Caffeic Acid in Spent Coffee Grounds as a Dual Inhibitor for MMP-9 and DPP-4 Enzymes.

Type 2 diabetes mellitus and diabetic foot ulcers remain serious worldwide health problems. Caffeic acid is one of the natural products that has been experimentally proven to have diverse pharmacological properties. This study aimed to assess the inhibitory activity of caffeic acid and ethanolic extract of spent coffee grounds targeting DPP-4 and MMP-9 enzymes and evaluate the molecular interactions through 50-ns molecular dynamics simulations. This study also introduced our new version of PyPLIF HIPPOS, PyPLIF HIPPOS 0.2.0, which allowed us to identify protein-ligand interaction fingerprints and interaction hotspots resulting from molecular dynamics simulations. Our findings revealed that caffeic acid inhibited the DPP-4 and MMP-9 activity with an IC50 of 158.19 ± 11.30 µM and 88.99 ± 3.35 µM while ethanolic extract of spent coffee grounds exhibited an IC50 of 227.87 ± 23.80 µg/100 µL and 81.24 ± 6.46 µg/100 µL, respectively. Molecular dynamics simulations showed that caffeic acid interacted in the plausible allosteric sites of DPP-4 and in the active site of MMP-9. PyPLIF HIPPOS 0.2.0 identified amino acid residues interacting more than 10% throughout the simulation, which were Lys463 and Trp62 in the plausible allosteric site of DPP-4 and His226 in the active site of MMP-9.

PyPLIF HIPPOS and Receptor Ensemble Docking Increase the Prediction Accuracy of the Structure-Based Virtual Screening Protocol Targeting Acetylcholinesterase.

In this article, the upgrading process of the structure-based virtual screening (SBVS) protocol targeting acetylcholinesterase (AChE) previously published in 2017 is presented. The upgraded version of PyPLIF called PyPLIF HIPPOS and the receptor ensemble docking (RED) method using AutoDock Vina were employed to calculate the ensemble protein-ligand interaction fingerprints (ensPLIF) in a retrospective SBVS campaign targeting AChE. A machine learning technique called recursive partitioning and regression trees (RPART) was then used to optimize the prediction accuracy of the protocol by using the ensPLIF values as the descriptors. The best protocol resulting from this research outperformed the previously published SBVS protocol targeting AChE.

Effect of supplementation of Rhodomyrtus tomentosa fruit juice in preventing hypercholesterolemia and atherosclerosis development in rats fed with high fat high cholesterol diet.

Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Nutraceuticals, mainly based on natural products, have been proven to control the risk factors of CVDs effectively. Rhodomyrtus tomentosa is an underutilized fruit that is rich in phenolic compounds and has antioxidant activities. Scientific investigation was needed to verify the pharmacological properties of R. tomentosa fruit juice in Sprague-Dawley rats fed with high fat high cholesterol (HFHC) as antihypercholesterolemic and antiatherosclerotic agents. The experiments were carried out using male albino rats fed with HFHC diet for 75 days and at the same time orally supplemented with R. tomentosa fruit juice (RTFJ) in doses of 0.5, 1, and 2 g/kg body weight (BW) daily for 75 days. Simvastatin was used as a positive control. At the end of the experiment, the blood was collected, and the serum was assayed for total triglycerides (TG), total cholesterol (TC), low-density lipoprotein (LDL-C), and high-density lipoprotein (HDL-C). The histopathology of coronary and aorta arteries was observed under the light microscope. The results demonstrated that the supplementation of RTFJ significantly prevented the increase of total triglycerides, total cholesterol, low-density lipoprotein, and the decrease of high-density lipoprotein in serum. Supplementation of RTFJ also prevents atherosclerosis development by preventing the thickening of the blood vessel wall, deposition of lipid formation, and foam cells in the tunica intima of the aorta and coronary arteries. These findings suggested that supplementation of R. tomentosa fruit juice prevents hypercholesterolemia and atherosclerosis.

