Molecular docking and dynamic simulation studies evidenced plausible immunotherapeutic anticancer property by Withaferin A targeting indoleamine 2,3-dioxygenase

Computational Evaluation of Phytocompounds From Selective Medicinal Plants as Potential Antidiabetic Agents

The distinguishing characteristic of diabetes mellitus (DM), chronic hyperglycemia emphasizes the need for safer, more efficient antidiabetic treatments. This study employs computational approaches to explore the therapeutic potential of phytochemicals from medicinal plants as antidiabetic drugs. Molecular docking against phosphorylated insulin receptor (IR) tyrosine kinase and human dipeptidyl peptidase IV (DPP-IV) identified eriodictyol (-7.13 kcal/mol) and petunidin (-6.61 kcal/mol) as potent inhibitors. Molecular dynamics simulations confirmed the structural stability of these complexes, with root mean square deviation values stabilizing within 2.8-4.5 Å. Binding free energy calculations using Molecular Mechanics Generalized Born Surface Area evealed strong binding affinities of eriodictyol-IR (ΔGbinding = -44.63 ± 4.05 kcal/mol), and petunidin-DPP-IV complex (ΔGbinding = -49.86 ± 6.13 kcal/mol). Additionally, pharmacokinetic assessments showed that these compounds adhered to Lipinski's rule, with no significant hepatotoxicity or cytotoxicity. These findings underscore the potential of these phytocompounds as antidiabetic candidates, warranting further in vitro and in vivo investigations.

Discovery of novel PDGFR inhibitors targeting non-small cell lung cancer using a multistep machine learning assisted hybrid virtual screening approach

Non-Small Cell Lung Cancer (NSCLC) is a formidable global health challenge, responsible for the majority of cancer-related deaths worldwide. The Platelet-Derived Growth Factor Receptor (PDGFR) has emerged as a promising therapeutic target in NSCLC, given its crucial involvement in cell growth, proliferation, angiogenesis, and tumor progression. Among PDGFR inhibitors, avapritinib has garnered attention due to its selective activity against mutant forms of PDGFR, particularly PDGFRA D842V and KIT exon 17 D816V, linked to resistance against conventional tyrosine kinase inhibitors. In recent years, Machine Learning has emerged as a powerful tool in pharmaceutical research, offering data-driven insights and accelerating lead identification for drug discovery. In this research article, we focus on the application of Machine Learning, alongside the RDKit toolkit, to identify potential anti-cancer drug candidates targeting PDGFR in NSCLC. Our study demonstrates how smart algorithms efficiently narrow down large screening collections to target-specific sets of just a few hundred small molecules, streamlining the hit discovery process. Employing a Machine Learning-assisted virtual screening strategy, we successfully preselected 220 compounds with potential PDGFRA inhibitory activity from a vast library of 1.048 million compounds, representing a mere 0.013% of the original library. To validate these candidates, we employed traditional genetic algorithm-based virtual screening and docking methods. Remarkably, we found that ZINC000002931631 exhibited comparable or even superior inhibitory potential against PDGFRA compared to Avapritinib, which highlights the value of our Machine Learning approach. Moreover, as part of our lead validation studies, we conducted molecular dynamic simulations, revealing critical molecular-level interactions responsible for the conformational changes in PDGFRA necessary for substrate binding. Our study exemplifies the potential of Machine Learning in the drug discovery process, providing a more efficient and cost-effective means of identifying promising drug candidates for NSCLC treatment. The success of this approach in preselecting compounds with potent PDGFRA inhibitory potential highlights its significance in advancing personalized and targeted therapies for cancer treatment.

In-Silico discovery of 17alpha-hydroxywithanolide-D as potential neuroprotective allosteric modulator of NMDA receptor targeting Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder marked by cognitive decline, memory impairment, and behavioral alterations. The N-methyl-D-aspartate (NMDA) receptor has emerged as a promising target for AD pharmacotherapy due to its role in the disease's pathogenesis. This study leverages advanced computational methods to screen 80 active constituents of Withania somnifera (Ashwagandha), a traditional herb known for its neuroprotective effects, against the NMDA receptor, using FDA-approved Ifenprodil as a reference. Our blind virtual screening results demonstrated that all tested compounds could bind to various domains of the NMDA receptor, with binding energies ranging from - 4.1 to -11.9 kcal/mol, compared to Ifenprodil's -7.8 kcal/mol. Binding preference analysis revealed 7 compounds bound to the A-chain, 37 to the B-chain, 7 to the C-chain, and 29 to the D-chain of the receptor. Notable binding was observed predominantly at the Amino Terminal Domain (ATD) core site, some at the ATD-Ligand Binding Domain (LBD) interface, and a few at the Transmembrane Domain (TMD). Particularly, 17alpha-hydroxywithanolide D, with a binding energy of -11.9 kcal/mol, emerged as a prime candidate for further investigation. Molecular dynamics simulations of this compound revealed key interactions, including direct hydrogen bonding with residues ASP165, ARG431, THR433, LYS466, and TYR476 on the D-chain, as well as additional hydrophobic and water-bridging interactions. These simulations highlighted the compound's influence on dynamic conformational states of the GluN1b-GluN2B receptor complex, modulating interactions between GluN1b Lys178 and GluN2B Asn184. Furthermore, the compound affected the distance between LBD heterodimers and the tension within the LBD-M30 linker, demonstrating its potential to modulate NMDA receptor activity. This comprehensive study not only underscores the therapeutic promise of Withania somnifera derivatives for AD but also provides a detailed molecular basis for their efficacy, offering valuable insights for targeted drug development and innovative therapeutic strategies against Alzheimer's disease.

