Computational and In Vitro Investigation of (-)-Epicatechin and Proanthocyanidin B2 as Inhibitors of Human Matrix Metalloproteinase 1

Small molecular exogenous modulators of active forms of MMPs

Matrix metalloproteinases (MMPs) are endopeptidases, and their activity depends on calcium and zinc metal ions. These enzymes are expressed originally in zymogenic form, where the active site of proteins is closed by a prodomain which is removed during activation. A homeostatic balance of their activity is primarily regulated by a 'cysteine switch' located on a consensus sequence of the prodomain and natural endogenous inhibitors, called tissue inhibitors of metalloproteinases (TIMPs). Breakage of this homeostasis may lead to various pathological conditions, which may require further activation and/or inhibition of these enzymes to regenerate that balance. Here, we report four modulators, more specifically, three inhibitors (I1, I2 and I3), and one exogenous activator (L) of the active form of human collagenase MMP-1 (without prodomain). The results were confirmed by binding studies using fluorescence-based enzyme assays.

Five New Tamarixetin Glycosides from Astragalus thracicus Griseb. Including Some Substituted with the Rare 3-Hydroxy-3-methylglutaric Acid and Their Collagenase Inhibitory Effects In Vitro

Along with the known kaempferol-3-O-α-l-rhamnopyranosyl-(1 → 2)-[6-O-(3-hydroxy-3-methylglutaryl)]-β-d-galactopyranoside (1), five new flavonoids, containing the rarely isolated aglycon tamarixetin, were isolated from a methanolic extract of the endemic Balkan species Astragalus thracicus Griseb. Three of the new compounds are substituted with 3-hydroxy-3-methylglutaryl residue (HMG), untypical for the genus Astragalus. The compounds were identified as tamarixetin-3-O-α-l-rhamnopyranosyl-(1 → 2)-[6-O-(3-hydroxy-3-methylglutaryl)]-β-d-galactopyranoside (2), tamarixetin-3-O-(2,6-di-O-α-l-rhamnopyranosyl)-β-d-galactopyranoside (3), tamarixetin 3-O-β-d-apiofuranosyl-(1 → 2)-β-d-galactopyranoside (4), tamarixetin-3-O-β-d-apiofuranosyl-(1 → 2)-[6-O-(3-hydroxy-3-methylglutaryl)]-β-d-galactopyranoside (5), and tamarixetin-3-O-β-d-apiofuranosyl-(1 → 2)-[α-l-rhamnopyranosyl-(1 → 6)]-β-d-galactopyranoside (6). Selected compounds from A. thracicus were tested to evaluate their anticollagenase activity. The greatest effect was observed for quercetin-3-O-β-d-apiofuranosyl-(1 → 2)-β-d-galactopyranoside, possibly due to the presence of an ortho-dihydroxy arrangement of flavonoid ring B. The effect on collagenase and elastase was further evaluated also by in silico study, and the test compounds showed some level of in silico interaction.

Unlocking Potentially Therapeutic Phytochemicals in Capadulla (Doliocarpus dentatus) from Guyana Using Untargeted Mass Spectrometry-Based Metabolomics

Doliocarpus dentatus is thought to have a wide variety of therapeutic phytochemicals that allegedly improve libido and cure impotence. Although a few biomarkers have been identified with potential antinociceptive and cytotoxic properties, an untargeted mass spectrometry-based metabolomics approach has never been undertaken to identify therapeutic biofingerprints for conditions, such as erectile dysfunction, in men. This study executes a preliminary phytochemical screening of the woody vine of two ecotypes of D. dentatus with renowned differences in therapeutic potential for erectile dysfunction. Liquid chromatography-mass spectrometry-based metabolomics was used to screen for flavonoids, terpenoids, and other chemical classes found to contrast between red and white ecotypes. Among the metabolite chemodiversity found in the ecotype screens, using a combination of GNPS, MS-DIAL, and SIRIUS, approximately 847 compounds were annotated at levels 2 to 4, with the majority of compounds falling under lipid and lipid-like molecules, benzenoids and phenylpropanoids, and polyketides, indicative of the contributions of the flavonoid, shikimic acid, and terpenoid biosynthesis pathways. Despite the extensive annotation, we report on 138 tentative compound identifications of potentially therapeutic compounds, with 55 selected compounds at a level-2 annotation, and 22 statistically significant therapeutic biomarkers, the majority of which were polyphenols. Epicatechin methyl gallate, catechin gallate, and proanthocyanidin A2 had the greatest significant differences and were also relatively abundant among the red and white ecotypes. These putatively identified compounds reportedly act as antioxidants, neutralizing damaging free radicals, and lowering cell oxidative stress, thus aiding in potentially preventing cellular damage and promoting overall well-being, especially for treating erectile dysfunction (ED).

