Molecular Modeling Applied to the Discovery of New Lead Compounds for P2 Receptors Based on Natural Sources

Investigating cannabinoids as P2X purinoreceptor 4 ligands by using surface plasmon resonance and computational docking

P2X purinoceptor 4 (P2X4) is an ATP-gated ion channel receptor with diverse neurophysiological functions, and P2X4 modulators hold promise as potential therapeutics for neuropathic pain, neuroinflammation, and neurodegenerative diseases. While several cannabinoids have been reported as modulators of purinoreceptors, their specific purinoreceptor-binding characteristics remain elusive. In this study, we established a comprehensive workflow that included a binding screening platform and a novel surface plasmon resonance (SPR) competitive assay, complemented by computational docking, to identify potential P2X4 binders among a panel of twenty-eight cannabinoids. Through SPR, we determined the binding affinities of cannabinoids (KD values ranging from 3.4 × 10-4 M to 1 × 10-6 M), along with two known P2X4 antagonists, BX430 (KD = 4.5 × 10-6 M) and 5-BDBD (KD = 7.8 × 10-6 M). The competitive SPR assay validated that BX430 and 5-BDBD acted as non-competitive binders with P2X4. In the following competitive assays, two cannabinoids including cannabidiol (CBD) and cannabivarin (CBV) were identified as competitive P2X4-binders with 5-BDBD, while the remaining cannabinoids exhibited non-competitive binding with either BX430 or 5-BDBD. Our molecular docking experiments further supported these findings, demonstrating that both CBD and CBV shared identical binding sites with residues in the 5-BDBD binding pocket on P2X4. In conclusion, this study provides valuable insights into the P2X4-binding affinity of cannabinoids through SPR and sheds light on the interactions between cannabinoids (CBD and CBV) and P2X4.

Antihyperglycemic Potential of Spondias mangifera Fruits via Inhibition of 11β-HSD Type 1 Enzyme: In Silico and In Vivo Approach

The 11 β- hydroxysteroid dehydrogenase 1 (11 β-HSD1) is hypothesized to play a role in the pathogenesis of type 2 diabetes and its related complications. Because high glucocorticoid levels are a risk factor for metabolic disorders, 11β-HSD1 might be a viable therapeutic target. In this investigation, docking experiments were performed on the main constituents of Spondias mangifera (SM) oleanolic acid, β-amyrin, and β-sitosterol to ascertain their affinity and binding interaction in the human 11β-hydroxysteroid dehydrogenase-1 enzyme’s active region. The results of in vitro 11β HSD1 inhibitory assay demonstrated that the extract of S. mangifera had a significant (p < 0.05) decrease in the 11-HSD1% inhibition (63.97%) in comparison to STZ (31.79%). Additionally, a non-insulin-dependent diabetic mice model was used to examine the sub-acute anti-hyperlipidemic and anti-diabetic effects of SM fruits. Results revealed that, in comparison to the diabetic control group, SM fruit extract (SMFE) extract at doses of 200 and 400 mg/kg body weight considerably (p < 0.05 and p < 0.01) lowered blood glucose levels at 21 and 28 days, as well as significantly decreased total cholesterol (TC) and triglycerides (TG) and enhanced the levels of high-density lipoprotein (HDL). After 120 and 180 s of receiving 200 and 400 mg/kg SMFE, respectively, disease control mice showed significantly poorer blood glucose tolerance (p < 0.05 and p < 0.01). SMFE extract 200 (p < 0.05), SMFE extract 400 (p < 0.01), and Glibenclamide at a dosage of 5 mg/kg body weight all resulted in statistically significant weight increase (p < 0.01) when compared to the diabetic control group after 28 days of treatment. According to in silico, in vitro, and in vivo validation, SMFE is a prospective medication with anti-diabetic and hypoglycemic effects.

Computer especially AI-assisted drug virtual screening and design in traditional Chinese medicine

BACKGROUND

Traditional Chinese medicine (TCM), as a significant part of the global pharmaceutical science, the abundant molecular compounds it contains is a valuable potential source of designing and screening new drugs. However, due to the un-estimated quantity of the natural molecular compounds and diversity of the related problems drug discovery such as precise screening of molecular compounds or the evaluation of efficacy, physicochemical properties and pharmacokinetics, it is arduous for researchers to design or screen applicable compounds through old methods. With the rapid development of computer technology recently, especially artificial intelligence (AI), its innovation in the field of virtual screening contributes to an increasing efficiency and accuracy in the process of discovering new drugs.

PURPOSE

This study systematically reviewed the application of computational approaches and artificial intelligence in drug virtual filtering and devising of TCM and presented the potential perspective of computer-aided TCM development.

STUDY DESIGN

We made a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Then screening the most typical articles for our research.

METHODS

The systematic review was performed by following the PRISMA guidelines. The databases PubMed, EMBASE, Web of Science, CNKI were used to search for publications that focused on computer-aided drug virtual screening and design in TCM.