Efficient and regioselective synthesis of ortho-diiodinated homobenzylic alcohol derivatives: in silico evaluation as potential anticancer IDO/TDO inhibitors

A simple and direct synthesis of 2,6-diiodophenylethanol building blocks through highly regioselective metalation (MIE)/oxirane SN2-type ring opening of 1,2,3-triiodobenzene is described. A significant impact of the nature of the R1 group on the reactivity of the reaction was discovered but not in terms of site-selectivity. The MIE quenching step is easily controlled by the use of slow-reacting electrophiles "oxiranes" providing solely the ortho-diiodinated homobenzylic alcohol derivatives (internal products) in excellent site-selectivity and with stereoretention. The reaction proceeded without any additives to activate the oxiranes and tolerated a wide range of substrates. The reaction of electron-deficient 1,2,3-triiodoarene systems and neutral oxiranes under the optimized conditions provided the highest isolated yields. The reaction is facile, scalable, efficient, general in scope, and generates handy precursors for further chemical manipulation. In silico interaction analysis revealed that compounds 7a, 7p, 7t and 7z established favourable interactions with the receptors IDO and TDO. Moreover, the molecular simulation results revealed stable dynamics, minimal internal fluctuations, tighter packing and more favourable dynamic features. Furthermore, the 7a-IDO reported a TBE of -26.22 ± 0.24 kcal mol-1, 7t-TDO reported a TBE of -46.66 ± 0.27 kcal mol-1, 7p-TDO reported a TBE of -48.02 ± 0.29 kcal mol-1 while 7z-TDO reported a TBE of -48.51 ± 0.28 kcal mol-1. This shows that these compounds potentially interact with IDO and TDO and consequently cause the inhibition of these targets. Moreover, the BFE results also revealed that this combination suggests that the gas-phase interactions between the components are favorable, but the solvation of the system is unfavorable. In the context of binding, it further means that the protein and ligand have attractive forces when in close proximity as seen in the gas phase, but when solvated, the system experiences an increase in free energy due to interactions with the solvent. This further implies that the binding might be enthalpically favorable due to favorable gas-phase interactions but entropically unfavorable due to unfavorable solvation effects. Our analysis shows that our designed compounds have unmatched pharmacological potential, far surpassing previously reported compounds. This highlights the innovative nature of these derivatives and sets a new benchmark in IDO and TDO drug discovery, indicating their significant potential as effective anticancer inhibitors.

In silico elucidation for the identification of potential phytochemical against ACE-II inhibitors

CONTEXT

The present study aims to investigate the therapeutic potential of phytocompounds derived from Annona reticulata leaves for the treatment of hypertension, utilizing computational methodologies. Gaining a comprehensive understanding of the molecular interactions between neophytadiene and γ-sitosterol holds significant importance in the advancement of innovative therapeutic approaches. This study aims to examine the inhibitory effects of neophytadiene and γ-sitosterol using molecular docking and dynamics simulations. Additionally, we will evaluate their stability and predict their drug-like properties as well as their ADME/toxicity profiles. Neophytadiene and γ-sitosterol have a substantial binding affinity with 1O8A, as shown by the docking study. The stability of the complexes was confirmed through molecular dynamics simulations, while distinct clusters were identified using PCA. These findings suggest the presence of potential stabilizers. The drug-likeness and ADME/toxicity predictions revealed positive characteristics, such as efficient absorption rates, limited distribution volume and non-hazardous profiles. The neophytadiene and γ-sitosterol exhibit potential as hypertension medication options. Computational investigations reveal that these compounds exhibit high affinity for binding, stability and favourable pharmacokinetic properties. The results of this study lay the groundwork for additional experimental verification and highlight the promising prospects of utilizing natural compounds in the field of pharmaceutical research.

METHODS

Target proteins (1O8A) were used to perform molecular docking with representative molecules. Stability, conformational changes and binding energies were assessed through molecular dynamics simulations lasting 100 ns. Principal component analysis (PCA) was utilized to analyze molecular dynamics (MD) simulation data, to identify potential compounds that could stabilize the main protease. The safety and pharmacokinetic profiles of the compounds were evaluated through drug-likeness and ADME/toxicity predictions.

Molecular docking and dynamic simulation studies of α4β2 and α7 nicotinic acetylcholine receptors with tobacco smoke constituents nicotine, NNK and NNN

Smoking constitutes a major global health problem. As it triggers various health hazards including cancers, cardiac and pulmonary illness, it is imperative to understand the mechanism of action of various smoke constituents on our cellular processes. Various in vitro studies have compiled the affinity of cigarette smoke constituents on various nicotinic acetylcholine receptors (nAChRs). But the nature of the intermolecular interactions contributing to this affinity and the key amino acids in the receptor active sites involved in this are not investigated so far. Here, we are examining the interaction of α7nAChR and α4β2nAChR on nicotine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N-nitrosornicotine (NNN), the physiologically significant constituents in smoke, through molecular docking and dynamics simulations study. The docking of α4β2nAChR structure with the ligands nicotine, NNK and NNN yielded docking scores of -41.45 kcal/mol, -59.28 kcal/mol and -54.60 kcal/mol, respectively, and that of α7nAChR receptor molecule with the ligands yielded docking scores of -59.54 kcal/mol, -71.06 kcal/mol and -70.86 kcal/mol, respectively. The study showed that NNK exhibited the highest affinity with the ligands which was confirmed by dynamics simulation. But higher stability of interactions as surmised from Molecular dynamics simulations was found for nicotine with α4β2nAChR and NNN with α7nAChR. The findings validate the in vitro studies comparing the affinities of these compounds. The study will be useful in formulating effective nAChR agonists to treat neurological disorders and antagonists for smoke deaddiction and improve health standards.Communicated by Ramaswamy H. Sarma.

Phytochemical Analysis, In Vitro Biological Activities, and Computer-Aided Analysis of Potentilla nepalensis Hook Compounds as Potential Melanoma Inhibitors Based on Molecular Docking, MD Simulations, and ADMET

Potentilla nepalensis Hook is a perennial Himalayan medicinal herb of the Rosaceae family. The present study aimed to evaluate biological activities such as the antioxidant, antibacterial, and anticancer activities of roots and shoots of P. nepalensis and its synergistic antibacterial activity with antibacterial drugs. Folin-Ciocalteau and aluminium chloride methods were used for the calculation of total phenolic (TPC) and flavonoid content (TFC). A DPPH radical scavenging assay and broth dilution method were used for the determination of the antioxidant and antibacterial activity of the root and shoot extracts of P. nepalensis. Cytotoxic activity was determined using a colorimetric MTT assay. Further, phytochemical characterization of the root and shoot extracts was performed using the Gas chromatography-mass spectrophotometry (GC-MS) method. The TPC and TFC were found to be higher in the methanolic root extract of P. nepalensis. The methanolic shoot extract of P. nepalensis showed good antioxidant activity, while then-hexane root extract of P. nepalensis showed strong cytotoxic activity against tested SK-MEL-28 cells. Subsequently, in silico molecular docking studies of the identified bioactive compounds predicted potential anticancer properties. This study can lead to the production of new herbal medicines for various diseases employing P. nepalensis, leading to the creation of new medications.

