as drug candidates in the future.

Alpinumisoflavone against cancer pro-angiogenic targets: In silico, In vitro, and In ovo evaluation

BACKGROUND

Breast cancer is currently the world's most predominant malignancy. In cancer progression, angiogenesis is a requirement for tumor growth and metastasis.Alpinumisoflavone (AIF), a bioactive isoflavonoid, exhibited good binding affinity with the angiogenesis pathway's druggable target through molecular docking.

OBJECTIVES

To confirm AIF's angiogenesis inhibitory activity, cytotoxic potential toward breast cancer cells, and druggability.

METHODS

Antiangiogenic activity was evaluated in six pro-angiogenic proteins in vitro, duck chorioallantoic membrane (CAM) in ovo, molecular docking and druggability in silico.

RESULTS

Findings showed that AIF significantly inhibited (p =  < 0.001) the HER2(IC50 = 2.96 µM), VEGFR-2(IC50 = 4.80 µM), MMP-9(IC50 = 23.00 µM), FGFR4(IC50 = 57.65 µM), EGFR(IC50 = 92.06 µM) and RET(IC50 =  > 200 µM) activity in vitro.AIF at 25 µM-200 µM significantly inhibited (p =  < 0.001) the total number of branch points (IC50 = 14.25 μM) and mean length of tubule complexes (IC50 = 3.52 μM) of duck CAM comparable (p =  > 0.001) with the positive control 200 µM celecoxib on both parameters.AIF inhibited the growth of the estrogen-receptor-positive (ER +) human breast cancer cells (MCF-7) by 44.92 ± 1.79% at 100 µM while presenting less toxicity to human dermal fibroblast neonatal (HDFn) normal cells.The positive control 100 µM doxorubicin showed 86.66 ± 0.93% and 92.97 ± 1.27% inhibition with MCF-7 (IC50 = 3.62 μM) and HDFn, (IC50 = 27.16 μM) respectively.In docking, AIF has the greatest in silico binding affinity on HER2 (-10.9 kcal/mol) among the key angiogenic molecules tested. In silico rat oral LD50 calculation indicates that AIF is moderate to slightly toxic at 146.4 mg/kg with 1.1 g/kg and 20.1 mg/kg upper and lower 95% confidence limits. Lastly, it sufficiently complies with Lipinski's, Veber's, Egan's, Ghose's, and Muegge's Rule, supporting its oral drug-like property.

CONCLUSION

This study revealed that AIF possesses characteristics of a phytoestrogen compound with significant binding affinity, inhibitory activity against pro-angiogenic proteins, and cytotoxic potential against ER + breast cancer cells.The acceptable and considerable safety and drug-likeness profiles of AIF are worthy of further confirmation in vivo and advanced pre-clinical studies so that AIF can be elevated as a promising molecule for breast cancer therapy.

Matrix Metalloproteinases: From Molecular Mechanisms to Physiology, Pathophysiology, and Pharmacology

The first matrix metalloproteinase (MMP) was discovered in 1962 from the tail of a tadpole by its ability to degrade collagen. As their name suggests, matrix metalloproteinases are proteases capable of remodeling the extracellular matrix. More recently, MMPs have been demonstrated to play numerous additional biologic roles in cell signaling, immune regulation, and transcriptional control, all of which are unrelated to the degradation of the extracellular matrix. In this review, we will present milestones and major discoveries of MMP research, including various clinical trials for the use of MMP inhibitors. We will discuss the reasons behind the failures of most MMP inhibitors for the treatment of cancer and inflammatory diseases. There are still misconceptions about the pathophysiological roles of MMPs and the best strategies to inhibit their detrimental functions. This review aims to discuss MMPs in preclinical models and human pathologies. We will discuss new biochemical tools to track their proteolytic activity in vivo and ex vivo, in addition to future pharmacological alternatives to inhibit their detrimental functions in diseases. SIGNIFICANCE STATEMENT: Matrix metalloproteinases (MMPs) have been implicated in most inflammatory, autoimmune, cancers, and pathogen-mediated diseases. Initially overlooked, MMP contributions can be both beneficial and detrimental in disease progression and resolution. Thousands of MMP substrates have been suggested, and a few hundred have been validated. After more than 60 years of MMP research, there remain intriguing enigmas to solve regarding their biological functions in diseases.

