Molecular interaction studies of green tea catechins as multitarget drug candidates for the treatment of Parkinson's disease: computational and structural insights

Curvilinear regression analysis of benzenoid hydrocarbons and computation of some reduced reverse degree based topological indices for hyaluronic acid-paclitaxel conjugates

Graph theoretical molecular descriptors alias topological indices are a convenient means for expressing in numerical form the chemical structure encoded in a molecular graph. The structure descriptors derived from molecular graphs are widely used in quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR) studies. The reason for introducing new indices is to obtain predictions of target properties of considered molecules that are better than the predictions obtained using already known indices. In this paper, we apply the reduced reverse degree based indices introduced in 2021 by Vignesh et al. In the QSPR analysis, we first compute the reduced reverse degree based indices for a family of benzenoid hydrocarbon molecules and then we obtain the correlation with the Physico-chemical properties of the considered molecules. We show that all the properties taken into consideration for the benzenoid hydrocarbons can be very effectively predicted by the reduced reverse degree based indices. Also, we have compared the predictive capability of reduced reverse degree based topological descriptors against 16 existing degree based indices. Further, we compute the defined reduced reverse degree based topological indices for Hyaluronic Acid-Paclitaxel Conjugates [Formula: see text], [Formula: see text].

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.

Targeting SARS-CoV-2 main protease by teicoplanin: A mechanistic insight by docking, MM/GBSA and molecular dynamics simulation

First emerged in late December 2019, the outbreak of novel severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) pandemic has instigated public-health emergency around the globe. Till date there is no specific therapeutic agent for this disease and hence, the world is craving to identify potential antiviral agents against SARS-CoV-2. The main protease (M^Pro) is considered as an attractive drug target for rational drug design against SARS-CoV-2 as it is known to play a crucial role in the viral replication and transcription. Teicoplanin is a glycopeptide class of antibiotic which is regularly used for treating Gram-positive bacterial infections, has shown potential therapeutic efficacy against SARS-CoV-2 in vitro. Therefore, in this study, a mechanistic insight of intermolecular interactions between teicoplanin and SARS-CoV-2 M^Pro has been scrutinized by molecular docking. Both monomeric and dimeric forms of M^Pro was used in docking involving blind as well as defined binding site based on the known inhibitor. Binding energies of teicoplanin-M^Pro complexes were estimated by Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) computations from docking and simulated trajectories. The dynamic and thermodynamics constraints of docked drug in complex with target proteins under specific physiological conditions was ascertained by all-atom molecular dynamics simulation of 100 ns trajectory. Root mean square deviation and fluctuation of carbon α chain justified the stability of the bound complex in biological environments. The outcomes of current study are supposed to be fruitful in rational design of antiviral drugs against SARS-CoV-2.

Impact of dietary polyphenols on neuroinflammation-associated disorders

Neurodegenerative disorders like Alzheimer's, Parkinson's, and associated dementia typically originate with altered protein folding and aggregation of their β structures in the neurons. This self-aggregation leads to glial activation in the brain, causing neuroinflammation and leads to neuronal death. According to statistics provided by WHO, there are around 50 million people with dementia worldwide and every year, 10 million more cases are projected to increase. Also, around 5-8 percentage of people who are aged above 60 globally has dementia or associated disorders. Over 82 million in 2030 and 152 in 2050 are expected to have dementia. Most of these patients fall into low-middle-income countries which makes it even more essential to find an affordable and effective treatment method. Polyphenols of different origin are studied for their potential role as anti-neuro-inflammatory molecules. This review would summarize recent advances in three widely researched dietary polyphenols projected as potential therapeutic agents for disorders like Alzheimer's, Parkinson's, etc. They are Resveratrol, Catechins, and Tannins. The review would discuss the recent advances and challenges in using these polyphenols using specific examples as potential therapeutic agents against neuroinflammation associated disorders. An abstract of neuroinflammation-associated events and the effects by selected polyphenols.

