Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase

Discovery of potential VEGFR-2 inhibitors from natural products by virtual screening and molecular dynamics simulation

Hepatocellular carcinoma (HCC) is the most common cancer worldwide and vascular endothelial growth factor receptor-2 (VEGFR-2) is an important target in the development of inhibitors for the treatment of liver cancer. So far, however, there are no effective drugs targeting VEGFR-2 to achieve complete treatment of liver cancer. In this study, we employed molecular docking, molecular dynamics simulations, molecular mechanics generalized Born surface area (MM-GBSA) method, quantum mechanics/molecular mechanics (QM/MM) calculations and steered molecular dynamics simulations to discover the potential inhibitors from COCONUT database targeting VEGFR-2. The molecular docking analyses of 13 743 natural compounds targeting VEGFR-2 identified 96 molecules as promising candidates. Our molecular dynamics simulations revealed that only 5 candidate-docking systems remained stable over 100 ns of production run. Then, steered molecular dynamics simulations showed that CNP0076764, CNP0028810, CNP0177683 and CNP0107283 had higher mean force values than that of sorafenib, reflecting the high potential of candidate molecules. A detailed analysis of the binding modes revealed that Leu840, Val848, Lys868, Glu885, Leu889, Val899, Val916, Leu1035, Cys1045, Asp1046 and Phe1047 play key roles in binding the inhibitors. Overall, this study shows evidence that the four natural products obtained from the COCONUT database could be further used as anti-cancer inhibitors, which provides theoretical guidance for designing new drugs.

Discovery of Ureido-Substituted 4-Phenylthiazole Derivatives as IGF1R Inhibitors with Potent Antiproliferative Properties

The existing kinase inhibitors for hepatocellular carcinoma (HCC) have conferred survival benefits but are hampered by adverse effects and drug resistance, necessitating the development of novel agents targeting distinct pathways. To discover potent new anti-HCC compounds, we leveraged scaffold hopping from Sorafenib and introduced morpholine/piperidine moieties to develop ureido-substituted 4-phenylthiazole analogs with optimized physicochemical properties and binding interactions. Notably, compound 27 exhibited potent cytotoxicity against HepG2 cells (IC50 = 0.62 ± 0.34 μM), significantly exceeding Sorafenib (IC50 = 1.62 ± 0.27 μM). Mechanistic investigations revealed that compound 27 potently inhibited HCC cell migration and colony formation, and it induced G2/M arrest and early-stage apoptosis. Kinase profiling revealed IGF1R as a key target, which compound 27 potently inhibited (76.84% at 10 μM). Molecular modeling substantiated compound 27's strong binding to IGF1R via multiple hydrogen bonds. Computational predictions indicate favorable drug-like properties for compound 27. These findings provide a promising drug candidate for the treatment of HCC patients.

Potential Inhibitors of Lumpy Skin Disease's Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches

Lumpy skin disease (LSD), caused by a virus within the Poxviridae family and Capripoxvirus genus, induces nodular skin lesions in cattle. This spreads through direct contact and insect vectors, significantly affecting global cattle farming. Despite the availability of vaccines, their efficacy is limited by poor prophylaxis and adverse effects. Our study aimed to identify the potential inhibitors targeting the LSDV-encoded DNA polymerase protein (gene LSDV039) for further investigation through comprehensive analysis and computational methods. Virtual screening revealed rhein and taxifolin as being potent binders among 380 phytocompounds, with respective affinities of -8.97 and -7.20 kcal/mol. Canagliflozin and tepotinib exhibited strong affinities (-9.86 and -8.86 kcal/mol) among 718 FDA-approved antiviral drugs. Simulating the molecular dynamics of canagliflozin, tepotinib, rhein, and taxifolin highlighted taxifolin's superior stability and binding energy. Rhein displayed compactness in RMSD and RMSF, but fluctuated in Rg and SASA, while canagliflozin demonstrated stability compared to tepotinib. This study highlights the promising potential of using repurposed drugs and phytocompounds as potential LSD therapeutics. However, extensive validation through in vitro and in vivo testing and clinical trials is crucial for their practical application.