PyPLIF HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors.

Identification of molecular determinants of receptor-ligand binding could significantly increase the quality of structure-based virtual screening protocols. In turn, drug design process, especially the fragment-based approaches, could benefit from the knowledge. Retrospective virtual screening campaigns by employing AutoDock Vina followed by protein-ligand interaction fingerprinting (PLIF) identification by using recently published PyPLIF HIPPOS were the main techniques used here. The ligands and decoys datasets from the enhanced version of the database of useful decoys (DUDE) targeting human G protein-coupled receptors (GPCRs) were employed in this research since the mutation data are available and could be used to retrospectively verify the prediction. The results show that the method presented in this article could pinpoint some retrospectively verified molecular determinants. The method is therefore suggested to be employed as a routine in drug design and discovery.

Effect of Annona muricata Leaf Extract Towards the Sertoli Cells on Alloxan-Induced Mice.

<b>Background and Objective:</b> Prolonged and uncontrolled hyperglycemia in diabetes mellitus can increase the production of reactive oxygen and enhance the risk of male infertility by reducing the number of Sertoli cells. This study aimed to investigate the potential effect of Ethanol Extract of <i>Annona muricata </i>leaf (EEAL) on the amount of Sertoli cells in alloxan-induced mice antioxidant to prevent reducing the number of Sertoli cells. <b>Materials and Methods:</b> The samples used for this study are 30 alloxan-induced Swiss Webster mice divided into a negative control group, a positive control group (glibenclamide 0.65 mg kg¹) and three plant extract groups (EEAL 150, 300 and 600 mg kg¹). Every solution was given every day for 14 days. Histological examination using HE-stained preparations was performed on 40x magnification to evaluate many Sertoli cells counted using Image J software. <b>Results:</b> three EEAL groups of 150, 300 and 600 mg kg¹ have significant effects (p<0.05) to increase the amounts of Sertoli cells compared to a negative control group. In contrast, it does not significantly affect the amounts of Sertoli cells than the positive control group. <b>Conclusion:</b> The administration of <i>A. muricata</i> leaf extract during 14 days significantly reduced the number of Sertoli cells on alloxan-induced mice.

PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS.

We describe here our tool named PyPLIF HIPPOS, which was newly developed to analyze the docking results of AutoDock Vina and PLANTS. Its predecessor, PyPLIF (https://github.com/radifar/pyplif), is a molecular interaction fingerprinting tool for the docking results of PLANTS, exclusively. Unlike its predecessor, PyPLIF HIPPOS speeds up the computational times by separating the reference generation and docking analysis. PyPLIF HIPPOS also offers more options compared to PyPLIF. PyPLIF HIPPOS for Linux is stored as the Supporting Information in this application note and can be accessed in GitHub (https://github.com/radifar/PyPLIF-HIPPOS). Additionally, we present here the application of the tool in a retrospective structure-based virtual screening campaign targeting neuraminidase.

The Antiviral Effect of Indonesian Medicinal Plant Extracts Against Dengue Virus In Vitro and In Silico.

