Homology modelling, vHTS, pharmacophore, molecular docking and molecular dynamics studies for the identification of natural compound-derived inhibitor of MRP3 in acute leukaemia treatment

Inhibition of erectile dysfunction-related enzymes by ginger (Zingiber officinale)-derived compounds: molecular docking and dynamics studies

Erectile dysfunction (ED) is one of the common forms of sexual disorder that significantly impacts the psychosocial quality of life amongst male folks. Previous studies have evidenced the role of arginase-1 (Arg-1), angiotensin-I-converting enzyme (ACE), phosphodiesterase-5 (PDE-5) and acetylcholinesterase (AChE) in the progression of this pathology. In the current investigation, a library of compounds present in Zingiber officinale was screened to discover lead therapeutic agents for potential inhibitors of these metabolic enzymes. The compounds were subjected to molecular docking analysis with the various proteins' standard inhibitors. Subsequently, the thermodynamic stability of the protein-ligand complexes of two top-docked compounds with the highest binding affinities for each protein was studied further via molecular dynamics (MD) using the CHARMM-GUI website. Moreover, the Absorption-Distribution-Metabolism-Excretion-Toxicity (ADMET) pharmacological properties and drug-likeness of the top-docked 5 compounds from the plant were investigated with the SuperPred and the SwissADME web servers. From the compounds' library, diacetoxy-6-gingerdiol, 10-gingerdione, alloaromadendrene, valencene, and 6-gingerdiol showed the strongest inhibitory capacities with the amino acids present at the catalytic pocket of the selected proteins. Nonetheless, valencene and alloaromadendrene displayed better stability with the various protein complexes. Given that all these compounds were predicted to be non-toxic and have acceptable drug-likeness profiles, this investigation revealed their potential as a source of lead phytochemicals from regularly consumed food substances to mitigate the pathophysiology of erectile dysfunction. However, additional lab-based experiments are required before these phytochemicals can be developed into clinically approved commercially available drugs.

Lead optimization of Allium sativum L. compounds for PTP1B inhibition in diabetes treatment: in silico molecular docking and dynamics simulation

Protein tyrosine phosphatase 1B (PTP1B) has been identified as a promising drug target for the development of diabetes medications via an inhibition mechanism. Using a computational approach, this study investigates the binding mechanism of lead optimized natural compounds from Allium sativum against the human PTP1B. The molecular docking, induced-fit docking, and binding free energy calculations were analyzed using Schrödinger Suite 2021-2. MD simulation, and gene enrichment analysis was achieved via the Desmond module of Schrödinger to identify best compounds as inhibitors against PTP1B in diabetes management. The docking scores of the lead optimized compounds were good; 5280443_121 from apigenin had the best binding score of -9.345 kcal/mol, followed by 5280443_129 with a binding score of -9.200 kcal/mol, and 5280863_177 from kaempferol had a binding score of -8.528 kcal/mol, followed by 5280863_462 with a binding score of -8.338 kcal/mol. The top two lead optimized compounds, docked better than the standard PTP1B inhibitor (-7.155 kcal/mol), suggesting them as potent inhibitors than the standard PTP1B inhibitor. The outcomes of the induced-fit docking were consistent with the increased binding affinity used in the Glide computation of the five conformed poses between the derivatives (5280443_121, 5280443_129, 5280863_177, and 5280863_462) and the protein (PTP1B). Based on the binding fee energies (MM-GBSA), the lead optimized compounds from kaempferol exhibited more stability than those from apigenin. In the pharmacophore development, all the models exhibit good results across the different metrics. The best performing model with five of five matches on a 1.34 and 1.33 phase score was DDRRR_1, DDRRR_2, and DDDRR_1. The average BEDROC value (= 160.9) was 1, while the average EF 1% value across all models was 101. There were no substantial conformational modifications during the MD simulation process, indicating that the apigenin derivatives (5280443_121) was stable in the protein's active site in 100 ns. IGF1R, EGFR, INSR, PTPN1, SRC, JAK2, GRB2, BCAR1, and IRS1 are among the 11 potential targets found in the protein-protein interaction (PPI) of A. sativum against PTP1B that may be important in A. sativum's defense against PTP1B. Sixty-four (64) pathways were found by KEGG pathway enrichment analysis to be potentially involved in the anti-PTP1B of A. sativum. Consequently, data obtained indicates the effectiveness of the in silico studies in identifying potential lead compounds in A. sativum against PTP1B target.

Identification of promising dipeptidyl peptidase-4 and protein tyrosine phosphatase 1B inhibitors from selected terpenoids through molecular modeling

Motivation

Investigating novel drug-target interactions is crucial for expanding the chemical space of emerging therapeutic targets in human diseases. Herein, we explored the interactions of dipeptidyl peptidase-4 and protein tyrosine phosphatase 1B with selected terpenoids from African antidiabetic plants.