Mechanistic study of Coriandrum sativum on neuritogenesis and synaptogenesis based on computationally guided in vitro analyses

ETHNOPHARMACOLOGICAL RELEVANCE

Acceleration of neurite outgrowth and halting neurodegeneration are the most critical factors that are negatively regulated in various neurodegenerative diseases or injuries in the central nervous system (CNS). Functional foods or nutrients are considered alternative sources of bioactive components to alleviate various CNS injuries by promoting neuritogenesis and synaptogenesis, while their exact molecular mechanism remains unexplored.

AIM OF THE STUDY

Coriandrum sativum L. (CS) is one of the popular herbs in the Apiaceae family, of which CNS modulating action is a well-documented traditionally but detailed study on memory boosting function yet remains unexplored. Consequently, this study aims to analyze the neurogenic and synaptogenic modulation of CS aqueous ethanol (CSAE) extract in the primary hippocampal neurons.

MATERIALS AND METHODS

Primary hippocampal neurons were cultured and allowed to incubate with CSAE or vehicle. To observe the early neuronal differentiation, axonal and dendritic arborization, and synapse formation, neurons were immune-stained against indicated antibodies or stained directly with a lipophilic dye (1, 1'-dioctadecyl-3, 3, 3', 3'-tetramethyl indocarbocyanine perchlorate, DiL). Meanwhile, western blot was used to validate the synaptogenesis effect of CSAE compared to vehicle. Additionally, molecular docking and system pharmacology approaches were applied to confirm the possible secondary metabolites and pathways by which CSAE promotes neuritogenesis.

RESULTS

Results show that CSAE can induce neuritogenesis and synaptogenesis at 30 μg/mL concentration. The treatment impacts early neuronal polarization, axonal and dendritic arborization, synaptogenesis, and synaptic plasticity via NMDARs expressions in primary neurons. In silico network pharmacology of CS metabolites show that the CSAE-mediated neurogenic effect is likely dependent on the NTRK2 (TrkB) mediated neurotrophin signaling pathway. Indeed, the observed neurogenic activity of CSAE is markedly reduced upon the co-treatment with a TrkB-specific inhibitor. Furthermore, molecular docking following binding energy calculation shows that one of the CS metabolites, scoparone, has a high affinity to bind in the BDNF mimetic binding site of TrkB, suggesting its role in TrkB activation. Scoparone was found to enhance neuritogenesis, but not to the same extent as CSAE. Moreover, the expression of TrkB signaling-related proteins (BCL2, CASP3, GSK3, and BDNF), which was found to be modulated by scoparone, was significantly affected by the co-treatment of TrkB inhibitor (ANA-12). These results further suggest that the modulation of neuritogenesis by scoparone is TrkB-dependent.

CONCLUSIONS

This study provides deeper insights into the molecular mechanism of CS in boosting neuronal growth and memory function, which might implicate the prevention of many neurological disorders.

Cyclohexane-1,3-dione Derivatives as Future Therapeutic Agents for NSCLC: QSAR Modeling, In Silico ADME-Tox Properties, and Structure-Based Drug Designing Approach

The abnormal expression of the c-Met tyrosine kinase has been linked to the proliferation of several human cancer cell lines, including non-small-cell lung cancer (NSCLC). In this context, the identification of new c-Met inhibitors based on heterocyclic small molecules could pave the way for the development of a new cancer therapeutic pathway. Using multiple linear regression (MLR)-quantitative structure-activity relationship (QSAR) and artificial neural network (ANN)-QSAR modeling techniques, we look at the quantitative relationship between the biological inhibitory activity of 40 small molecules derived from cyclohexane-1,3-dione and their topological, physicochemical, and electronic properties against NSCLC cells. In this regard, screening methods based on QSAR modeling with density-functional theory (DFT) computations, in silico pharmacokinetic/pharmacodynamic (ADME-Tox) modeling, and molecular docking with molecular electrostatic potential (MEP) and molecular mechanics-generalized Born surface area (MM-GBSA) computations were used. Using physicochemical (stretch-bend, hydrogen bond acceptor, Connolly molecular area, polar surface area, total connectivity) and electronic (total energy, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels) molecular descriptors, compound 6d is identified as the optimal scaffold for drug design based on in silico screening tests. The computer-aided modeling developed in this study allowed us to design, optimize, and screen a new class of 36 small molecules based on cyclohexane-1,3-dione as potential c-Met inhibitors against NSCLC cell growth. The in silico rational drug design approach used in this study led to the identification of nine lead compounds for NSCLC therapy via c-Met protein targeting. Finally, the findings are validated using a 100 ns series of molecular dynamics simulations in an aqueous environment on c-Met free and complexed with samples of the proposed lead compounds and Foretinib drug.