Oligomeric Proanthocyanidins: An Updated Review of Their Natural Sources, Synthesis, and Potentials

Oligomeric Proanthocyanidins (OPCs), as a class of compounds widely found in plants, are particularly abundant in grapes and blueberries. It is a polymer comprising many different monomers, such as catechins and epicatechins. The monomers are usually linked to each other by two types of links, A-linkages (C-O-C) and B-linkages (C-C), to form the polymers. Numerous studies have shown that compared to high polymeric procyanidins, OPCs exhibit antioxidant properties due to the presence of multiple hydroxyl groups. This review describes the molecular structure and natural source of OPCs, their general synthesis pathway in plants, their antioxidant capacity, and potential applications, especially the anti-inflammatory, anti-aging, cardiovascular disease prevention, and antineoplastic functions. Currently, OPCs have attracted much attention, being non-toxic and natural antioxidants of plant origin that scavenge free radicals from the human body. This review would provide some references for further research on the biological functions of OPCs and their application in various fields.

The Anti-Photoaging Activity of Peptides from Pinctada martensii Meat

Long-term exposure to ultraviolet-B (UVB) can cause photoaging. Peptides from Pinctada martensii meat have been shown to have anti-photoaging activities, but their mechanism of action is rarely studied. In this study, Pinctada martensii meat hydrolysates (PME) were prepared by digestive enzymes and then separated by ultrafiltration and Sephadex G-25 gel filtration chromatography to obtain a purified fraction (G2). The fraction G2 was identified by ultra-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS), and peptide sequences were synthesized by solid-phase synthesis. The mechanism of anti-photoaging activities was investigated using a human immortalised epidermal (HaCaT) cell model. Results showed that peptides from Pinctada martensii meat increased UVB-induced cell viability and reduced the contents of interstitial collagenase (MMP-1) and matrix lysing enzyme (MMP-3) in HaCaT cells. Furthermore, the fraction of G2 significantly downregulated the expression of p38, EKR, JNK, MMP-1, and MMP-3 in HaCaT cells. The peptide sequences Phe-His (FH), Ala-Leu (AL), Met-Tyr (MY), Ala-Gly-Phe (AGF), and Ile-Tyr-Pro (IYP) were identified and synthesized. Besides, FH reduced the contents of MMP-1 and MMP-3 in HaCaT cells, combining them effectively in molecular docking analysis. Thus, peptides from Pinctada martensii meat showed anti-photoaging activities and might have the potential to be used as an anti-photoaging agent in functional foods.

Computational Investigations on the Natural Small Molecule as an Inhibitor of Programmed Death Ligand 1 for Cancer Immunotherapy

Several therapeutic monoclonal antibodies approved by the FDA are available against the PD-1/PD-L1 (programmed death 1/programmed death ligand 1) immune checkpoint axis, which has been an unprecedented success in cancer treatment. However, existing therapeutics against PD-L1, including small molecule inhibitors, have certain drawbacks such as high cost and drug resistance that challenge the currently available anti-PD-L1 therapy. Therefore, this study presents the screening of 32,552 compounds from the Natural Product Atlas database against PD-L1, including three steps of structure-based virtual screening followed by binding free energy to refine the ideal conformation of potent PD-L1 inhibitors. Subsequently, five natural compounds, i.e., Neoenactin B1, Actinofuranone I, Cosmosporin, Ganocapenoid A, and 3-[3-hydroxy-4-(3-methylbut-2-enyl)phenyl]-5-(4-hydroxybenzyl)-4-methyldihydrofuran-2(3H)-one, were collected based on the ADMET (absorption, distribution, metabolism, excretion, and toxicity) profiling and binding free energy (>−60 kcal/mol) for further computational investigation in comparison to co-crystallized ligand, i.e., JQT inhibitor. Based on interaction mapping, explicit 100 ns molecular dynamics simulation, and end-point binding free energy calculations, the selected natural compounds were marked for substantial stability with PD-L1 via intermolecular interactions (hydrogen and hydrophobic) with essential residues in comparison to the JQT inhibitor. Collectively, the calculated results advocate the selected natural compounds as the putative potent inhibitors of PD-L1 and, therefore, can be considered for further development of PD-L1 immune checkpoint inhibitors in cancer immunotherapy.

In Silico and In Vitro Screening of Natural Compounds as Broad-Spectrum β-Lactamase Inhibitors against Acinetobacter baumannii New Delhi Metallo-β-lactamase-1 (NDM-1)

Antibiotic resistance is one of the significant problems globally; there is an increase in resistance with introducing every new class of antibiotics. Further, this has become one of the reasons for arising of new resistance mechanisms in Acinetobacter baumannii. In this study, we have screened natural compounds as a possible inhibitor against the NDM-1 β-lactamase enzyme from A. baumannii using a combination of in silico methods and in vitro evaluation. The database of natural compounds was screened against NDM-1 protein, using Glide docking, followed by QM-polarised ligand docking (QPLD). When the screened hits were validated in vitro, withaferin A and mangiferin had good IC₅₀ values in reducing the activity of NDM-1 enzymes, and their fractional inhibitory concentration index (FICI) was ascertained in combination with imipenem. The withaferin A and mangiferin-NDM-1 docking complexes were analyzed for structural stability by molecular dynamic simulation analysis using GROMACS for 100 ns. The molecular properties of the natural compounds were then calculated using density functional theory (DFT). Withaferin A and mangiferin showed promising inhibitory activity and can be a natural compound candidate inhibitor synergistically used along with carbapenems against NDM-1 producing A. baumannii.