Potential benefits of phytochemicals from Azadirachta indica against neurological disorders

Azadirachta indica or Neem has been extensively used in the Indian traditional medical system because of its broad range of medicinal properties. Neem contains many chemically diverse and structurally complex phytochemicals such as limonoids, flavonoids, phenols, catechins, gallic acid, polyphenols, nimbins. These phytochemicals possess vast array of therapeutic activities that include anti-feedant, anti-viral, anti-malarial, anti-bacterial, anti-cancer properties. In recent years, many phytochemicals from Neem have been shown to be beneficial against various neurological disorders like Alzheimer's and Parkinson's disease, mood disorders, ischemic-reperfusion injury. The neuroprotective effects of the phytochemicals from Neem are primarily mediated by their anti-oxidant, anti-inflammatory and anti-apoptotic activities along with their ability to modulate signaling pathways. However, extensive studies are still required to fully understand the molecular mechanisms involved in neuropotective effects of phytochemicals from Neem. This review is an attempt to cover the neuroprotective properties of various phytochemicals from Neem along with their mechanism of action so that the potential of the compounds could be realized to reduce the burden of neurodegenerative diseases.

Role of natural products for the treatment of Alzheimer's disease

Negative psychological and physiological consequences of neurodegenerative disorders represent a high social and health cost. Among the neurodegenerative disorders Alzheimer's disease (AD) is recognized as a leading neurodegenerative condition and a primary cause of dementia in the elderlys. AD is considered as neurodegenerative disorder that progressively impairs cognitive function and memory. According to current epidemiological data, about 50 milLion people worldwide are suffering from AD. The primary symptoms of AD are almost inappreciable and usually comprise forgetfulness of recent events. Numerous processes are involved in the development of AD, for example oxidative stress (OS) mainly due to mitochondrial dysfunction, intracellular the accumulation of hyperphosphorylated tau (τ) proteins in the form of neurofibrillary tangles, excessive the accumulation of extracellular plaques of beta-amyloid (Aβ), genetic and environmental factors. Running treatments only attenuate symptoms and temporarily reduce the rate of cognitive progression associated with AD. This means that most treatments focus only on controlLing symptoms, particularly in the initial stages of the disease. In the past, the first choice of treatment was based on natural ingredients. In this sense, diverse natural products (NPs) are capable to decrease the symptoms and alleviate the development of several diseases including AD attracting the attention of the scientific community and the pharmaceutical industry. Specifically, numerous NPs including flavonoids, gingerols, tannins, anthocyanins, triterpenes and alkaloids have been shown anti-inflammatory, antioxidant, anti-amyloidogenic, and anti-choLinesterase properties. This review provide a summary of the pathogenesis and the therapeutic goals of AD. It also discusses the available data on various plants and isolated natural compounds used to prevent and diminish the symptoms of AD.

An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α

Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IMP)α directly and averts interaction with IMPβ1, leading to the prevention of nuclear localization signal (NLS) recognition. Therefore, the current study seeks to employ molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) analysis and molecular dynamics simulation studies for decrypting the binding mode, key interacting residues as well as mechanistic insights on IVM interaction with 15 potential drug targets associated with COVID-19 as well as IMPα. Among all COVID-19 targets, the non-structural protein 9 (Nsp9) exhibited the strongest affinity to IVM showing -5.30 kcal/mol and -84.85 kcal/mol binding energies estimated by AutoDock Vina and MM-GBSA, respectively. However, moderate affinity was accounted for IMPα amounting -6.9 kcal/mol and -66.04 kcal/mol. Stability of the protein-ligand complexes of Nsp9-IVM and IMPα-IVM was ascertained by 100 ns trajectory of all-atom molecular dynamics simulation. Structural conformation of protein in complex with docked IVM exhibited stable root mean square deviation while root mean square fluctuations were also found to be consistent. In silico exploration of the potential targets and their interaction profile with IVM can assist experimental studies as well as designing of COVID-19 drugs.

Design and synthesis of pyrazole-pyrazoline hybrids as cancer-associated selective COX-2 inhibitors