Unveiling the Potentiality of Shikonin Derivatives Inhibiting SARS-CoV-2 Main Protease by Molecular Dynamic Simulation Studies

Shikonin, a phytochemical present in the roots of Lithospermum erythrorhizon, is well-known for its broad-spectrum activity against cancer, oxidative stress, inflammation, viruses, and anti-COVID-19 agents. A recent report based on a crystallographic study revealed a distinct conformation of shikonin binding to the SARS-CoV-2 main protease (M^pro), suggesting the possibility of designing potential inhibitors based on shikonin derivatives. The present study aimed to identify potential shikonin derivatives targeting the M^pro of COVID-19 by using molecular docking and molecular dynamics simulations. A total of 20 shikonin derivatives were screened, of which few derivatives showed higher binding affinity than shikonin. Following the MM-GBSA binding energy calculations using the docked structures, four derivatives were retained with the highest binding energy and subjected to molecular dynamics simulation. Molecular dynamics simulation studies suggested that alpha-methyl-n-butyl shikonin, beta-hydroxyisovaleryl shikonin, and lithospermidin-B interacted with two conserved residues, His41 and Cys145, through multiple bonding in the catalytic sites. This suggests that these residues may effectively suppress SARS-CoV-2 progression by inhibiting M^pro. Taken together, the present in silico study concluded that shikonin derivatives may play an influential role in M^pro inhibition.

Multitarget Potential of Phytochemicals from Traditional Medicinal Tree, Terminalia arjuna (Roxb. ex DC.) Wight & Arnot as Potential Medicaments for Cardiovascular Disease: An In-Silico Approach

Cardiovascular diseases (CVDs) are the leading cause of mortality worldwide. Terminalia arjuna (Roxb. ex DC.) Wight & Arnot of the Combretaceae family is one of the most frequently approved and utilized medicinal trees in the traditional medicinal system, which was used for the treatment of a variety of diseases, including cardiovascular disorders. The present study aims to identify phytochemicals from T. arjuna, that do not exhibit any toxicity and have significant cardioprotective activity using an in-silico technique. Four different cardiovascular proteins, namely human angiotensin receptor (PDB ID: 4YAY), P38 mitogen-activated protein kinase (MAPK, PDB ID: 4DLI), 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-Co A) reductase (PDB ID: 1HW9), and human C-reactive protein (PDB ID: 1B09), were used as target proteins to identify potential inhibitors using a virtual screening of the phytochemicals in T. arjuna revealed casuarinin as a potential inhibitor of all selected target proteins with strong binding energy. Furthermore, MD simulations for a 100 ns time scale also revealed that most of the key protein contacts of all target proteins were retained throughout the simulation trajectories. Binding free energy calculations using the MM-GBSA approach also support a strong inhibitory effect of casuarinin on target proteins. Casuarinin's effective binding to these proteins lays the groundwork for the development of broad-spectrum drugs as well as the understanding of the underlying mechanism against cardiovascular diseases through in vivo and clinical studies.

In vitro and in silico antioxidant and anti-inflammatory potential of essential oil of Cymbopogon citratus (DC.) Stapf. of North-Western Himalaya

Cymbopogon citratus (DC.) Stapf is an aromatic perennial herb of Gramineae (Poaceae) family and is known for its application in food and healthcare industry. The present study aimed to evaluate anti-inflammatory and antioxidant potential of C. citratus essential oil (CEO) through in vitro and in silico studies. Chemical characterization of CEO was done using Gas chromatography-mass spectrophotometry (GC-MS) method. In vitro antioxidant activity was evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and ferric ion reducing antioxidant power (FRAP) assays, while egg albumin denaturation method was used to evaluate in vitro anti-inflammatory activity of CEO. Molecular docking investigation of major phytocompounds of CEO was done using Autodock vina software against human peroxiredoxin 5 (PDB ID: 1HD2) and human cyclooxygenase 2 (PDB ID: 5IKQ) proteins, which were further analyzed through molecular dynamics (MD) simulation using YASARA. GC-MS analysis of CEO showed the presence of geranial (48%) neral (34.04%), β-myrcene (9.77%), geraniol (1.88%), linalool (0.84%), isogeranial (0.81%), β-caryophyllene (0.80%), D-limonene (0.51%) as major constituents. CEO showed significant antioxidant activity with DPPH (IC₅₀-47.53 ± 2.16 µg/ml), FRAP (IC₅₀-30.7 ± 0.31 µM), and ABTS assays (IC₅₀-27.87 ± 0.09 µg/ml). CEO also exhibited significant in-vitro anti-inflammatory activity with IC₅₀-29.71 ± 1.95 µg/ml as compared to that of Diclofenac sodium (IC₅₀-36.52 ± 1.95 µg/ml). Molecular docking revealed that β-caryophyllene showed considerable binding potential with human peroxiredoxin 5 receptor (-6.0 kcal/mol) and human cyclooxygenase 2 receptor (-10.1 kcal/mol). Further, MD simulations demonstrated considerable and stable interactions of β-caryophyllene with 1HD2 and 5IKQ proteins up to 100 ns. Drug-likeness and ADME/T features also showed that β-caryophyllene can be used as a potential candidate to replace the synthetic anti-inflammatory drugs with side effects and also act as natural antioxidants.Communicated by Ramaswamy H. Sarma.

Evaluation of the Antifungal, Antioxidant, and Anti-Diabetic Potential of the Essential Oil of Curcuma longa Leaves from the North-Western Himalayas by In Vitro and In Silico Analysis

