Analysis of plant-derived phytochemicals as anti-cancer agents targeting cyclin dependent kinase-2, human topoisomerase IIa and vascular endothelial growth factor receptor-2

Molecular docking of curcumin and curcuminoids as human Zn+ dependent histone deacetylase (HDAC) enzyme inhibitors

Chemotherapy is one of the most well-established and effective cancer treatments available. However, non-tumor-associated damage restrict the treatment's effectiveness and safety. Our growing understanding of cancer epigenetics has resulted in new therapeutic options and the potential of better patient outcomes in recent decades. In cancer, epigenetic changes are widespread, particularly increased expression and activity of histone deacetylases (HDACs). Epi-drugs are chemical agents that modify the structure of DNA and chromatin facilitating disruption of transcriptional and post-transcriptional changes. First generation epi-drugs include HDAC inhibitors (HDACi) (approved to treat hematological malignancies) harbor various adverse effects demanding the discovery and development of potential natural HDACi that might benefit cancer treatment especially in hematological malignancies. Curcumin (diferuloylmethane), a polyphenolic, component of Curcuma longa, is a well-known anti-inflammatory, anti-oxidative, and anti-lipidemic agent and has recently been shown to be a pan HDACi. Yet the potential of other curcuminoids in Curcuma longa as pan HDACi remains unexplored. (i) To virtually screen curcumin and curcuminoids (Desmethoxycurcumin [DMC] & Bisdemethoxycurcumin [BDMC]) against human Histone deacetylase (HDAC) class I, II and IV enzymes in comparison to their pan HDAC inhibition activity with FDA approved human HDACis available in market and also (ii) to predict the drug likeness property and ADME/ toxicity of curcumin, curcuminoids and approved HDACis via computational approach. Homology modelling followed by docking was performed for human HDAC class I, II and IV enzymes with curcumin, Desmethoxycurcumin, Bisdemethoxycurcumin and with 5 reference HDACi compounds Vorinostat (SAHA), Trichostatin A (TSA), Chidamide, Romidepsin, and Panobinostat to understand the protein -ligand interactions and binding efficiencies. Further, the study ligands with low binding energy were predicted for pharmacokinetic properties and Lipinski's rule of 5. Our study revealed that BDMC followed by DMC and curcumin had high inhibitory effect by interacting at the active site of Zn+ HDACs similar to that of the standard HDACi (curcumin, DMC, BDMC, Belinostat, Chidamide, Romidepsin, Panobinostat, Trichostatin A and Vorinostat). Likewise, all of the chosen ligand molecules, with the exception of Romidepsin (refractive index > 130 m3mol-1), adhered to Lipinski's rule of five and none of the natural compounds (curcumin, DMC, BDMC) did report any toxicity and mutagenic property also, the lethal doses (LD50) of all the natural compounds were higher when compared to chemical drugs. BDMC could be a potential pan HDACi than curcumin and DMC owing to high binding affinity among human Zn+ HDACs. The results of our present study can be useful for the design and development of novel compounds having better HDAC inhibitory activity against several types of cancers. Moreover, these findings could be validated with invitro investigations and by clinical trials to evaluate the survival outcomes in cancer patients when treated with the natural HDACi along with standard chemo regimen.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00221-4.

In-vitro antibacterial, antioxidant and anti-inflammatory and In-silico ADMET, molecular docking study on Hardwickia binata phytocompunds with potential inhibitor of skin cancer protein

The new sources of antimicrobial and antioxidant agents for methanol extracts of Hardwickia binata Roxb were evaluated systematically. The present investigation is antibacterial, antioxidant, ADMET and molecular docking studies. Our results show the good polyphenol content (total phenol, total flavonoid) and antioxidant capacity of methanol extracts. The free radical scavenging activities of the methanol extracts also were highest, with the antioxidant activity becoming significantly greater. Furthermore, in-vitro antibacterial experiments against phytopathogens, Enterococcus faecalis have a high zone of inhibition (14 ± 0.54) compared with other pathogens. The functional groups of methanol extract were identified using FTIR. The active molecules from GCMS involved in ADMET and docking study for skin cancer proteins (1P7K and 5OTE) among the phytocompounds, Hexadecanoic acid, methyl ester (- 6.2; - 6.6 kcal/mol) and 5-Phenyl-2,4-pyrimidinediamine, 2TMS derivative (- 7.50; - 8.11 kcal/mol) is the best compound for the human skin cancer possessed higher binding energy. Our results indicate that the plants can provide sources of natural compounds used for moderate good anticancer drug.