In silico design of epitope-based peptide vaccine against non-typhoidal Salmonella through immunoinformatic approaches

Non-typhoidal Salmonella (NTS) is one of the leading bacterial causes of many invasive human infections with a high antibiotic resistance profile. With this concern, the current study aimed to design an effective epitope-based peptide vaccine against NTS species as a successive and substitutive protective measure of invasive NTS disease. To design rationally, the current study considered a comprehensive in silico workflow combination of both immunoinformatics and molecular modeling approaches, including molecular docking and molecular dynamics (MD) simulation. We identified the two most promising T cell epitopes KVLYGIFAI and YGIFAITAL, and three B cell epitopes AAPVQVGEAAGS, TGGGDGSNT, and TGGGDGSNTGTTTT, in the outer membrane of NTS. Using these epitopes, a multiepitope vaccine was subsequently constructed along with appropriate adjuvant and linkers, which showed a good binding affinity and stability with toll-like receptor 2 (TLR2) in both molecular docking and MD simulation. Furthermore, in silico immune simulation described a strong immune response with a high number of antibodies, interferon-γ, and activated B and T cells. This study collectively suggests that predicted vaccine constructs could be considered potential vaccine candidates against common NTS species.Communicated by Ramaswamy H. Sarma.

Molecular Docking and Dynamics Simulation of Natural Compounds from Betel Leaves (Piper betle L.) for Investigating the Potential Inhibition of Alpha-Amylase and Alpha-Glucosidase of Type 2 Diabetes

Piper betle L. is widely distributed and commonly used medicinally important herb. It can also be used as a medication for type 2 diabetes patients. In this study, compounds of P. betle were screened to investigate the inhibitory action of alpha-amylase and alpha-glucosidase against type 2 diabetes through molecular docking, molecular dynamics simulation, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis. The molecule apigenin-7-O-glucoside showed the highest binding affinity among 123 (one hundred twenty-three) tested compounds. This compound simultaneously bound with the two-target proteins alpha-amylase and alpha-glucosidase, with high molecular mechanics-generalized born surface area (MM/GBSA) values (ΔG Bind = -45.02 kcal mol^-1 for alpha-amylase and -38.288 for alpha-glucosidase) compared with control inhibitor acarbose, which had binding affinities of -36.796 kcal mol^-1 for alpha-amylase and -29.622 kcal mol^-1 for alpha-glucosidase. The apigenin-7-O-glucoside was revealed to be the most stable molecule with the highest binding free energy through molecular dynamics simulation, indicating that it could compete with the inhibitors' native ligand. Based on ADMET analysis, this phytochemical exhibited a wide range of physicochemical, pharmacokinetic, and drug-like qualities and had no significant side effects, making them prospective drug candidates for type 2 diabetes. Additional in vitro, in vivo, and clinical investigations are needed to determine the precise efficacy of drugs.