Essential oils (EOs) have gained immense popularity due to considerable interest in the health, food, and pharmaceutical industries. The present study aimed to evaluate the antimicrobial and antioxidant activity and the anti-diabetic potential of Curcuma longa leaf (CLO) essential oil. Further, major phytocompounds of CLO were analyzed for their in-silico interactions with antifungal, antioxidant, and anti-diabetic proteins. CLO was found to have a strong antifungal activity against the tested Candida species with zone of inhibition (ZOI)-11.5 ± 0.71 mm to 13 ± 1.41 mm and minimum inhibitory concentration (MIC) was 0.63%. CLO also showed antioxidant activity, with IC₅₀ values of 5.85 ± 1.61 µg/mL using 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging assay and 32.92 ± 0.64 µM using ferric reducing antioxidant power (FRAP) assay. CLO also showed anti-diabetic activity with an IC₅₀ of 43.06 ± 1.24 µg/mL as compared to metformin (half maximal inhibitory concentration, IC₅₀-16.503 ± 0.66 µg/mL). Gas chromatography-mass spectrometry (GC-MS) analysis of CLO showed the presence of (-)-zingiberene (17.84%); 3,7-cyclodecadien-1-one, 3,7-dimethyl-10-(1-methylethylidene)-(15.31%); cyclohexene, 4-methyl-3-(1-methylethylidene) (12.47%); and (+)-4-Carene (11.89%) as major phytocompounds. Molecular docking of these compounds with antifungal proteins (cytochrome P450 14 alpha-sterol demethylase, PDB ID: 1EA1, and N-myristoyl transferase, PDB ID: 1IYL), antioxidant (human peroxiredoxin 5, PDB ID: 1HD2), and anti-diabetic proteins (human pancreatic alpha-amylase, PDB ID: 1HNY) showed strong binding of 3,7-cyclodecadien-1-one with all the selected protein targets. Furthermore, molecular dynamics (MD) simulations for a 100 ns time scale revealed that most of the key contacts of target proteins were retained throughout the simulation trajectories. Binding free energy calculations using molecular mechanics generalized born surface area (MM/GBSA), and drug-likeness and toxicity analysis also proved the potential for 3,7-cyclodecadien-1-one, 3,7-dimethyl-10-(1-methylethylidene) to replace toxic synthetic drugs and act as natural antioxidants.

Plant‐Based Natural Bioactive Compounds 2,4‐Ditert‐Butylphenolas: A Potential Candidates Against SARS‐Cov‐2019

The novel coronavirus 2019 is spreading around the world and causing serious concern. However, there is limited information about novel coronavirus that hinders the design of effective drug. Bioactive compounds are rich source of chemo preventive ingredients. In our present research focuses on identifying and recognizing bioactive chemicals in Lantana camara, by evaluating their potential toward new coronaviruses and confirming the findings using molecular docking, ADMET, network analysis and dynamics investigations.. The spike protein receptor binding domain were docked with 25 identified compounds and 2,4-Ditertbutyl-phenol (-6.3kcal/mol) shows highest docking score, its interactions enhances the increase in binding and helps to identify the biological activity. The ADME/toxicity result shows that all the tested compounds can serve as inhibitors of the enzymes CYP1A2 and CYP2D6. In addition, Molecular dynamics simulations studies with reference inhibitors were carried out to test the stability. This study identifies the possible active molecules against the receptor binding domain of spike protein, which can be further exploited for the treatment of novel coronavirus 2019. The results of the toxicity risk for phytocompounds and their active derivatives showed a moderate to good drug score.

Evaluation of in vitro and in silico anti-inflammatory potential of some selected medicinal plants of Bangladesh against cyclooxygenase-II enzyme

ETHNOPHARMACOLOGICAL RELEVANCE

Medicinal plants are sources of chemical treasures that can be used in treatment of different diseases, including inflammatory disorders. Traditionally, Heritiera littoralis, Ceriops decandra, Ligustrum sinense, and Polyscias scutellaria are used to treat pain, hepatitis, breast inflammation. The present research was designed to explore phytochemicals from the ethanol extracts of H. littoralis, C. decandra, L. sinense, and P. scutellaria to discern the possible pharmacophore (s) in the treatment of inflammatory disorders.

MATERIAL AND METHODS

The chemical compounds of experimental plants were identified through GC-MS analysis. Furthermore, in-vitro anti-inflammatory activity was assessed in human erythrocytes and an in-silico study was appraised against COX-2.

RESULTS

The experimental extracts totally revealed 77 compounds in GC-MS analysis and all the extracts showed anti-inflammatory activity in in-vitro assays. The most favorable phytochemicals as anti-inflammatory agents were selected via ADMET profiling and molecular docking with specific protein of the COX-2 enzyme. Molecular dynamics simulation (MDS) confirmed the stability of the selected natural compound at the binding site of the protein. Three phytochemicals exhibited the better competitive result than the conventional anti-inflammatory drug naproxen in molecular docking and MDS studies.

CONCLUSION

Both experimental and computational studies have scientifically revealed the folklore uses of the experimental medicinal plants in inflammatory disorders. Overall, N-(2-hydroxycyclohexyl)-4-methylbenzenesulfonamide (PubChem CID: 575170); Benzeneethanamine, 2-fluoro-. beta., 3, 4-trihydroxy-N-isopropyl (PubChem CID: 547892); and 3,5-di-tert-butylphenol (PubChem CID: 70825) could be the potential leads for COX-2 inhibitor for further evaluation of drug-likeliness.

Inhibition of GSK_3β by Iridoid Glycosides of Snowberry (Symphoricarpos albus) Effective in the Treatment of Alzheimer's Disease Using Computational Drug Design Methods

The inhibition of glycogen synthase kinase-3β (GSK-3β) activity prevents tau hyperphosphorylation and binds it to the microtubule network. Therefore, a GSK-3β inhibitor may be a recommended drug for Alzheimer's treatment. In silico methods are currently considered as one of the fastest and most cost-effective available alternatives for drug/design discovery in the field of treatment. In this study, computational drug design was conducted to introduce compounds that play an effective role in inhibiting the GSK-3β enzyme by molecular docking and molecular dynamics simulation. The iridoid glycosides of the common snowberry (Symphoricarpos albus), including loganin, secologanin, and loganetin, are compounds that have an effect on improving memory and cognitive impairment and the results of which on Alzheimer's have been studied as well. In this study, in the molecular docking phase, loganin was considered a more potent inhibitor of this protein by establishing a hydrogen bond with the ATP-binding site of GSK-3β protein and the most negative binding energy to secologanin and loganetin. Moreover, by molecular dynamics simulation of these ligands and GSK-3β protein, all structures were found to be stable during the simulation. In addition, the protein structure represented no change and remained stable by binding ligands to GSK-3β protein. Furthermore, loganin and loganetin have higher binding free energy than secologanin; thus, these compounds could effectively bind to the active site of GSK-3β protein. Hence, loganin and loganetin as iridoid glycosides can be effective in Alzheimer's prevention and treatment, and thus, further in vitro and in vivo studies can focus on these iridoid glycosides as an alternative treatment.

