Conjugated β-Cyclodextrin Enhances the Affinity of Folic Acid towards FRα: Molecular Dynamics Study

ADME profiling, molecular docking, DFT, and MEP analysis reveal cissamaline, cissamanine, and cissamdine from Cissampelos capensis L.f. as potential anti-Alzheimer's agents

The current pharmacotherapies for Alzheimer's disease (AD) demonstrate limited efficacy and are associated with various side effects, highlighting the need for novel therapeutic agents. Natural products, particularly from medicinal plants, have emerged as a significant source of potential neuroprotective compounds. In this context, Cissampelos capensis L.f., renowned for its medicinal properties, has recently yielded three new proaporphine alkaloids; cissamaline, cissamanine, and cissamdine. Despite their promising bioactive profiles, the biological targets of these alkaloids in the context of AD have remained unexplored. This study undertakes a comprehensive in silico examination of the binding affinity and molecular interactions of these alkaloids with human protein targets implicated in AD. The drug likeness and ADME analyses indicate favorable pharmacokinetic profiles for these compounds, suggesting their potential efficacy in targeting the central nervous system. Molecular docking studies indicate that cissamaline, cissamanine, and cissamdine interact with key AD-associated proteins. These interactions are comparable to, or in some aspects slightly less potent than, those observed with established AD drugs, highlighting their potential as novel therapeutic agents for Alzheimer's disease. Crucially, Density Functional Theory (DFT) calculations offer deep insights into the electronic and energetic characteristics of these alkaloids. These calculations reveal distinct electronic properties, with differences in total energy, binding energy, HOMO-LUMO gaps, dipole moments, and electrophilicity indices. Such variations suggest unique reactivity profiles and molecular stability, pertinent to their pharmacological potential. Moreover, Molecular Electrostatic Potential (MEP) analyses provide visual representations of the electrostatic characteristics of these alkaloids. The analyses highlight areas prone to electrophilic and nucleophilic attacks, indicating their potential for specific biochemical interactions. This combination of DFT and MEP results elucidates the intricate electronic, energetic, and electrostatic properties of these compounds, underpinning their promise as AD therapeutic agents. The in silico findings of this study shed light on the promising potential of cissamaline, cissamanine, and cissamdine as agents for AD treatment. However, further in vitro and in vivo studies are necessary to validate these theoretical predictions and to understand the precise mechanisms through which these alkaloids may exert their therapeutic effects.

In Vitro and In Silico Analysis of the Anticancer Effects of Eurycomanone and Eurycomalactone from Eurycoma longifolia

Eurycomanone and eurycomalactone are known quassinoids present in the roots and stems of Eurycoma longifolia. These compounds had been reported to have cytotoxic effects, however, their mechanism of action in a few cancer cell lines have yet to be elucidated. This study was aimed at investigating the anticancer effects and mechanisms of action of eurycomanone and eurycomalactone in cervical (HeLa), colorectal (HT29) and ovarian (A2780) cancer cell lines via Sulforhodamine B assay. Their mechanism of cell death was evaluated based on Hoechst 33342 assay and in silico molecular docking toward DHFR and TNF-α as putative protein targets. Eurycomanone and eurycomalactone exhibited in vitro anticancer effects manifesting IC50 values of 4.58 ± 0.090 µM and 1.60 ± 0.12 µM (HeLa), 1.22 ± 0.11 µM and 2.21 ± 0.049 µM (HT-29), and 1.37 ± 0.13 µM and 2.46 ± 0.081 µM (A2780), respectively. They induced apoptotic cancer cell death in dose- and time-dependent manners. Both eurycomanone and eurycomalactone were also predicted to have good inhibitory potential as demonstrated by the docking into TNF-α with binding affinity of -8.83 and -7.51 kcal/mol, respectively, as well as into DHFR with binding affinity results of -8.05 and -8.87 kcal/mol, respectively. These results support the evidence of eurycomanone and eurycomalactone as anticancer agents via apoptotic cell death mechanism that could be associated with TNF-α and DHFR inhibition as among possible protein targets.