Suppressing VEGF-A/VEGFR-2 Signaling Contributes to the Anti-Angiogenic Effects of PPE8, a Novel Naphthoquinone-Based Compound

Natural naphthoquinones and their derivatives exhibit a broad spectrum of pharmacological activities and have thus attracted much attention in modern drug discovery. However, it remains unclear whether naphthoquinones are potential drug candidates for anti-angiogenic agents. The aim of this study was to evaluate the anti-angiogenic properties of a novel naphthoquinone derivative, PPE8, and explore its underlying mechanisms. Determined by various assays including BrdU, migration, invasion, and tube formation analyses, PPE8 treatment resulted in the reduction of VEGF-A-induced proliferation, migration, and invasion, as well as tube formation in human umbilical vein endothelial cells (HUVECs). We also used an aorta ring sprouting assay, Matrigel plug assay, and immunoblotting analysis to examine PPE8’s ex vivo and in vivo anti-angiogenic activities and its actions on VEGF-A signaling. It has been revealed that PPE8 inhibited VEGF-A-induced micro vessel sprouting and was capable of suppressing angiogenesis in in vivo models. In addition, PPE8 inhibited VEGF receptor (VEGFR)-2, Src, FAK, ERK1/2, or AKT phosphorylation in HUVECs exposed to VEGF-A, and it also showed significant decline in xenograft tumor growth in vivo. Taken together, these observations indicated that PPE8 may target VEGF-A–VEGFR-2 signaling to reduce angiogenesis. It also supports the role of PPE8 as a potential drug candidate for the development of therapeutic agents in the treatment of angiogenesis-related diseases including cancer.

Unveiling the effect of Withania somnifera on neuronal cytoarchitecture and synaptogenesis: A combined in vitro and network pharmacology approach

Withania somnifera (WS), is known for its remarkable contribution in herbal medicine and Ayurveda, which is therapeutically applied to improve memory and anxiety in patients. However, the pharmacological details of this plant on memory boosting yet remained undefined. This study provides mechanistic insights on the effect of ethanol solution extract of the whole plant of WS (WSEE) on neuritogenesis by combining in vitro and in silico network pharmacology approaches. WSEE promoted significant neuronal growth through early differentiation, axodendritic arborization, and synaptogenesis on primary hippocampal neurons. The network pharmacological study confirmed that the neuritogenic activity is potentially mediated by modulating the neurotrophin signaling pathway, where NRTK1 (TrkA) was revealed as the primary target of WS secondary metabolites. This neurotrophic activity of WSEE was significantly stifled by the presence of TrkA inhibitor, which further confirms the TrkA-dependent activity of WSEE. In addition, a molecular docking study suggested steroidal lactones present in the WS might act as nerve growth factor (NGF)-mimetics, activating TrkA by binding to the NGF-binding domain. As a whole, the findings of the study suggest a significant role of WSEE on neuritogenesis and its potential to function as a therapeutic agent and in drug designing for the prevention and treatment of memory-related neurological disorders.

Structural Consequence of Non-Synonymous Single-Nucleotide Variants in the N-Terminal Domain of LIS1

Disruptive neuronal migration during early brain development causes severe brain malformation. Characterized by mislocalization of cortical neurons, this condition is a result of the loss of function of migration regulating genes. One known neuronal migration disorder is lissencephaly (LIS), which is caused by deletions or mutations of the LIS1 (PAFAH1B1) gene that has been implicated in regulating the microtubule motor protein cytoplasmic dynein. Although this class of diseases has recently received considerable attention, the roles of non-synonymous polymorphisms (nsSNPs) in LIS1 on lissencephaly progression remain elusive. Therefore, the present study employed combined bioinformatics and molecular modeling approach to identify potential damaging nsSNPs in the LIS1 gene and provide atomic insight into their roles in LIS1 loss of function. Using this approach, we identified three high-risk nsSNPs, including rs121434486 (F31S), rs587784254 (W55R), and rs757993270 (W55L) in the LIS1 gene, which are located on the N-terminal domain of LIS1. Molecular dynamics simulation highlighted that all variants decreased helical conformation, increased the intermonomeric distance, and thus disrupted intermonomeric contacts in the LIS1 dimer. Furthermore, the presence of variants also caused a loss of positive electrostatic potential and reduced dimer binding potential. Since self-dimerization is an essential aspect of LIS1 to recruit interacting partners, thus these variants are associated with the loss of LIS1 functions. As a corollary, these findings may further provide critical insights on the roles of LIS1 variants in brain malformation.

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.