Discovery of Aryloxyphenyl-Heptapeptide Hybrids as Potent and Selective Matrix Metalloproteinase-2 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis

Matrix metalloproteinase-2 (MMP2) is a zinc-dependent endopeptidase that plays important roles in the degradation of extracellular matrix proteins. MMP2 is considered to be an attractive target for the treatment of various diseases such as cancer, arthritis, and fibrosis. In this study, we have developed a novel class of MMP2-selective inhibitors by hybridizing the peptide that binds to a zinc ion and S2-S5 pockets with small molecules that bind to the S1' pocket. Structural modifications based on X-ray crystallography revealed that the introduction of 2,4-diaminobutanoic acid (Dab) at position 4 dramatically enhanced MMP2 selectivity by forming an electrostatic interaction with Glu130. After improving the metabolic and chemical stability, TP0556351 (9) was identified. It exhibited potent MMP2 inhibitory activity (IC₅₀ = 0.20 nM) and extremely high selectivity. It suppressed the accumulation of collagen in a bleomycin-induced idiopathic pulmonary fibrosis model in mice, demonstrating the efficacy of MMP2-selective inhibitors for fibrosis.

First-in-Class Star-Shaped Triazine Dendrimers Endowed with MMP-9 Inhibition and VEGF Suppression Capacity: Design, Synthesis, and Anticancer Evaluation

Off-target side effects are major challenges hindering the clinical success of matrix metalloproteinase (MMP) inhibitors. Various targeting strategies revitalized MMP research to eliminate this drawback. Herein, we developed s-triazine-based dendrimeric architecture not only amenable to tumor targeting but also decorated with pharmacophoric entities to endow MMP-9 inhibition for halting cancer progression. The design rationale utilized hydrazide branching chains as well as carboxylic and hydroxamic acid termini as Zn-binding groups to confer substantial MMP inhibitory potential. The carboxylic acids are tetherable to tumor targeting ligands and other cargo payloads as synergistic drugs via biodegradable linkages. The synthesized series were screened for cytotoxicity against normal fibroblasts (Wi-38) and two selected cancers (MDA-MB 231 and Caco-2) via MTT assay. The most active hexacarboxylic acid dendrimer 8a was more potent and safer than Dox against MDA-MB 231 and Caco-2 cells. It intrinsically inhibited MMP-9 with selectivity over MMP-2. Docking simulations demonstrated that the extended carboxylic acid termini of 8a could possibly chelate the active site Zn of MMP-9 and form hydrogen-bonding interactions with the ligand essential backbone Tyr423. In addition, it suppressed the correlated oncogenic mediators VEGF and cyclin D, upregulated p21 expression, induced apoptosis (>75%), and inhibited the tumor cell migration (∼84%) in the treated cancer cells. Thus, up to our knowledge, it is the first triazine-based MMP-9 inhibitor dendrimer endowed with VEGF suppression potential that can be employed as a bioactive carrier.

Metalloproteinase-Dependent and TMPRSS2-Independent Cell Surface Entry Pathway of SARS-CoV-2 Requires the Furin Cleavage Site and the S2 Domain of Spike Protein