Impact of Mutation on the Structural Stability and the Conformational Landscape of Inhibitor-Resistant TEM β-Lactamase: A High-Performance Molecular Dynamics Simulation Study

Gain-of-function mutations and structural adjustment toward β-lactamase inhibitors in the TEM-type β-lactamases among the uropathogenic E. coli (UPEC) culminate in treatment complications and demands detailed investigation. In this study, uncharacterized amino acid substitutions, M69L/I84V/W165G/V184A/V262I/N276S, in inhibitor-resistant TEM (IRT) β-lactamase isolated from clinical UPEC were subjected to extensive molecular dynamics (EMD) simulations for 100 ns to estimate parameters such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), the radius of gyration (R_g), contour plot (R_g/RMSD), secondary structure element (SSE), etc. Residue interaction networks, principal component analysis (PCA), and correlation heatmaps were generated to predict the relation between functionally important atomic motions to uncover the structural stability of the mutants. To avoid the false positive conclusion of the simulation study, we performed three identically parameterize replicas of 100 ns each. Alterations in hydrophobic interactions resulted in conformation changes exhibited as comparable residue interaction networks. Besides, PCA and porcupine plot analysis based on the ensemble of structure from molecular dynamics trajectories revealed the collective atomic motions of the IRT variants that impart structural flexibility to their active site loop. This study conducted on IRT mutants that delineate intricate protein motions contributes to their stability and folding, which is an absolute necessity for designing candidate molecules owing to the clinical threat of emerging resistance against potent β-lactam antibiotics.

Cantilever-centric mechanism of cooperative non-active site mutations in HIV protease: Implications for flap dynamics

The HIV-1 protease is an important drug target in antiretroviral therapy due to the crucial role it plays in viral maturation. A greater understanding of the dynamics of the protease as a result of drug-induced mutations has been successfully elucidated using computational models in the past. We performed induced-fit docking studies and molecular dynamics simulations on the wild-type South African HIV-1 subtype C protease and two non-active site mutation-containing protease variants; HP3 PR and HP4 PR. The HP3 PR contained the I13V, I62V, and V77I mutations while HP4 PR contained the same mutations with the addition of the L33F mutation. The simulations were initiated in a cubic cell universe containing explicit solvent, with the protease variants beginning in the fully closed conformation. The trajectory for each simulation totalled 50 ns. The results indicate that the mutations increase the dynamics of the flap, hinge, fulcrum and cantilever regions when compared to the wild-type protease while in complex with protease inhibitors. Specifically, these mutations result in the protease favouring the semi-open conformation when in complex with inhibitors. Moreover, the HP4 PR adopted curled flap tip conformers which coordinated several water molecules into the active site in a manner that may reduce inhibitor binding affinity. The mutations affected the thermodynamic landscape of inhibitor binding as there were fewer observable chemical contacts between the mutated variants and saquinavir, atazanavir and darunavir. These data help to elucidate the biophysical basis for the selection of cooperative non-active site mutations by the HI virus.

Review on anticancerous therapeutic potential of Withania somnifera (L.) Dunal

ETHNOPHARMACOLOGICAL RELEVANCE

Withania somnifera, commonly known as Ashwagandha, is an important medicinal herb belonging to family Solanaceae. It is widely used in folkloric and Ayurvedic medicines since antiquity. Traditionally, the plant is highly practiced throughout the globe as immunomodulator, anti-inflammatory, anti-stress, anti-parkinson, anti-alzheimer, cardio protective, neural and physical health enhancer, neurodefensive, anti-diabetic, aphrodisiac, memory boosting etc. The plant is also effective in combating various types of cancer and other related problems of colon, mammary, lung, prostate, skin, blood, liver and kidney.

AIM OF THIS REVIEW

The present review represents the critical assessment of the literature available on the anticancerous role of W. somnifera. The present study throws light on its diverse chemical compounds and the possible mechanisms of action involved. This review also suggests further research strategies to harness the therapeutic potential of this plant.

MATERIALS AND METHODS

The present review is the outcome of a systematic search of scientific literature about 'Withania somnifera and its role in cancer prevention'. The scientific databases viz. Google Scholar, Science Direct, Pubmed and Web of Science were searched from 2001 to 2019. Textbooks, magazines and newspapers were also consulted. This review summarizes all the published literature about its therapeutic potential for the treatment of different types of cancers.

RESULTS

W. somnifera has been widely used in traditional and ayurvedic medicines for treatment of numerous problems related to health and vitality. The plant is a reservoir of diverse phytoconstituents like alkaloids, steroids, flavonoids, phenolics, nitrogen containing compounds and trace elements. Withanolides are the major alkaloids which renders its anticancer potential due to its highly oxygenated nature. The plant is highly effective in combating various types of cancers viz. colon, mammary, lung, prostate, skin, blood, liver and kidney. Previous studies depict that this plant is more effective against breast cancer followed by colon, lung, prostate and blood cancer. Furthermore, from different clinical studies it has been observed that the active constituents of the plant like withaferin-A, withanolide-D have least toxic effects.

CONCLUSION

The present review confirms the various medicinal values of W. somnifera without any significant side effects. Withaferin-A (WA) and Withanolides are its most promising anticancer compounds that play a major role in apoptosis induction. Keeping in mind the anticancerous potential of this plant, it is suggested that this plant may further be investigated and more clinical studies can be performed.

Untangling the multi-regime molecular mechanism of verbenol-chemotype Zingiber officinale essential oil against Aspergillus flavus and aflatoxin B1

Aflatoxin B1 (AFB1), the natural polyketide produced by Aspergillus flavus, has a potent carcinogenic effect on humans as well as animals. In the present study, the antifungal and anti-aflatoxigenic B1 activity of chemically characterized Zingiber officinale essential oil (ZOEO) was investigated via in vitro analysis aided with molecular dynamics (MD) approaches. The GC-MS results revealed verbenol (52.41%) as the major component of oil. The antifungal and anti-aflatoxigenic activity of ZOEO was found to be 0.6 µl/ml and 0.5 µl/ml respectively. In-vitro analysis targeting the cell membrane, mitochondria and carbohydrate catabolism elucidated the probable antifungal mode of action. Further, docking and MD simulation results confirmed the inhibitory action of verbenol on the structural gene products (Nor-1, Omt-1, and Vbs) of aflatoxin biosynthetic machinery. Biochemical assays revealed the fungitoxic potential of the ZOEO while, computational results infers the stabilizing effects on the gene products upon verbenol binding leads to the impairment in its functionality. This is the first attempt to assess the multi-regime anti-AFB1 mechanism of verbenol chemotype-ZOEO targeting the Nor-1, Omt-1, and Vbs via computational approaches.