Dengue infections are still a worldwide burden, especially in Indonesia. There is no specific medication against the dengue virus. Recently, many types of research have been conducted to discover a new drug for dengue virus using natural resource extracts. Indonesia, as a tropical country, has a wide biodiversity. There are several medicinal plants in Indonesia that are believed to possess anti-dengue activity, such as Myristica fatua, Cymbopogon citratus, and Acorus calamus plants. We conducted an in vitro laboratory experiment of several extracts from Indonesian herbs combined with in silico analysis. The extracts were evaluated for safety and antiviral activity in Huh7it-1 cell lines, using a single dose of 20 µg/mL and dose-dependent (5, 10, 20, 40, 80 and 160 µg/mL) of plant extracts against dengue virus serotype 2 (DENV-2) NGC strain. The DMSO 0.1% was used as a negative control. The cytotoxic aspect was assessed by counting the cell viability, while the antiviral activity was calculated by counting the average inhibition. The selectivity index (SI) of plant extracts were performed from a ratio of CC50/EC50 value. In silico analysis was conducted to determine the free energy of binding between NS5 of dengue virus with bioactive compounds contained in Myristica fatua, Cymbopogon citratus and Acorus calamus extract plants. We determined that all extracts were not toxic against Huh7it-1 cell lines. The methanolic extracts of A. calamus, C. citratus, and M. fatua showed inhibition of DENV-2 at a dose of 20 µg/mL to 96.5%, 98.9%, and 122.7%, respectively. The dose-dependent effects showed that M. fatua has the best inhibition activity towards DENV-2. Molecular docking result showed that artesunic acid within M. fatua has the best free energy of binding (-7.2 kcal/mol), followed by homoegonol (-7.1 kcal/mol) which was slightly different from artesunic acid among others. The methanolic extracts of A. calamus, C. citratus, and M. fatua showed prospective anti-dengue activities both in vitro and in silico. Future research should be conducted to find the pure extracts of all useful herbs as a new candidate of antiviral drug.

Probing the interaction between cHAVc3 peptide and the EC1 domain of E-cadherin using NMR and molecular dynamics simulations.

The goal of this work is to probe the interaction between cyclic cHAVc3 peptide and the EC1 domain of human E-cadherin protein. Cyclic cHAVc3 peptide (cyclo(1,6)Ac-CSHAVC-NH2) binds to the EC1 domain as shown by chemical shift perturbations in the 2D 1H,-15N-HSQC NMR spectrum. The molecular dynamics (MD) simulations of the EC1 domain showed folding of the C-terminal tail region into the main head region of the EC1 domain. For cHAVc3 peptide, replica exchange molecular dynamics (REMD) simulations generated five structural clusters of cHAVc3 peptide. Representative structures of cHAVc3 and the EC1 structure from MD simulations were used in molecular docking experiments with NMR constraints to determine the binding site of the peptide on EC1. The results suggest that cHAVc3 binds to EC1 around residues Y36, S37, I38, I53, F77, S78, H79, and I94. The dissociation constants (Kd values) of cHAVc3 peptide to EC1 were estimated using the NMR chemical shifts data and the estimated Kds are in the range of .5 × 10-5-7.0 × 10-5 M.

(1)H, (13)C and (15)N backbone assignment of the EC-1 domain of human E-cadherin.

The Extracellular 1 (EC1) domain of E-cadherin has been shown to be important for cadherin-cadherin homophilic interactions. Cadherins are responsible for calcium-mediated cell-cell adhesion located at the adherens junction of the biological barriers (i.e., intestinal mucosa and the blood-brain barrier (BBB)). Cadherin peptides can modulate cadherin interactions to improve drug delivery through the BBB. However, the mechanism of modulating the E-cadherin interactions by cadherin peptides has not been fully elucidated. To provide a basis for subsequent examination of the structure and peptide-binding properties of the EC1 domain of human E-cadherin using solution NMR spectroscopy, the (1)H, (13)C and (15)N backbone resonance of the uniformly labeled-EC1 were assigned and the secondary structure was determined based on the chemical shift values. These resonance assignments are essential for assessing protein-ligand interactions and are reported here.

Pathways and progress in improving drug delivery through the intestinal mucosa and blood-brain barriers.

One of the major hurdles in developing therapeutic agents is the difficulty in delivering drugs through the intestinal mucosa and blood-brain barriers (BBB). The goal here is to describe the general structures of the biological barriers and the strategies to enhance drug delivery across these barriers. Prodrug methods used to improve drug penetration via the transcellular pathway have been successfully developed, and some prodrugs have been used to treat patients. The use of transporters to improve absorption of some drugs (e.g., antiviral agents) has also been successful in treating patients. Other methods, including blocking the efflux pumps to improve transcellular delivery, and modulation of cell-cell adhesion in the intercellular junctions to improve paracellular delivery across biological barriers, are still in the investigational stage.