Study of folate-based carbon nanotube drug delivery systems targeted to folate receptor α by molecular dynamic simulations

We designed targeted drug delivery systems containing folate (FOL), the functionalized carbon nanotube (f-CNT) and doxorubicin (DOX), and studied the targeting properties of folate, f-CNT-FOL and DOX/f-CNT-FOL to folate receptor α (FRα). Folate was actively targeted to FRα in molecular dynamics simulations, and the dynamic process, effect of folate receptor evolution, and characteristics were analyzed. On this basis, the f-CNT-FOL and DOX/f-CNT-FOL nano-drug-carrier systems were designed, and the drug delivery process targeted to FRα was studied by 4 times MD simulations. The system evolution and detailed interactions of f-CNT-FOL and DOX/f-CNT-FOL with FRα residues were examined. We found that though the connection of CNT with the FOL could decrease the insertion depth of the pterin of FOL into the pocket of FRα, the loading of drug molecules could reduce this effect. Representative snapshots from the MD simulations were analyzed, showing that the location of DOX on the surface of CNT was constantly changed during the MD simulation, but the surface of the four rings of DOX were almost always parallel to the surface of CNT. The RMSD and RMSF were used to further analyze. The results may provide new insights for the design of novel targeted nano-drug-delivery systems.

Investigating small molecule compounds targeting psoriasis based on cMAP database and molecular dynamics simulation

OBJECTIVE

Psoriasis (PSO) is a chronic inflammatory skin disease that severely affects the physical and mental health of patients. Drug resistance has been developed upon current drug treatments, and there is no specific therapy. The aim of this study was to screen promising novel drug candidates for PSO using molecular dynamics (MD) simulations.

METHODS

The data of PSO were downloaded from gene expression omnibus (GEO) database and subjected to variance analysis. Target proteins and small molecule compounds targeting PSO were predicted in the connective map (cMAP) database. Molecular docking, MD simulation, and trajectory analysis were conducted to predict the binding of target proteins to compounds.

RESULTS

1999 differentially expressed genes in PSO were obtained by differential analysis. Through cMAP database prediction, a low Score value of -45.69 for lymphocyte cell-specific protein-tyrosine kinase (LCK) was revealed, and aminogenistein was identified as the compound targeting LCK, and LCK was notably highly expressed in the PSO samples. The drugScore of the binding pocket P_0 was 0.814656, which was docked with aminogenistein. The results showed that there were more than one binding site between LCK and aminogenistein with binding energy less than -7.0 kJ/mol, and the docking was relatively stable. The results of root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), Gyrate, number of hydrogen bonds and total free binding energy in MD simulations showed that the binding of aminogenistein to LCK was relatively solid.

CONCLUSION

Aminogenistein has good protein-ligand interaction and stability with LCK, a target of PSO, and is a novel drug candidate for PSO.

tLyp-1: A peptide suitable to target NRP-1 receptor

Targeting vascular endothelial growth factor receptor (VEFGR) and its co-receptor neuropilin-1 (NRP-1) is an interesting vascular strategy. tLyp-1 is a tumor-homing and penetrating peptide of 7 amino acids (CGNKRTR). It is a truncated form of Lyp-1 (CGNKRTRGC), which is known to target NRP-1 receptor, with high affinity and specificity. It is mediated by endocytosis via C-end rule (CendR) internalization pathway. The aim of this study is to evaluate the importance of each amino acid in the tLyp-1 sequence through alanine-scanning (Ala-scan) technique, during which each of the amino acid in the sequence was systematically replaced by alanine to produce 7 different analogues. In silico approach through molecular docking and molecular dynamics are employed to understand the interaction between the peptide and its analogues with the NRP-1 receptor, followed by in vitro ligand binding assay study. The C-terminal Arg is crucial in the interaction of tLyp-1 with NRP-1 receptor. Substituting this residue dramatically reduces the affinity of this peptide which is clearly seen in this study. Lys-4 is also important in the interaction, which is confirmed via the in vitro study and the MM-PBSA analysis. The finding in this study supports the CendR, in which the presence of R/K-XX-R/K motif is essential in the binding of a ligand with NRP-1 receptor. This presented work will serve as a guide in the future work pertaining the development of active targeting agent towards NRP-1 receptor.