Anti-angiogenic potential of bioactive phytochemicals from Helicteres isora targeting VEGFR-2 to fight cancer through molecular docking and molecular dynamics simulation

Cancer is one of the leading causes of death due to its very high rate of morbidity and mortality, and there is a constant demand of effective drugs for cancer therapy. Vascular endothelial growth factor receptor-2 (VEGFR-2) plays a significant role as central modulator of angiogenesis and is targeted frequently for developing anti-angiogenic agents to fight cancer. Helicteres isora L. (Malvaceae) is reported to possess diverse medicinal properties including anti-cancer potentials. In the current investigation, 38 bioactive phytochemicals of H. isora were screened virtually to evaluate their anti-angiogenic potentials targeting VEGFR-2. The study unveiled three potential candidates such as, Diosgenin (-9.8 Kcal//mol), Trifolin (-8.4 Kcal/mol) and Yohimbine (-8.1 Kcal/mol) that showed favorable pharmacokinetic, pharmacodynamic and toxicity properties with no significant side effects. Molecular dynamics simulation employing 100 ns revealed noteworthy structural stability and compactness for all the top three candidates. The MM/GBSA binding free energy estimation corroborated the docking interactions where Yohimbine (-30.47 Kcal/mol) scored better than Diosgenin (-27.54 Kcal/mol) and Trifolin (-29.58 Kcal/mol). Target class prediction revealed enzymes in most of the cases and some FDA approved drugs were found as structurally similar analogs for Trifolin and Yohimbine. These findings could lead to the development of novel and effective anti-angiogenic agents.Communicated by Ramaswamy H. Sarma.

Synthesis and biological evaluation of novel pteridin-7(8H)-one derivatives as potent CDK2 inhibitors

Cyclin-dependent kinase 2 (CDK2) is considered as an important target in the research of antitumor drugs. Taking the CDK2/4/6 inhibitor Ebvaciclib as the positive control and an in-house library compound (23) as the lead compound, three classes of 30 target compounds with pteridin-7(8H)-one as the core structure were designed to establish structure-activity relationships (SAR). In general, SAR of pteridin-7(8H)-one CDK2 inhibitors is systematically described in this paper, resulting in the discovery of two compounds (KII-17 and KII-21) with further research value. After the above compounds were tested for CDK2/4/6 kinase selectivity, we found that compound KII-21 was about 3 and 4 times more selective to CDK2-cyclinE2 than CDK4-cyclinD1 and CDK6-cyclinD3, respectively. This work also provides a reference basis for the subsequent research on CDK2 inhibitors.

Bioactive Compounds from Nyctanthes arbor tristis Linn as Potential Inhibitors of Janus Kinases (JAKs) Involved in Rheumatoid Arthritis

Nyctanthes arbor tristis L (NAT) is one of the herbal plants whose parts are commonly used to treat diverse ailment including RA. Although the etiology of the autoimmune disorder RA is still unclear, actions of cytokines have been greatly associated with the mechanism of RA. Despite the huge development of drugs to combat this disorder, the search for alternative medicine is increasing due to the adverse effects of these synthetic drugs. Here, the ability of 30 selected bioactive compounds from the parts of NAT to bind effectively to target proteins of the Janus kinases as a potent inhibitor was predicted in an in silico manner through molecular docking procedure using Autodock 4.2.6 and their interactions visualized using Discovery Studio, followed by evaluating the physiochemical and ADMET properties of compounds of the lowest binding energy comparable to the reference drug baricitinib. Comparing the predicted target information with the standard drug baricitinib, 7 bioactive compounds may be potential lead drug for the treatment of RA owing to their lowest binding energy ranging from - 7.0 kcal/mol to - 10.49 kcal/mol and their pharmacokinetics properties. This can be used for further in vivo and in vitro studies to establish their potency as JAKs inhibitors to treat RA.

An In-Silico Identification of Potential Flavonoids against Kidney Fibrosis Targeting TGFβR-1

Fibrosis is a hallmark of progressive kidney diseases. The overexpression of profibrotic cytokine, namely transforming growth factor β (TGF-β) due to excessive inflammation and tissue damage, induces kidney fibrosis. The inhibition of TGF-β signaling is markedly limited in experimental disease models. Targeting TGF-β signaling, therefore, offers a prospective strategy for the management of kidney fibrosis. Presently, the marketed drugs have numerous side effects, but plant-derived compounds are relatively safer and more cost-effective. In this study, TGFβR-1 was targeted to identify the lead compounds among flavonoids using various computational approaches, such as ADME/T (absorption, distribution, metabolism, and excretion/toxicity) analysis, molecular docking, and molecular dynamics simulation. ADME/T screening identified a total of 31 flavonoids with drug-like properties of 31 compounds, a total of 5 compounds showed a higher binding affinity to TGFβR-1, with Epicatechin, Fisetin, and Luteolin ranking at the top three (-13.58, -13.17, and -10.50 kcal/mol, respectively), which are comparable to the control drug linagliptin (-9.074 kcal/mol). The compounds also exhibited outstanding protein-ligand interactions. The molecular dynamic simulations revealed a stable interaction of these compounds with the binding site of TGFβR-1. These findings indicate that flavonoids, particularly Epicatechin, Fisetin, and Luteolin, may compete with the ligand-binding site of TGFβR-1, suggesting that these compounds can be further evaluated for the development of potential therapeutics against kidney fibrosis. Further, in-vitro and in-vivo studies are recommended to support the current findings.