Microsecond simulation analysis of carbonic anhydrase - II in complex with (+)-cathechin revealed molecular interactions responsible for its amelioration effect on fluoride toxicity

Fluorosis is a chronic condition caused by overexposure to fluoride, marked by impaired dental, skeletal, and non-skeletal health. In presence of excess fluoride ions, in severe cases calcification of the ligaments observed. Earlier studies have suggested that the disruption of carbonic anhydrase activity via ionic homeostasis change was associated with F toxicity. In a recent study, it was demonstrated that Tamarind fruit extract was effective in increasing the urinary F excretion in male Wistar rats via studying the mRNA expression of carbonic anhydrase II (CA II) in kidney homogenates using western blotting, immunohistochemistry and quantitative Realtime PCR based studies. We have carried out this study to understand the detailed molecular level interactions responsible for this tamarind extract based (+)-cathechin compound towards lowering the F toxicity via targeting CA-II. From our study, it was revealed that due to the ability of (+)-cathechin compound to bind tightly filling complete available space at the catalytically important site forming metal coordinated ionic bonds with His94, His96 and His119 residues helps in restricting F ions to interact with Zn ion located at the core of catalytic site responsible for its functionality. On the other hand, interaction of (+)-cathechin compound with Gln92 was observed to be critically important towards inducing conformational changes in CA-II, thus allowing (+)-cathechin compound to burry even deeply inside the catalytic site.Communicated by Ramaswamy H. Sarma.

Molecular docking studies of phytocompounds of Rheum emodi Wall with proteins responsible for antibiotic resistance in bacterial and fungal pathogens: in silico approach to enhance the bio-availability of antibiotics

Rheum emodi Wall. (Himalayan rhubarb) has many pharmacological activities such as antioxidant, antimicrobial, antiviral, anticancer and wound healing. The present study was aimed to understand if major phytocompounds of Rheum emodi could bind proteins responsible for antibiotic resistance in bacterial and fungal pathogens and enhance the potency of antibiotics. The major phytocompounds of R. emodi (emodin, rhein-13c6 and chrysophenol dimethy ether) were retrieved from the Pubchem and target proteins were retrieved from RCSB protein data bank. The docking study was performed by using AutoDock vina software and Molinspiration, swiss ADME servers were used for the determination of Lipinski rule of 5, drug-likeness prediction respectively, whereas, admetSAR and Protox-II tools were used for toxicity prediction. To study the docking accuracy of protein-ligand complexes, MD simulation for 100 ns was done by using Desmond program version 2.0 (Academic version). Among all the selected phytocompounds, emodin showed the best binding affinity against bacterial (Penicillin binding protein 3, 3VSL and fungal target (cytochrome P450 14 alpha-sterol demethylase 1EA1) with binding energy -8.2 and -8.0 Kcal mol^-1 respectively. Similarly, rhein-13C6 showed the best binding affinity against fungal target (n-myristoyl transferase 1IYL) with binding energy -8.0 Kcal mol^-1 which is higher than antibacterial and antifungal antibiotics. All the selected phytocompounds also fulfill Lipinski rule, non-carcinogenic and non-cytotoxic in nature. These compounds also showed high LD₅₀ value showing non-toxicity of these phytocompounds. MD simulation studies of phytocompounds (emodin and rhein-13C6) define the stability of protein-ligand complexes with in 100 ns time scale.Communicated by Freddie R. Salsbury.

Synthesis, characterization, in silico, and in vitro biological screening of coordination compounds with 1,2,4-triazine based biocompatible ligands and selected 3d-metal ions

A bidentate Schiff base ligand, MHMMT, obtained from 1,2,4-triazine derivative and 4-hydroxy-3-methoxy benzaldehyde and its Fe(III), Co(II), Ni(II), Cu(II), and Zn(II) complexes were synthesised in ethanolic media and characterized by various analytical techniques like elemental analyses, magnetic susceptibility measurements, FTIR, UV-VIS, proton NMR, ESR, spectroscopic and thermogravimetric studies. Various geometries like a tetrahedral for Co(II) and Zn(II) complexes, an octahedral for Fe(III) and Ni(II) complexes, and square planar for Cu(II) complex has been assigned. For all metals complexes except Co(II), a 2:1 ligand to metal ratio is observed, while Co(II) complex has a 1:1 ratio. In accordance with the probable activity spectra of substances as obtained from PASS analysis, in vitro α-amylase inhibition studies by starch-iodine method for ligand and complexes except that of Fe(III) and anticancer screening against human breast cancer cell lines MCF-7 using MTT assay for Fe(III) complex were conducted. The tested compounds were found to be good α-amylase inhibitors, characteristically similar to most of the antidiabetic drugs. Among the compounds, Cu(II) complex exhibited the highest α-amylase inhibitory activity. Furthermore, ligand and complexes were also exposed to in vitro antimicrobial activities, drug-likeness, bioactivity score prediction by Molinspiration software. Molecular docking analysis of selected compounds on α-amylase and VEGFR-2 kinase were carried out for confirming the experimental observations.

In-silico anti-inflammatory potential of guaiane dimers from Xylopia vielana targeting COX-2

Natural products of herbal origin are prodigious to display diverse pharmacological activities. In the present study, five guaiane-type sesquiterpene dimers, xylopidimers A - E (1-5), isolated from Xylopia vielana species were tested against COX-2 protein target (PDB: 1CX2), a potent target for anti-inflammatory agents. To better understand the pharmacological properties of all these compounds, in this work, a systemic in silico study was performed on xylopidimers A-E using molecular docking, ADMET analysis and MD simulations. During ADMET predictions the two compounds xylopidimer C, D displayed best results as compared to others. The compound xylopidimer C was further evaluated for its MD simulations and its molecular interactions with COX2 complex showed clear interactions with active gorge of the enzyme through hydrogen bonding as well as hydrophobic contacts. The xylopidimer C has shown the best binding potential with -10.57Kcal/mol energy with 17.92 nano molar of predicted inhibition constant better than Ibuprofen and Felbinac. These findings provide enough significant information for designing and developing novel targeted base anti-inflammatory drugs from guaiane dimers.