In continuation of our previous work on cancer and inflammation, 15 novel pyrazole-pyrazoline hybrids (WSPP1-15) were synthesized and fully characterized. The formation of the pyrazoline ring was confirmed by the appearance of three doublets of doublets in ¹ H nuclear magnetic resonance spectra exhibiting an AMX pattern for three protons (H_A , H_M , and H_X ) of the pyrazoline ring. All the synthesized compounds were screened for their in vitro anticancer activity against five cell lines, that is, MCF-7, A549, SiHa, COLO205, and HepG2 cells, using the MTT growth inhibition assay. 5-Fluorouracil was taken as the positive control in the study. It was observed that, among them, WSPP11 was found to be active against A549, SiHa, COLO205, and HepG2 cells, with IC₅₀ values of 4.94, 4.54, 4.86, and 2.09 µM. All the derivatives were also evaluated for their cytotoxicity against HaCaT cells. WSPP11 was also found to be nontoxic against normal cells (cell line HaCaT), with an IC₅₀ value of more than 50 µM. The derivatives were also evaluated for their in vitro anti-inflammatory activity by the protein (egg albumin) denaturation assay and the red blood cell membrane stabilizing assay, using diclofenac sodium and celecoxib as standard. Compounds that showed significant anticancer and anti-inflammatory activities were further studied for COX-2 inhibition. The manifestation of a higher COX-2 selectivity index of WSPP11 as compared with other derivatives and an in vitro anticancer activity against four cell lines further established that compounds that were more selective toward COX-2 also exhibited a better spectrum of activity against various cancer cell lines.

Nano-engineered nerolidol loaded lipid carrier delivery system attenuates cyclophosphamide neurotoxicity - Probable role of NLRP3 inflammasome and caspase-1

Neuroinflammation is one of the most common etiology in various neurological disorders and responsible for multi-array neurotoxic manifestations such as neurodegeneration, neurotransmitters alteration and cognitive dysfunction. NR (Nerolidol) is a natural bioactive molecule which possesses significant antioxidant and anti-inflammatory potential, but suffers from glitches of low solubility, low bioavailability and fast hepatic metabolism. In the current study, we fabricated nano-engineered lipid carrier of nerolidol (NR-NLC) for its effective delivery into the brain and explored its effect on neuroinflammation, neurotransmitters level and on dysfunctional behavioral attributes induced by CYC (cyclophosphamide). The binding affinity of nerolidol with NLRP3 and TLR-4 was performed which showed stong interaction between them. NR-NLC was prepared by the ultrasonication methods and particle size was determined by Zeta-sizer. Swiss Albino mice were divided into 5 groups (n = 6), assessed for behavioral dysfunction, and sacrificed on the fifteenth day following cyclophosphamide treatment. Brains were then removed and used for biochemical, histopathological, immunohistochemical and fluorescence microscopic analysis. Biochemical analysis showed increased levels of MDA, TNF-α, IL-6, IL-1β, acetylcholine esterase, BDNF, 5-HT and dopamine, and reduced levels of SOD, CAT, GSH, IL-10, along with significant behavioral dysfunction in cyclophosphamide-treated animals. Significant neuronal damage was also observed in the histological study. Immunohistochemical analysis demonstrated increased expression of NLRP3 and caspase-1. Fluorescence microscopic analysis showed significant availability of NR-NLC in the hippocampus and cortex region. In contrast, treatment with NR-NLC effectively mitigated the aforementioned neurotoxic manifestation as compared to NR suspension. Our results showed potent neuroprotective effect of NR-NLC via modulation of oxidative stress, NLRP3 inflammasome, caspase-1 and neurotransmitter status.

Degree-based topological indices and polynomials of hyaluronic acid-curcumin conjugates

Quantitative structure–activity relationship (QSAR) represents quantitative correlation of chemical structural features called as molecular descriptors and pharmacological activity as response endpoints. Topological index is a molecular descriptor extensively used to study QSAR of pharmaceuticals to assess their molecular characteristics by numerical computation. Theoretical assessment of drug like molecules helps to expedite the drug design and discovery process by rationalizing the lead identification, lead optimization and understanding their mechanism of actions. Therefore, in this article, we have computed the general inverse sum indeg index, ISIα,β of Hyaluronic acid-curcumin conjugates by using molecular structure analysis and edge partitioning technique. Many standard topological indices are obtained as a special case of ISIα,β. We also proposed general inverse sum indeg polynomial ISIα,β(Gn,x) of Hyaluronic acid-curcumin conjugates from which many well-known polynomials are deduced.