Molecular Docking of Phytochemicals Targeting GFRs as Therapeutic Sites for Cancer: an In Silico Study

Drug delivery in a safe manner is a major challenge in the drug development process. Growth factor receptors (GFRs) are known to have profound roles in the growth and progression of cancerous cells making these receptors a therapeutic target in the effective treatment of cancer. This work focused on exploring bioactive compounds that can target GFRs using in silico method. In this study, 50 bioactive compounds from different plant sources were screened as anticancer agent against GFRs using drug likeness parameters of Lipinski's rule of five. The molecular docking was performed between phytochemicals and GFRs. Ligands with acceptable drug likeness and binding energy comparable to the standard drugs were further screened to determine their pharmacokinetic activities. This study showed phytochemicals with the binding energy comparable with the standard drugs (Dovitinib and Gefitinib), while ADME, bioactivity score, and bioavailability radar analysis gave further insight on these compounds as potent anticancer agents.

In silico investigations on curcuminoids from Curcuma longa as positive regulators of the Wnt/β-catenin signaling pathway in wound healing

Background

Curcuma longa (Turmeric) is a traditionally used herb in wound healing. The efficacy of fresh turmeric paste to heal wounds has already been investigated in multiple ethnobotanical studies. Wnt/β-catenin signaling pathway plays a significant role in wound healing and injury repair processes which has been evident in different in vitro studies. This study aims to analyze the potentiality of curcuminoids (curcumin I, curcumin II and curcumin III) from Curcuma longa to bind and enhance the activity of two intracellular signaling proteins- casein kinase-1 (CK1) and glycogen synthase kinase-3β (GSK3B) involved in Wnt/β-catenin signaling pathway. This study is largely based on a computer-based molecular docking program which mimics the in vivo condition and works on a specific algorithm to interpret the binding affinity and poses of a ligand molecule to a receptor. Subsequently, drug likeness property, ADME/Toxicity profile, pharmacological activity, and site of metabolism of the curcuminoids were also analyzed.

Results

Curcumin I showed better affinity of binding with CK1 (− 10.31 Kcal/mol binding energy) and curcumin II showed better binding affinity (− 7.55 Kcal/mol binding energy) for GSK3B. All of the ligand molecules showed quite similar pharmacological properties.

Conclusion

Curcumin has anti-oxidant, anti-carcinogenic, anti-mutagenic, anti-coagulant, and anti-infective properties. Curcumin has also anti-inflammatory and wound healing properties. It hastens wound healing by acting on different stages of the natural wound healing process. In this study, three curcumins from Curcuma longa were utilized in this experiment in a search for a drug to be used in wound healing and injury repair processes. Hopefully, this study will raise research interest among researchers.

Identification of the most potent acetylcholinesterase inhibitors from plants for possible treatment of Alzheimer’s disease: a computational approach

Background

Being one of the rapidly growing dementia type diseases in the world, Alzheimer’s disease (AD) has gained much attention from researchers in the recent decades. Many hypotheses have been developed that describe different reasons for the development of AD. Among them, the cholinergic hypothesis depicts that the degradation of an important neurotransmitter, acetylcholine by the enzyme acetylcholinesterase (AChE), is responsible for the development of AD. Although, many anti-AChE drugs are already available in the market, their performance sometimes yields unexpected results. For this reason, research works are going on to find out potential anti-AChE agents both from natural and synthetic sources. In this study, 50 potential anti-AChE phytochemicals were analyzed using numerous tools of bioinformatics and in silico biology to find out the best possible anti-AChE agents among the selected 50 ligands through molecular docking, determination of the druglikeness properties, conducting the ADMET test, PASS and P450 site of metabolism prediction, and DFT calculations.

Result

The predictions of this study suggested that among the selected 50 ligands, bellidifolin, naringenin, apigenin, and coptisine were the 4 best compounds with quite similar and sound performance in most of the experiments.

Conclusion

In this study, bellidifolin, naringenin, apigenin, and coptisine were found to be the most effective agents for treating the AD targeting AChE. However, more in vivo and in vitro analyses are required to finally confirm the outcomes of this research.