The ongoing global vaccination program to prevent SARS-CoV-2 infection, the causative agent of COVID-19, has had significant success. However, recently, virus variants that can evade the immunity in a host achieved through vaccination have emerged. Consequently, new therapeutic agents that can efficiently prevent infection from these new variants, and hence COVID-19 spread, are urgently required. To achieve this, extensive characterization of virus-host cell interactions to identify effective therapeutic targets is warranted. Here, we report a cell surface entry pathway of SARS-CoV-2 that exists in a cell type-dependent manner and is TMPRSS2 independent but sensitive to various broad-spectrum metalloproteinase inhibitors such as marimastat and prinomastat. Experiments with selective metalloproteinase inhibitors and gene-specific small interfering RNAS (siRNAs) revealed that a disintegrin and metalloproteinase 10 (ADAM10) is partially involved in the metalloproteinase pathway. Consistent with our finding that the pathway is unique to SARS-CoV-2 among highly pathogenic human coronaviruses, both the furin cleavage motif in the S1/S2 boundary and the S2 domain of SARS-CoV-2 spike protein are essential for metalloproteinase-dependent entry. In contrast, the two elements of SARS-CoV-2 independently contributed to TMPRSS2-dependent S2 priming. The metalloproteinase pathway is involved in SARS-CoV-2-induced syncytium formation and cytopathicity, leading us to theorize that it is also involved in the rapid spread of SARS-CoV-2 and the pathogenesis of COVID-19. Thus, targeting the metalloproteinase pathway in addition to the TMPRSS2 and endosomal pathways could be an effective strategy by which to cure COVID-19 in the future. IMPORTANCE To develop effective therapeutics against COVID-19, it is necessary to elucidate in detail the infection mechanism of the causative agent, SARS-CoV-2. SARS-CoV-2 binds to the cell surface receptor ACE2 via the spike protein, and then the spike protein is cleaved by host proteases to enable entry. Here, we found that the metalloproteinase-mediated pathway is important for SARS-CoV-2 infection in addition to the TMPRSS2-mediated pathway and the endosomal pathway. The metalloproteinase-mediated pathway requires both the prior cleavage of spike into two domains and a specific sequence in the second domain, S2, conditions met by SARS-CoV-2 but lacking in the related human coronavirus SARS-CoV. Besides the contribution of metalloproteinases to SARS-CoV-2 infection, inhibition of metalloproteinases was important in preventing cell death, which may cause organ damage. Our study provides new insights into the complex pathogenesis unique to COVID-19 and relevant to the development of effective therapies.

Integrated Whole-Transcriptome Profiling and Bioinformatics Analysis of the Polypharmacological Effects of Ganoderic Acid Me in Colorectal Cancer Treatment

Ganoderic acid Me (GA-Me) is a natural bioactive compound derived from Ganoderma lucidum. Our present results suggested that GA-Me inhibited proliferation, induced DNA fragmentation and significantly activated caspase-9 and caspase-3 in HCT116 cells. As shown in our previous studies, GA-Me targets several genes to prevent cancer, including colorectal cancer (CRC). Thus, we hypothesized that GA-Me might be a multitarget ligand against cancer. However, its exact mechanism in CRC remains unclear. Here, whole-transcriptome sequencing was employed to assess the long noncoding RNA (lncRNA), circular RNA (circRNA), microRNA (miRNA), and messenger RNA (mRNA) profiles of GA-Me-treated HCT116 cells. In total, 1572 differentially expressed (DE) lncRNAs, 123 DEcircRNAs, 87 DEmiRNAs, and 1508 DEmRNAs were identified. DCBLD2 and RAPGEF5 were validated as two core mRNAs in the DElncRNA, DEcircRNA, and DEmiRNA networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed the biological functions and potential mechanisms of TCONS-00008997, XR-925056.2, circRNA-07908, hsa-miR-100-3p, hsa-miR-1257, hsa-miR-3182, NAV3, ADAM20, and STARD4, which were altered after GA-Me treatment. The regulatory relationships of the XR-925056.2-hsa-miR-3182-NAV3/ADAM20/STARD4, circRNA-07908|Chr22:38986298-39025349-hsa-miR-3182-NAV3/ADAM20, ENST00000414039/ENST00000419190-novel874_mature-MMP9 and circRNA-00314|Chr1:35470863-35479212/circRNA-05460|Chr17:72592203-72649268-novel874_mature-MMP9 immune-regulatory networks involved both noncoding RNAs (ncRNAs) and mRNAs. Molecular docking studies showed that Zn2+ and the His201, His205, His211, Glu202, and Ala165 residues of MMP2 contributed to its high affinity for GA-Me. Zn2+ and the Glu402 and Gly186 residues of MMP9 are important for its interaction with GA-Me. Our results suggested and confirmed that GA-Me is a potential multitarget lead compound for CRC treatment with unique polypharmacological advantages.