Zerumbone binding to estrogen receptors: an in-silico investigation

Breast cancer is the most frequent malignancy among females worldwide. Estrogen receptor (ER) mediate important pathophysiological signaling pathways induced by estrogens, and is regarded as a promising target for the treatment of breast cancer. Zerumbone (2,6,9,9-tetramethylcycloundeca-2,6,10-trien-1-one; ZER), a chemical constituent present in the Zingiber zerumbet is known to exhibit anti-breast cancer activity by modulating several proteins to induce apoptosis. Medicinal chemists usually exploit lead compounds of natural origin to develop molecules with improved pharmacological properties. Current study is intended to utilize molecular modeling techniques to investigate the interaction of ZER with estrogen receptors. AutoDock was used to predict the binding modes of ZER and target receptors. Stability of the ZER-ER complex was verified by molecular dynamics simulation using Desmond software. Docked ZER was further optimized by density functional theory (DFT) using Gaussian09 program. Analysis of docked conformations in terms of binding energy disclosed estrogen receptor-β (ERβ) as more promising than estrogen receptor-α (ERα). Evaluation of MD trajectories of ZER bound to both ERα and ERβ showed appreciable stability with minimum Cα-atom root mean square deviation shifts. DFT based global reactivity descriptors such as electron affinity, hardness, chemical potential, electronegativity and electrophilicity index, calculated from the energies of highest occupied and lowest unoccupied molecular orbitals underscored the electronic features governing viability of the ZER for interaction with the target receptors. In conclusion, these findings can be exploited to design and develop novel anticancer agents based on the lead compound, ZER.

Anti-Inflammatory, Anti-Diabetic, and Anti-Alzheimer's Effects of Prenylated Flavonoids from Okinawa Propolis: An Investigation by Experimental and Computational Studies

Okinawa propolis (OP) and its major ingredients were reported to have anti-cancer effects and lifespan-extending effects on Caenorhabditis elegans through inactivation of the oncogenic kinase, p21-activated kinase 1 (PAK1). Herein, five prenylated flavonoids from OP, nymphaeol-A (NA), nymphaeol-B (NB), nymphaeol-C (NC), isonymphaeol-B (INB), and 3'-geranyl-naringenin (GN), were evaluated for their anti-inflammatory, anti-diabetic, and anti-Alzheimer's effects using in vitro techniques. They showed significant anti-inflammatory effects through inhibition of albumin denaturation (half maximal inhibitory concentration (IC₅₀) values of 0.26⁻1.02 µM), nitrite accumulation (IC₅₀ values of 2.4⁻7.0 µM), and cyclooxygenase-2 (COX-2) activity (IC₅₀ values of 11.74⁻24.03 µM). They also strongly suppressed in vitro α-glucosidase enzyme activity with IC₅₀ values of 3.77⁻5.66 µM. However, only INB and NA inhibited acetylcholinesterase significantly compared to the standard drug donepezil, with IC₅₀ values of 7.23 and 7.77 µM, respectively. Molecular docking results indicated that OP compounds have good binding affinity to the α-glucosidase and acetylcholinesterase proteins, making non-bonded interactions with their active residues and surrounding allosteric residues. In addition, none of the compounds violated Lipinski's rule of five and showed notable toxicity parameters. Density functional theory (DFT)-based global reactivity descriptors demonstrated their high reactive nature along with the kinetic stability. In conclusion, this combined study suggests that OP components might be beneficial in the treatment of inflammation, type 2 diabetes mellitus, and Alzheimer's disease.

Cocoa beans improve mitochondrial biogenesis via PPARγ/PGC1α dependent signalling pathway in MPP+ intoxicated human neuroblastoma cells (SH-SY5Y)

Polyphenols are shown to protect from or delay the progression of chronic neurodegenerative diseases. Mitochondrial dysfunction plays a key role in the pathogenesis of Parkinson's disease (PD). This study was aims to gain insight into the role of ahydroalcoholic extract of cocoa (standardised for epicatechin content) on mitochondrial biogenesis in MPP⁺ intoxicated human neuroblastoma cells (SHSY5Y). The effects of cocoa on PPARγ, PGC1α, Nrf2 and TFAM protein expression and mitochondrial membrane potential were evaluated. A pre-exposure to cocoa extract decreased reactive oxygen species formation and restored mitochondrial membrane potential. The cocoa extract was found to up-regulate the expression of PPARγ and the downstream signalling proteins PGC1α, Nrf2 and TFAM. It increased the expression of the anti-apoptotic protein BCl2 and increased superoxide dismutase activity. Further, the cocoa extract down-regulated the expression of mitochondria fission 1 (Fis1) and up-regulated the expression of mitochondria fusion 2 (Mfn2) proteins, suggesting an improvement in mitochondrial functions in MPP⁺ intoxicated cells upon treatment with cocoa. Interestingly, cocoa up-regulates the expression of tyrosine hydroxylase, the rate limiting enzyme in dopamine synthesis. No change in the expression of PPARγ on treatment with cocoa extract was observed when the cells were pre-treated with PPARγ antagonist GW9662. This data suggests that cocoa mediates mitochondrial biogenesis via a PPARγ/PGC1α dependent signalling pathway and also has the ability to improve dopaminergic functions by increasing tyrosine hydroxylase expression. Based on our data, we propose that a cocoa bean extract and products thereof could be used as potential nutritional supplements for neuroprotection in PD.