Identification of bioactive molecule from Withania somnifera (Ashwagandha) as SARS-CoV-2 main protease inhibitor

SARS-CoV-2 is the causative agent of COVID-19 and has been declared as pandemic disease by World Health Organization. Lack of targeted therapeutics and vaccines for COVID-2019 have triggered the scientific community to develop new vaccines or drugs against this novel virus. Many synthetic compounds and antimalarial drugs are undergoing clinical trials. The traditional medical practitioners widely use Indian medicinal plant Withania somnifera (Ashwagandha) natural constituents, called withanolides for curing various diseases. The main protease (M^pro) of SARS-CoV-2 plays a vital role in disease propagation by processing the polyproteins which are required for its replication. Hence, it denotes a significant target for drug discovery. In the present study, we evaluate the potential of 40 natural chemical constituents of Ashwagandha to explore a possible inhibitor against main protease of SARS-CoV-2 by adopting the computational approach. The docking study revealed that four constituents of Ashwagandha; Withanoside II (-11.30 Kcal/mol), Withanoside IV (-11.02 Kcal/mol), Withanoside V (-8.96 Kcal/mol) and Sitoindoside IX (-8.37 Kcal/mol) exhibited the highest docking energy among the selected natural constituents. Further, MD simulation study of 100 ns predicts Withanoside V possess strong binding affinity and hydrogen-bonding interactions with the protein active site and indicates its stability in the active site. The binding free energy score also correlates with the highest score of -87.01 ± 5.01 Kcal/mol as compared to other selected compounds. In conclusion, our study suggests that Withanoside V in Ashwagandha may be serve as a potential inhibitor against M^pro of SARS-CoV-2 to combat COVID-19 and may have an antiviral effect on nCoV.Communicated by Ramaswamy H. Sarma.

Unveiling the Structural Insights into the Selective Inhibition of Protein Kinase D1

BACKGROUND

Although protein kinase D1 (PKD1) has been proved to be an efficient target for anticancer drug development, lack of structural details and substrate binding mechanisms are the main obstacles for the development of selective inhibitors with therapeutic benefits.

OBJECTIVE

The present study described the in silico dynamics behaviors of PKD1 in binding with selective and non-selective inhibitors and revealed the critical binding site residues for the selective kinase inhibition.

METHODS

Here, the three dimensional model of PKD1 was initially constructed by homology modeling along with binding site characterization to explore the non-conserved residues. Subsequently, two known inhibitors were docked to the catalytic site and the detailed ligand binding mechanisms and post binding dyanmics were investigated by molecular dynamics simulation and binding free energy calculations.

RESULTS

According to the binding site analysis, PKD1 serves several non-conserved residues in the G-loop, hinge and catalytic subunits. Among them, the residues including Leu662, His663, and Asp665 from hinge region made polar interactions with selective PKD1 inhibitor in docking simulation, which were further validated by the molecular dynamics simulation. Both inhibitors strongly influenced the structural dynamics of PKD1 and their computed binding free energies were in accordance with experimental bioactivity data.

CONCLUSION

The identified non-conserved residues likely to play critical role on molecular reorganization and inhibitor selectivity. Taken together, this study explained the molecular basis of PKD1 specific inhibition, which may help to design new selective inhibitors for better therapies to overcome cancer and PKD1 dysregulated disorders.

In Silico Elucidation of the Plausible Inhibitory Potential of Withaferin A of Withania Somnifera Medicinal Herb Against Breast Cancer Targeting Estrogen Receptor

BACKGROUND

Estrogen Receptors (ER) are members of the nuclear intracellular receptors family. ER once activated by estrogen, it binds to DNA via translocating into the nucleus and regulates the activity of various genes. Withaferin A (WA) - an active compound of a medicinal plant Withania somnifera was reported to be a very effective anti-cancer agent and some of the recent studies has demonstrated that WA is capable of arresting the development of breast cancer via targeting estrogen receptor.

OBJECTIVE

The present study is aimed at understanding the molecular level interactions of ER and Tamoxifen in comparison to Withaferin A using In-silico approaches with emphasis on Withaferin A binding capability with ER in presence of point mutations which are causing de novo drug resistance to existing drugs like Tamoxifen.

METHODS

Molecular modeling and docking studies were performed for the Tamoxifen and Withaferin A with the Estrogen receptor. Molecular docking simulations of estrogen receptor in complex with Tamoxifen and Withaferin A were also performed.

RESULTS

Amino acid residues, Glu353, Arg394 and Leu387 was observed as crucial for binding and stabilizing the protein-ligand complex in case of Tamoxifen and Withaferin-A. The potential of Withaferin A to overcome the drug resistance caused by the mutations in estrogen receptor to the existing drugs such as Tamoxifen was demonstrated.

CONCLUSION

In-silico analysis has elucidated the binding mode and molecular level interactions which are expected to be of great help in further optimizing Withaferin A or design / discovery of future breast cancer inhibitors targeting estrogen receptor.

Design and Molecular dynamic Investigations of 7,8-Dihydroxyflavone Derivatives as Potential Neuroprotective Agents Against Alpha-synuclein

Parkinson's disease (PD) is the second most common neurodegenerative disorder caused due to loss of dopaminergic neurons in substantia nigra pars compacta, which occurs the presence of Lewy bodies made up of Alpha-synuclein (ASN) aggregation resulting in neuronal death. This study aims to identify potent 7,8-Dihydroxyflavone (DHF) derivatives to inhibit the ASN aggregation from in silico analysis. Molecular docking study reveals that carbamic ester derivatives of DHF [DHF-BAHPC (8q), DHF-BAHPEC (8s), DHF-BAHEC (8p), DHF-BDOPC (8c), DHF-BAPEC (8n) and DHF-BAMC (8h)] have good binding affinity towards ASN, when compared with DHF and L-DOPA; their docking score values are -16.3120, -16.1875, -15.2223, -14.3118, -14.2893, -14.2810, -14.0383, and -9.1560 kcal/mol respectively. The in silico pharmacological evaluation shows that these molecules exhibit the drug-likeness and ADMET properties. Molecular dynamics simulation confirms the stability of the molecules with ASN. The intermolecular interaction analyzed under the dynamic condition, allows to identify the candidate which potentially inhibits ASN aggregation. Hence, we propose that DHF derivatives are the potential lead drug molecules and preclinical studies are needed to confirm the promising therapeutic ability against PD.