RESULT

Totally, 42 corresponding articles were included in literature reviewing. Aforementioned studies were of great significance to the treatment and cost control of many challenging diseases such as COVID-19, diabetes, Alzheimer's Disease (AD), etc. Computational approaches and AI were widely used in virtual screening in the process of TCM advancing, which include structure-based virtual screening (SBVS) and ligand-based virtual screening (LBVS). Besides, computational technologies were also extensively applied in absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction of candidate drugs and new drug design in crucial course of drug discovery.

CONCLUSIONS

The applications of computer and AI play an important role in the drug virtual screening and design in the field of TCM, with huge application prospects.

Can Crude Oil Exploration Influence the Phytochemicals and Bioactivity of Medicinal Plants? A Case of Nigerian Vernonia amygdalina and Ocimum gratissimum

The Nigerian Niger-Delta crude oil exploration often results in spills that affect indigenous medicinal plant biodiversity, likely changing the phytochemical profile of surviving species, their bioactivity or toxicity. In crude oil-rich Kokori and crude oil-free Abraka, classic examples of indigenous plants occupying the medicine-food interface include Vernonia amygdalina (VAL) and Ocimum gratissimum leaves (OGL). These plants are frequently utilised during pregnancy and in anaemia. To date, no scientific investigation has been reported on the potential changes to the phytochemical or bioactivity of the study plants. To discuss the similarities and dissimilarities in antisickling bioactivity and phytochemicals in VAL and OGL collected from Kokori (VAL-KK and OGL-KK) and Abraka (VAL-AB and OGL-AB), in silico, in vitro and comparative UPLC-QTOF-MS analysis was performed. Nine unique compounds were identified in OGL-KK, which have never been reported in the literature, while differences in antisickling potentials were observed in VAL-KK, OGL-KK and, VAL-AB, OGL-AB. Our findings show that VAL-AB and OGL-AB are richer and more diverse in phytochemicals and displayed a slightly higher antisickling activity than VAL-KK and OGL-KK. Ligand-based pharmacophore modelling was performed to understand the potential compounds better; this study may provide a basis for explaining the effect of crude oil spills on secondary metabolites and a reference for further research.

The Structural, Biological, and In-Silico Profiling of Novel Capryloyl Tetra-Glucoside and Aliphatic Ester Constituents from the Abutilon indicum Offers New Perspectives on the Treatment of Pain and Inflammation

Abutilon indicum L. (Malvaceae), more often referred to as Peeli booti, Kanghi, and Kakhi, is a perennial shrub found in many countries of Asia. Traditionally, this plant is used as a diuretic to treat inflammation, discomfort, urethral infections, and gout. Inflammation and pain are key topics of interest for researchers throughout the globe, since they are linked to almost every illness that could affect humans or animals. The present study was conducted to isolate the phytoconstituents from the methanolic extract of Abutilon indicum collected from the Bihar state Koshi river belt in India, and to evaluate the isolated phytoconstituents' ability to reduce nociception and inflammation. Furthermore, molecular docking was performed to investigate the molecular interaction profile, with possible therapeutic targets for anti-inflammatory medicines. A. indicum methanolic extract yielded two novel phytocompounds identified as 5'-hydroxyhexyl n-hexadecanoate (AB-01) and n-octanoyl-β-D-glucopyranosyl-(2'-1'')-β-D-glucopyranosyl-(2''-1''')-β-D-glucopyranosyl-(2'''-1'''')-β-D-glucopyranoside (AB-05), together with three previously recognized phytocompounds such as ester glucoside. All isolated molecules were tested for the efficacy of analgesic and anti-inflammatory characteristics at doses of 5 and 10 mg/kg body weight. The isolated compound's molecular interaction profile with anti-inflammatory drug targets cyclooxygenase-2 and tumor necrosis factor-alpha possessed high potential energy in molecular docking. These findings may aid in developing anti-inflammatory and analgesic drugs from A. indicum.

Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process

The conventional drug discovery approach is an expensive and time-consuming process, but its limitations have been overcome with the help of mathematical modeling and computational drug design approaches. Previously, finding a small molecular candidate as a drug against a disease was very costly and required a long time to screen a compound against a specific target. The development of novel targets and small molecular candidates against different diseases including emerging and reemerging diseases remains a major concern and necessitates the development of novel therapeutic targets as well as drug candidates as early as possible. In this regard, computational and mathematical modeling approaches for drug development are advantageous due to their fastest predictive ability and cost-effectiveness features. Computer-aided drug design (CADD) techniques utilize different computer programs as well as mathematics formulas to comprehend the interaction of a target and drugs. Traditional methods to determine small-molecule candidates as a drug have several limitations, but CADD utilizes novel methods that require little time and accurately predict a compound against a specific disease with minimal cost. Therefore, this review aims to provide a brief insight into the mathematical modeling and computational approaches for identifying a novel target and small molecular candidates for curing a specific disease. The comprehensive review mainly focuses on biological target prediction, structure-based and ligand-based drug design methods, molecular docking, virtual screening, pharmacophore modeling, quantitative structure-activity relationship (QSAR) models, molecular dynamics simulation, and MM-GBSA/MM-PBSA approaches along with valuable database resources and tools for identifying novel targets and therapeutics against a disease. This review will help researchers in a way that may open the road for the development of effective drugs and preventative measures against a disease in the future as early as possible.

