Antibacterial and Antioxidant Activities, in silico Molecular Docking, ADMET and DFT Analysis of Compounds from Roots of Cyphostemma cyphopetalum

Background

Cyphostemma cyphopetalum is a medicinal plant traditionally used to treat various ailments. Limited studies on C. cyphopetalum inspired us to investigate the chemical nature and therapeutic potential of the plant.

Methods

Silica gel column chromatographic separation was used for isolation. 1D and 2D NMR spectroscopic analysis and literature data were used for structural elucidation. Agar well diffusion assay was used for evaluation of antibacterial activity against E. coli, P. aeruginosa, and S. aureus. DPPH assay was used to evaluate radical scavenging activities. Molecular docking was done by AutoDock Vina 4.2 open-source program. DFT calculations were performed using the Gaussian 16 program package.

Results

Dichloromethane/methanol (1:1) roots extract afforded a new hydroxyl-spongiane diterpenoid lactone derivative, 3-hydroxyisoagatholactone (1), along with β-sitosterol (2) and ε-viniferin (3) whereas methanol extract afforded trans-resveratrol (4), gnetin H (5), tricuspidatol A (6), ε-viniferin-diol (7) and parthenostilbenin B (8). At 50 μg/mL, compound 3 recorded the highest inhibition against E. coli (8.55 ± 0.45 mm) and S. aureus (9.30 ±1.39 mm). Against P. aeruginosa, compound 5 consistently outperformed chloramphenicol (11.76 ± 0.77 mm, at 30 g/mL). Maximum binding affinity were observed by compound 3 against DNA gyrase B (-7.6 kcal/mol) where as compound 5 displayed maximum binding against PqsA (-8.8 kcal/mol) and S. aureus PK (-5.8 kcal/mol). Compounds 1, 3 and 4 satisfy Lipinski's rule of five. Trans-resveratrol (4) demonstrated strong DPPH scavenging activity at 12.5 g/mL, with IC50 values of 0.052 µg/mL, compared to ascorbic acid (IC50 value of 0.0012 µg/mL).

Conclusion

In this work, eight compounds were identified from the roots extracts of C. cyphopetalum including a new hydroxyl-spongiane diterpenoid lactone, 3-hydroxyisoagatholactone (1). Compounds 3 and 5 exhibited good antibacterial activity and binding affinities. The docking result is in agreement with the in vitro antibacterial study. Overall, the study result suggests that the isolated compounds have the potential to be used as therapeutic agents, which supports the traditional uses of C. cyphpetalum roots.

Exploration of Luteolin as Potential Anti-COVID-19 Agent: Molecular Docking, Molecular Dynamic Simulation, ADMET and DFT Analysis

Background:

Coronavirus disease-2019 (COVID-19) has recently emerged as a pandemic respiratory disease with mild to severe pneumonia symptoms. No clinical antiviral agent is available so far. However, several repurposing drugs and vaccines are being given to individuals or in clinical trials against SARS-CoV-2

Objective:

The aim of this study is to uncover the potential effects of Luteolin (Lut) as an inhibitor of SARS-CoV2 encoded proteins via utilizing computational tools.

Method:

Molecular modelling to unfold the anti-SARS-CoV2 potential of Lut along with reference drugs namely remdesivir and nafamostat was performed by the use of molecular docking, molecular dynamic (MD) simulation, absorption, distribution, metabolism, excretion, toxicity (ADMET) and density functional theory (DFT) methods against the five different SARS-CoV-2 encoded key proteins and one human receptor protein. The chemical reactivity of Luteolin is done through prediction of HOMO-LUMO gap energy and other chemical descriptors analysis.

Results:

In the present study, Lut binds effectively in the binding pockets of spike glycoprotein (6VSB), ADP phosphatase of NSP3 (6W02), and RNA dependent RNA polymerase (7AAP) protein receptors with significant values of docking scores -7.00, -7.25, and -6.46 respectively as compared to reference drugs remdesivir and nafamostat.

Conclusion::

Thus, Lut can act as a therapeutic agent and is orally safe for human consumption as predicted by molecular modelling against SARS-CoV-2 in the treatment of COVID-19.

High-Strength, Strongly Bonded Nanocomposite Hydrogels for Cartilage Repair

Polyacrylamide-based hydrogels are widely used as potential candidates for cartilage replacement. However, their bioapplicability is sternly hampered due to their limited mechanical strength and puncture resistance. In the present work, the strength of polyacrylamide (PAM) hydrogels was increased using titanium oxide (TiO₂) and carbon nanotubes (CNTs) separately and a combination of TiO₂ with CNTs in a PAM matrix, which was interlinked by the bonding between nanoparticles and polymers with the deployment of density functional theory (DFT) approach. The synergistic effect and strong interfacial bonding of TiO₂ and CNT nanoparticles with PAM are attributed to high compressive strength, elastic modulus (>0.43 and 2.340 MPa, respectively), and puncture resistance (estimated using the needle insertion test) for the PAM-TiO₂-CNT hydrogel. The PAM-TiO₂-CNT composite hydrogel revealed a significant self-healing phenomenon along with a sign toward the bioactivity and cytocompatibility by forming the apatite crystals in simulated body fluid as well as showing a cell viability of ∼99%, respectively. Furthermore, for new insights on interfacial bonding and structural and electronic features involved in the hydrogels, DFT was used. The PAM-TiO₂-CNT composite model, constructed by two interfaces (PAM-TiO₂ and PAM-CNT), was stabilized by H-bonding and van der Waals-type interactions. Employing the NCI plot, HOMO-LUMO gap, and natural population analysis tools, the PAM-TiO₂-CNT composite has been found to be most stable. Therefore, the prepared polyacrylamide hydrogels in combination with the TiO₂ and CNT can be a remarkable nanocomposite hydrogel for cartilage repair applications.

Theoretical (DFT) and experimental (Raman and FTIR) spectroscopic study on communic acids, main components of fossil resins

The objective of this work is to establish a spectral assignment of several communic acids. The most significant vibrational modes of three stereoisomers of communic acids [trans-, cis-, and iso- (or mirceo-)] are presented. They are showed throughout experimental Raman and IR spectra, and on the basis on calculations with Density Functional Theory (DFT) and the assignment of the spectral bands of different resins found in the literature. These three communic acids studied are the most important isomers present in the scaffold of the fossil resins Class I, as monomers or co-polymerized according to several authors. These kinds of terpenes are used as starting material, for example, for the synthesis of the fungicide and compounds bioactives. In a novel way, it is reported jointly the assignment of the experimental Infrared and Raman modes together with theoretical modes, since normally the authors tend to focus on one or another spectroscopic technique only. These results can be used as a reference for distinguishing amber from less matured resins as copal, determining the local origin of archaeological fossilized resins. Moreover, they will serve as help to differentiate between real and imitation ambers.