Design, molecular docking, and molecular dynamics of thiourea-iron (III) metal complexes as NUDT5 inhibitors for breast cancer treatment

In research, anticancer agents, such as thiourea derivative compounds, and metal complexes, such as those complexed with iron (III) metal, are often studied. The metal complexes are presumably more active than thiourea derivatives as free ligands; some negative effects may be reduced. The computational studies used in this study involved molecular docking with AutoDock and molecular dynamics (MD) simulations using Desmond to evaluate the stability of the interactions. The docking and MD analysis results showed that compounds 2 and 6 had stable interactions with NUDIX hydrolase type 5 (NUDT5)—one of the therapeutic targets for breast cancer—where they had the lowest root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values compared to the other compounds. Together, these compounds are anti-breast cancer drug candidates.

Naturally Occurring 8ß,13ß-kaur-15-en-17-al and Anti-Malarial Activity from Podocarpus polystachyus Leaves

Despite much interest and studies toward the genus Podocarpus, the anti-malarial evaluation of Podocarpus polystachyus’s phytoconstituents remains lacking. Herein, the phytoconstituents of P. polystachyus leaves and their anti-malarial effect against Plasmodium falciparum were investigated for the first time. One new natural product, 8ß,13ß-kaur-15-en-17-al (1), along with three known compounds, 8ß,13ß-kaur-15-en-17-ol (2) and 13ß-kaur-16-ene (3), and α-tocopherol hydroquinone (4) were isolated via HR-ESI-MS and NMR analyses. Compounds 1 and 2 inhibited P. falciparum growth at 12 and 52 µM of IC₅₀, respectively. Their anti-malarial activity was associated with the in silico P. falciparum lactate dehydrogenase (PfLDH) inhibition. Molecular docking of ligands 1 and 2 with the putative target PfLDH revealed ~−2 kcal/mol of binding energies more negative than the control. Molecular dynamic simulations (100 ns) showed equal or smaller deviation values (RMSD, RMSF, Rg) and stronger interactions of PfLDH-1 and PfLDH-2 complexes via at least one consistent H-bond than the control. Additionally, a slightly increased PfLDH H-bond profile in their interactions improved the PfLDH dynamic and structural stabilities. Overall, this study supports the relevance of 1 and 2 as plasmodial growth inhibitors with their putative anti-PfLDH activity, which could be a potential scaffold for developing anti-malarial drugs.

Interaction mechanism of novel fluorescent antifolates targeted with folate receptors α and β via molecular docking and molecular dynamic simulations

Eight novel fluorescent antifolates were designed and docked with folate receptors FRα and FRβ. The structures of the complexes were further calculated by molecular dynamic (MD) simulations. The binding energies were calculated by molecular docking and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) studies. The binding energy differences between FRα and FRβ (|E_bα|-|E_bβ|) values for compounds 3 and 8 were 1.3 and 1.1 kcal/mol calculated by molecular docking, and 13.9 and 10.4 kcal/mol by MM-PBSA simulation, respectively. The results indicated that compounds 3 and 8 may be the best candidates for targeted drug delivery to FRα. The binding structures, interaction residues, negatively charged pocket volume, and surface area were analyzed for all the complexes. We further calculated the root mean square displacement and secondary structural elements of the bound complexes using molecular dynamics simulations. The purpose of this study is to design novel antifolates targeted to FRα and FRβ, and to further distinguish between cancer cells and inflammation.