Ameliorative Sexual Behavior and Phosphodiesterase-5 Inhibitory Effects of Spondias mangifera Fruit Extract in Rodents: In Silico, In Vitro, and In Vivo Study

The ethanolic extracts of Spondias mangifera fruit (SMFE) were evaluated for aphrodisiac activity. The in-vitro phosphodiesterase-5 (PDE-5) inhibition was assessed based on in-silico molecular docking and simulation studies. In addition, the in-vivo sexual behavior was analyzed in the form of mount (MF, ML), intromission (IF, IL), and ejaculation (EF, EL) frequencies and latencies to validate the in-vitro results. Some biochemical parameters, including PDE-5, nitric oxide, and testosterone, were also observed. The above extract constituted β-amyrin, β-sitosterol, and oleanolic acid and showed tremendous binding with phosphodiesterase-5 and sildenafil. Both the sildenafil and ethanolic extracts (200 and 400 mg/kg/d bodyweight) significantly (p < 0.1, p < 0.05) increased MF, IF, and EF, respectively. In contrast, ML and IL significantly (p < 0.1) decreased, and EL significantly (p < 0.1) increased compared with a normal group of animals. The ethanolic extracts (200 and 400 mg/kg/d bodyweight) and sildenafil further significantly (p < 0.05, p < 0.1) diminished PDE-5 activity significantly (p < 0.05, p < 0.1) and enhanced nitric oxide and testosterone levels, as compared with normal rodents. Therefore, the S. mangifera ethanolic extract might be a valuable alternate aphrodisiac for erectile dysfunction.

Anti-Diabetic Activity of Bioactive Compound Extracted from Spondias mangifera Fruit: In-Vitro and Molecular Docking Approaches

Spondias mangifera is a drupaceous fruit popular for its flavour and health advantages. There is little scientific knowledge about S. mangifera, despite its widespread usage in traditional medicine, in the North-Eastern region of India. Inhibiting the key carbohydrate hydrolysing enzymes is one of the strategies for managing diabetes. Therefore, this study studied the antioxidant and anti-diabetic properties of different fraction S. mangifera fruit extract (SMFFs) from Indian geographical origin by in vitro experimental assays and silico docking simulation studies. The ADMET prediction for active substances was also investigated using the AdmetSAR database. Based on the binding affinity/molecular interactions between phytocompounds and target enzymes, in silico investigations were done to confirm the in vitro enzymatic inhibitory capability. β-sitosterol in EtOH-F was analysed using RP-HPLC with RP-C18 column as stationary phase and photo diode array detector. The percentage of β-sitosterol was found to be 1.21% ± 0.17% of total weight of extract (w/w). S. mangifera fruit ethanolic extract had a significant inhibitory concentration of 50% against free radicals produced by ABTS (89.71 ± 2.73%) and lipid peroxidation assay (88.26 ± 2.17%) tests. Similarly, the in vitro antidiabetic test findings indicated that S. mangifera inhibited alpha-amylase (73.42 ± 2.01%) and alpha-glucosidase (79.23 ± 1.98%) enzymes dose-dependently. The maximum glycosylated Hb percentage inhibitory activity shown in the ethanolic fraction was (83.97 ± 2.88%) at 500 µg/mL. The glucose uptake of the ethanolic fraction by the yeast cell showed significant (p < 0.05) at 500 µg/mL when compared with metformin (91.37 ± 1.59%), whereas the other fraction did not show the uptake of glucose by the yeast cell at the same concentration. In the docking study, the main phytoconstituents of S. mangifera fruit, such as oleanolic acid, beta-sitosterol, and beta amyrin, show strong affinity for pancreatic α-amylase. These results imply that S. mangifera has α-amylase and α-glucosidase inhibitory properties and may be used as antidiabetic with antioxidant characteristics.

Challenges and advances in clinical applications of mesenchymal stromal cells

Mesenchymal stromal cells (MSCs), also known as mesenchymal stem cells, have been intensely investigated for clinical applications within the last decades. However, the majority of registered clinical trials applying MSC therapy for diverse human diseases have fallen short of expectations, despite the encouraging pre-clinical outcomes in varied animal disease models. This can be attributable to inconsistent criteria for MSCs identity across studies and their inherited heterogeneity. Nowadays, with the emergence of advanced biological techniques and substantial improvements in bio-engineered materials, strategies have been developed to overcome clinical challenges in MSC application. Here in this review, we will discuss the major challenges of MSC therapies in clinical application, the factors impacting the diversity of MSCs, the potential approaches that modify MSC products with the highest therapeutic potential, and finally the usage of MSCs for COVID-19 pandemic disease.