Computational Molecular Docking and X-ray Crystallographic Studies of Catechins in New Drug Design Strategies

Epidemiological and laboratory studies have shown that green tea and green tea catechins exert beneficial effects on a variety of diseases, including cancer, metabolic syndrome, infectious diseases, and neurodegenerative diseases. In most cases, (-)-epigallocatechin gallate (EGCG) has been shown to play a central role in these effects by green tea. Catechins from other plant sources have also shown health benefits. Many studies have revealed that the binding of EGCG and other catechins to proteins is involved in its action mechanism. Computational docking analysis (CMDA) and X-ray crystallographic analysis (XCA) have provided detailed information on catechin-protein interactions. Several of these studies have revealed that the galloyl moiety anchors it to the cleft of proteins through interactions with its hydroxyl groups, explaining the higher activity of galloylated catechins such as EGCG and epicatechin gallate than non-galloylated catechins. In this paper, we review the results of CMDA and XCA of EGCG and other plant catechins to understand catechin-protein interactions with the expectation of developing new drugs with health-promoting properties.

Computational Approaches in Multitarget Drug Discovery

Current therapeutic strategies entail identifying and characterizing a single protein receptor whose inhibition is likely to result in the successful treatment of a disease of interest, and testing experimentally large libraries of small molecule compounds "in vitro" and "in vivo" to identify promising inhibitors in model systems and determine if the findings are extensible to humans. This highly complex process is largely based on tests, errors, risk, time, and intensive costs. The virtual computational study of compounds simulates situations predicting possible drug linkages with multiple protein target atomic structures, taking into account the dynamic protein inhibitor, and can help identify inhibitors efficiently, particularly for complex drug-resistant diseases. Some discussions will relate to the potential benefits of this approach, using HIV-1 and Plasmodium falciparum infections as examples. Some authors have proposed a virtual drug discovery that not only identifies efficient inhibitors but also helps to minimize side effects and toxicity, thus increasing the likelihood of successful therapies. This chapter discusses concepts and research of bioactive multitargets related to toxicology.

NSAIDs as potential treatment option for preventing amyloid β toxicity in Alzheimer's disease: an investigation by docking, molecular dynamics, and DFT studies

Aggregation of amyloid beta (Aβ) protein considered as one of contributors in development of Alzheimer's disease (AD). Several investigations have identified the importance of non-steroidal anti-inflammatory drugs (NSAIDs) as Aβ aggregation inhibitors. Here, we have examined the binding interactions of 24 NSAIDs belonging to eight different classes, with Aβ fibrils by exploiting docking and molecular dynamics studies. Minimum energy conformation of the docked NSAIDs were further optimized by density functional theory (DFT) employing Becke's three-parameter hybrid model, Lee-Yang-Parr (B3LYP) correlation functional method. DFT-based global reactivity descriptors, such as electron affinity, hardness, softness, chemical potential, electronegativity, and electrophilicity index were calculated to inspect the expediency of these descriptors for understanding the reactive nature and sites of the molecules. Few selected NSAID-Aβ fibrils complexes were subjected to molecular dynamics simulation to illustrate the stability of these complexes and the most prominent interactions during the simulated trajectory. All of the NSAIDs exhibited potential activity against Aβ fibrils in terms of predicted binding affinity. Sulindac was found to be the most active compound underscoring the contribution of indene methylene substitution, whereas acetaminophen was observed as least active NSAID. General structural requirements for interaction of NSAIDs with Aβ fibril include: aryl/heteroaryl aromatic moiety connected through a linker of 1-2 atoms to a distal aromatic group. Considering these structural requirements and electronic features, new potent agents can be designed and developed as potential Aβ fibril inhibitors for the treatment of AD.