Results

Using molecular docking, molecular dynamics simulations, molecular mechanics with generalized Born and surface area solvation-free energy, and density functional theory analyses, the study revealed dipeptidyl peptidase-4 as a promising target. Cucurbitacin B, 6-oxoisoiguesterin, and 20-epi-isoiguesterinol were identified as potential dipeptidyl peptidase-4 inhibitors with strong binding affinities. These triterpenoids interacted with key catalytic and hydrophobic pockets of dipeptidyl peptidase-4, demonstrating structural stability and flexibility under dynamic conditions, as indicated by dynamics simulation parameters. The free energy analysis further supported the binding affinities in dynamic environments. Quantum mechanical calculations revealed favorable highest occupied molecular orbital and lowest unoccupied molecular orbital energy profiles, indicating the suitability of the hits as proton donors and acceptors, which likely enhance their molecular interactions with the targets. Moreover, the terpenoids showed desirable drug-like properties, suggesting their potential as safe and effective dipeptidyl peptidase-4 inhibitors. These findings may pave the way for the development of novel antidiabetic agents and nutraceuticals based on these promising in silico hits.

Availability and implementation

Not applicable.

Therapeutic Role of Alkaloids and Alkaloid Derivatives in Cancer Management

Cancer is a neoplastic disease that remains a global challenge with a reported prevalence that is increasing annually. Though existing drugs can be applied as single or combined therapies for managing this pathology, their concomitant adverse effects in human applications have led to the need to continually screen natural products for effective and alternative anticancer bioactive principles. Alkaloids are chemical molecules that, due to their structural diversity, constitute a reserve for the discovery of lead compounds with interesting pharmacological activities. Several in vitro studies and a few in vivo findings have documented various cytotoxic and antiproliferative properties of alkaloids. This review describes chaetocochin J, neopapillarine, coclaurine, reflexin A, 3,10-dibromofascaplysin and neferine, which belong to different alkaloid classes with antineoplastic properties and have been identified recently from plants. Despite their low solubility and bioavailability, plant-derived alkaloids have viable prospects as sources of viable lead antitumor agents. This potential can be achieved if more research on these chemical compounds is directed toward investigating ways of improving their delivery in an active form close to target cells, preferably with no effect on neighboring normal tissues.

Inhibition mechanism of alpha-amylase, a diabetes target, by a steroidal pregnane and pregnane glycosides derived from Gongronema latifolium Benth

Alpha-amylase is widely exploited as a drug target for preventing postprandial hyperglycemia in diabetes and other metabolic diseases. Inhibition of this enzyme by plant-derived pregnanes is not fully understood. Herein, we used in vitro, in silico, and in vivo studies to provide further insights into the alpha-amylase inhibitory potential of selected pregnane-rich chromatographic fractions and four steroidal pregnane phytochemicals (SPPs), viz: marsectohexol (P1), 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→14)-β-D-oleandropyranosyl]-11,12-di-O-tigloyl-17β-marsdenin (P2), 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl]-17β-marsdenin (P3), and 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-canaropyranosyl]-17β-marsdenin (P4) derived from Gongronema latifolium Benth. The results revealed that the SPPs source pregnane-rich chromatographic fractions and the SPPs (P1–P4) exhibited inhibitory potential against porcine pancreatic alpha-amylase in vitro. Compounds P1 and P2 with IC50 values 10.01 and 12.10 µM, respectively, showed greater inhibitory potential than the reference acarbose (IC50 = 13.47 µM). Molecular docking analysis suggests that the SPPs had a strong binding affinity to porcine pancreatic alpha-amylase (PPA), human pancreatic alpha-amylase (HPA), and human salivary alpha-amylase (HSA), interacting with the key active site residues through an array of hydrophobic interactions and hydrogen bonds. The strong interactions of the SPPs with Glu233 and Asp300 residues may disrupt their roles in the acid-base catalytic mechanism and proper orientation of the polymeric substrates, respectively. The interactions with human pancreatic amylase were maintained in a dynamic environment as indicated by the root mean square deviation, radius of gyration, surface accessible surface area, and number of hydrogen bonds computed from the trajectories obtained from a 100-ns molecular dynamics simulation. Key loop regions of HPA that contribute to substrate binding exhibited flexibility and interaction potential toward the compounds as indicated by the root mean square fluctuation. Furthermore, P1 significantly reduced blood glucose levels and area under the curve in albino rats which were orally challenged with starch. Therefore, Gongronema latifolium and its constituent SPPs may be exploited as inhibitors of pancreatic alpha-amylase as an oral policy for impeding postprandial blood glucose rise.