Macrolactin A as a Novel Inhibitory Agent for SARS-CoV-2 Mpro: Bioinformatics Approach

COVID-19 is a disease that puts most of the world on lockdown and the search for therapeutic drugs is still ongoing. Therefore, this study used in silico screening to identify natural bioactive compounds from fruits, herbaceous plants, and marine invertebrates that are able to inhibit protease activity in SARS-CoV-2 (PDB: 6LU7). We have used extensive screening strategies such as drug likeliness, antiviral activity value prediction, molecular docking, ADME, molecular dynamics (MD) simulation, and MM/GBSA. A total of 17 compounds were shortlisted using Lipinski’s rule in which 5 compounds showed significant predicted antiviral activity values. Among these 5, only 2 compounds, Macrolactin A and Stachyflin, showed good binding energy of −9.22 and −8.00 kcal/mol, respectively, within the binding pocket of the M^pro catalytic residues (HIS 41 and CYS 145). These two compounds were further analyzed to determine their ADME properties. The ADME evaluation of these 2 compounds suggested that they could be effective in developing therapeutic drugs to be used in clinical trials. MD simulations showed that protein–ligand complexes of Macrolactin A and Stachyflin with the target receptor (6LU7) were stable for 100 nanoseconds. The MM/GBSA calculations of M^pro–Macrolactin A complex indicated higher binding free energy (−42.58 ± 6.35 kcal/mol). Dynamic cross-correlation matrix (DCCM) and principal component analysis (PCA) on the residual movement in the MD trajectories further confirmed the stability of Macrolactin A bound state with 6LU7. In conclusion, this study showed that marine natural compound Macrolactin A could be an effective therapeutic inhibitor against SARS-CoV-2 protease (6LU7). Additional in vitro and in vivo validations are strongly needed to determine the efficacy and therapeutic dose of Macrolactin A in biological systems.

Skin Antiaging Effects of the Fermented Outer Layers of Leaf Skin of Aloe barbadensis Miller Associated with the Enhancement of Mitochondrial Activities of UVb-Irradiated Human Skin Fibroblasts

This study is the first to show that increased mitochondrial activities improved the antiaging effects of Aloe vera leaf skin fermented by Lactobacillus plantarum on UVb-irradiated skin fibroblasts. The fermented extract (AF) increased the activities of mitochondrial reductase and the complex II and significantly reduced reactive oxygen species (ROS) production, even under UVb stress conditions, and also increased DPPH free radical scavenging activities compared with the hot water extract of outer layers of aloe leaf (AW) and quercetin itself. AF exerted a synergistic effect with quercetin and bioactive substances derived from the fermentation process. Moreover, mitochondrial activation of UVb-irradiated human skin fibroblasts by 0.3% (w/v) of the AF plays important roles in increasing collagen production up to 125 ± 5.45% and decreasing MMP-1 secretion down to 69.41 ± 2.63% of the control levels. The AF enhanced the upregulation of collagen gene expression, and this change was also greater than those induced by the AW and quercetin. Therefore, this study concludes that fermentation of the skin of aloe leaves increases the activation of mitochondria and inhibits the photo-aging of UVb-irradiated skin fibroblasts.

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.

Inhibitory insights of strawberry (Fragaria × ananassa var. Seolhyang) root extract on tyrosinase activity using computational and in vitro analysis

The strawberry (Fragaria × ananassa var. seolhyang) is commonly used as fruit but medicinal importance for the non-edible roots which contained a pool of bioactive compounds are not yet studied against tyrosinase inhibition. This study demonstrates the potential of bioactive compounds in root and rhizome of strawberry against tyrosinase inhibition using in silico and in vitro approaches. ADMET profiling and molecular docking analysis show druglikeness for the major bioactive compounds in strawberry root extract (SRE), i.e. procyanidin, procyanidin trimer, kaempferol 3-O-(4-O-p-coumaroyl)-glucoside, neochlorogenic acid, procyanidin tetramer, and quercetin-3-O-pentoside, and docking score between -7.8 to -6.3 kcal/mol with tyrosinase, respectively. Also, these docked complexes exhibit substantial stability contributed by strong hydrogen bonding, hydrophobic interactions, and polar interactions in 100 ns molecular dynamics simulation; further supported by essential dynamics and dynamic cross-correlation matrix analysis. Also, in vitro functional assays support in silico predicted results in terms of substantial cytoprotective and cellular antioxidant potential in Raw 264.7 macrophages challenged by H₂O₂ as well as non-significant toxicity in zebrafish. SRE exhibits the lowest (5.8%) and highest (42.8%) inhibition of tyrosinase at 100 and 500 μg/ml concentrations, respectively. These results advocated functional properties and tyrosinase inhibition potential of SRE; and hence, SRE can be used in medicinal or cosmetic applications.