Inhibitory proteins block substrate access by occupying the active site cleft of Bacillus subtilis intramembrane protease SpoIVFB

Intramembrane proteases (IPs) function in numerous signaling pathways that impact health, but elucidating the regulation of membrane-embedded proteases is challenging. We examined inhibition of intramembrane metalloprotease SpoIVFB by proteins BofA and SpoIVFA. We found that SpoIVFB inhibition requires BofA residues in and near a predicted transmembrane segment (TMS). This segment of BofA occupies the SpoIVFB active site cleft based on cross-linking experiments. SpoIVFB inhibition also requires SpoIVFA. The inhibitory proteins block access of the substrate N-terminal region to the membrane-embedded SpoIVFB active site, based on additional cross-linking experiments; however, the inhibitory proteins did not prevent interaction between the substrate C-terminal region and the SpoIVFB soluble domain. We built a structural model of SpoIVFB in complex with BofA and parts of SpoIVFA and substrate, using partial homology and constraints from cross-linking and co-evolutionary analyses. The model predicts that conserved BofA residues interact to stabilize a TMS and a membrane-embedded C-terminal region. The model also predicts that SpoIVFA bridges the BofA C-terminal region and SpoIVFB, forming a membrane-embedded inhibition complex. Our results reveal a novel mechanism of IP inhibition with clear implications for relief from inhibition in vivo and design of inhibitors as potential therapeutics.

Identification of Zinc-Binding Inhibitors of Matrix Metalloproteinase-9 to Prevent Cancer Through Deep Learning and Molecular Dynamics Simulation Approach

The overexpression of matrix metalloproteinase-9 (MMP-9) is associated with tumor development and angiogenesis, and hence, it has been considered an attractive drug target for anticancer therapy. To assist in drug design endeavors for MMP-9 targets, an in silico study was presented to investigate whether our compounds inhibit MMP-9 by binding to the catalytic domain, similar to their inhibitor or not. For that, in the initial stage, a deep-learning algorithm was used for the predictive modeling of the CHEMBL321 dataset of MMP-9 inhibitors. Several regression models were built and evaluated based on R2, MAE MSE, RMSE, and Loss. The best model was utilized to screen the drug bank database containing 9,102 compounds to seek novel compounds as MMP-9 inhibitors. Then top high score compounds were selected for molecular docking based on the comparison between the score of the reference molecule. Furthermore, molecules having the highest docking scores were selected, and interaction mechanisms with respect to S1 pocket and catalytic zinc ion of these compounds were also discussed. Those compounds, involving binding to the catalytic zinc ion and the S1 pocket of MMP-9, were considered preferentially for molecular dynamics studies (100 ns) and an MM-PBSA (last 30 ns) analysis. Based on the results, we proposed several novel compounds as potential candidates for MMP-9 inhibition and investigated their binding properties with MMP-9. The findings suggested that these compounds may be useful in the design and development of MMP-9 inhibitors in the future.

Effects of the Nature of the Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies

Matrix metalloproteinase-1 (MMP-1) is a Zn(II) dependent endopeptidase involved in the degradation of collagen, the most abundant structural protein in the extracellular matrix of connective tissues and the human body. Herein we performed a multilevel computational analysis including molecular dynamics (MD), combined quantum mechanics/molecular mechanics (QM/MM), and quantum mechanics (QM) calculations to characterize the structure and geometry of the catalytic Zn(II) within the MMP-1 protein environment in comparison to crystallographic and spectroscopic data. The substrate's removal fine-tuned impact on the conformational dynamics and geometry of the catalytic Zn(II) center was also explored. Finally, the study examined the effect of substituting catalytic Zn(II) by Co(II) on the overall structure and dynamics of the MMP-1 THP complex and specifically on the geometry of the catalytic metal center. Overall our QM/MM and QM studies were in good agreement with the MM description of the Zn(II) centers in the MD simulations.