Pyrrole derivatives as potential anti-cancer therapeutics: synthesis, mechanisms of action, safety

Pyrrole derivatives (PDs) chloro-1-(4-chlorobenzyl)-4-((3-(trifluoromethyl)phenyl)amino)-1H-pyrrole-2,5-dione (MI-1) and 5-amino-4-(1,3-benzothyazol-2-yn)-1-(3-methoxyphenyl)-1,2-dihydro-3H-pyrrole-3-one (D1) were synthesised as inhibitors of several protein kinases including EGFR and VEGFR. The aim of the study was to reveal the exact mechanisms of PDs' action EGFR and VEGFR are involved in. We observed, that both PDs could bind with EGFR and VEGFR and form stable complexes. PDs entered into electrostatic interactions with polar groups of phospholipid heads in cell membrane, and the power of interaction depended on the nature of PD radical substituents (greater for MI-1 and smaller for D1). Partial intercalation of MI-1 into the membrane hydrophobic zone also occurred. PDs concentrations induced apoptosis in malignant cells but normal ones had different sensitivity to those. MI-1 and D1 acted like antioxidants in inflamed colonic tissue, as evidenced by reduce of lipid and protein peroxidation products (by 43-67%) and increase of superoxide dismutase activity (by 40 and 58%) with restoring these values to control ones. MI-1 restored reduced haemoglobin and normalised elevated platelets and monocytes in settings of colorectal cancer, whereas D1 normalised only platelets. Thus, MI-1 and D1 could be used as competitive inhibitors of EGFR and VEGFR and antioxidants, which might contribute to realisation of their anti-inflammatory, proapoptotic and antitumor activity.

Cardiotonic steroids as potential Na+/K+-ATPase inhibitors - a computational study

Cardiotonic steroids (CTS) are steroidal drugs, processed from the seeds and dried leaves of the genus Digitalis as well as from the skin and parotid gland of amphibians. The most commonly known CTS are ouabain, digoxin, digoxigenin and bufalin. CTS can be used for safer medication of congestive heart failure and other related conditions due to promising pharmacological and medicinal properties. Ouabain isolated from plants is widely utilized in in vitro studies to specifically block the sodium potassium (Na⁺/K⁺-ATPase) pump. For checking, whether ouabain derivatives are robust inhibitors of Na⁺/K⁺-ATPase pump, molecular docking simulation was performed between ouabain and its derivatives using YASARA software. The docking energy falls within the range of 8.470 kcal/mol to 7.234 kcal/mol, in which digoxigenin was found to be the potential ligand with the best docking energy of 8.470 kcal/mol. Furthermore, pharmacophore modeling was applied to decipher the electronic features of CTS. Molecular dynamics simulation was also employed to determine the conformational properties of Na⁺/K⁺-ATPase-ouabain and Na⁺/K⁺-ATPase-digoxigenin complexes with the plausible structural integrity through conformational ensembles for 100 ns which promoted digoxigenin as the most promising CTS for treating conditions of congestive heart failure patients.

Virtual screening of National Cancer Institute database for claudin-4 inhibitors: Synthesis, biological evaluation, and molecular dynamics studies

Claudin-4 (CLDN4) is a vital member of tight-junction proteins that is often overexpressed in cancer and other malignancies. The three-dimensional structure of human CLDN4 was constructed based on homology modeling approach. A total of 265 242 molecules from the National Cancer Institute (NCI) database has been utilized as a dataset for this study. In the present work, structure-based virtual screening is performed with the NCI database using Glide. By molecular docking, 10 candidate molecules with high scoring functions, which binds to the active site of CLDN4 were identified. Subsequently, molecular dynamics simulations of membrane protein were used for optimization of the top-three lead compounds (NCI110039, NCI344682, and NCI661251) with CLDN4 in a dynamic system. The lead molecule from NCI database NCI11039 (purpurogallin carboxylic acid) was synthesized and cytotoxic properties were evaluated with A549, MCF7 cell lines. Our docking and dynamics simulations predicted that ARG31, ASN142, ASP146, and ARG158 as critically important residues involved in the CLDN4 activity. Finally, three lead candidates from the NCI database were identified as potent CLDN4 inhibitors. Cytotoxicity assays had proved that purpurogallin carboxylic acid had an inhibitory effect towards breast (MCF7) and lung (A549) cancer cell lines. Computational insights and in vitro (cytotoxicity) studies reported in this study are expected to be helpful for the development of novel anticancer agents.

Identification of potential drugs targeting L,L-diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach

Chlamydia trachomatis (C.t) is a gram-negative obligate intracellular bacteria, which is a major causative of infectious blindness and sexually transmitted diseases. A surge in multidrug resistance among chlamydial species has posed a challenge to adopt alternative drug targeting strategies. Recently, in C.t, L,L-diaminopimelate aminotransferase (CtDAP-AT) is proven to be a potential drug target due its essential role in cell survival and host nonspecificity. Hence, in this study, a multilevel precision-based virtual screening of CtDAP-AT was performed to identify potential inhibitors, wherein, an integrative stringent scoring and filtration were performed by coupling, glide docking score, binding free energy, ADMET (absorption, distribution, metabolism, and excretion, toxicity) prediction, density functional theory (quantum mechanics), and molecular dynamics simulation (molecular mechanics). On cumulative analysis, NSC_5485 (1,3-bis((7-chloro-4-quinolinyl)amino)-2-propanol) was found to be the most potential lead, as it showed higher order significance in terms of binding affinity, bonded interactions, favorable ADMET, chemical reactivity, and greater stabilization during complex formation. This is the first report on prioritization of small molecules from National Cancer Institute (NCI) and Maybridge data sets (341 519 compounds) towards targeting CtDAP-AT. Thus, the proposed compound shall aid in effective combating of a broad spectrum of C.t infections as it surpassed all the levels of prioritization.

Infectivity of Dengue Virus Serotypes 1 and 2 Is Correlated with E-Protein Intrinsic Dynamics but Not to Envelope Conformations

Dengue is a mosquito-borne virus with dire health and economic impacts. Dengue is responsible for an estimated 390 million infections per year, with dengue 2 (DENV2) being the most virulent strain among the four serotypes. Interestingly, it is also in strains of this serotype that temperature-dependent large-scale morphological changes, termed "breathing," have been observed. Although the structure of these morphologies has been solved to 3.5-Å resolution, the dynamics of the viral envelope are unknown. Here, we combine fluorescence and mass spectrometry with molecular dynamics simulations to provide insights into DENV2 (NGC strain) structural dynamics in comparison with DENV1 (PVP 159). We observe hitherto unseen conformational changes and structural dynamics of the DENV2 envelope that are influenced by both temperature and divalent cations. Our results show that for DENV2 and DENV1 the intrinsic dynamics, but not the specific morphologies, are correlated with viral infectivity.

Lead Optimization Studies Towards Finding NS2B/NS3 Protease Targetspecific Inhibitors as Potential Anti-dengue Drug-like Compounds

BACKGROUND

Dengue Fever is a major threatening global health issue caused by a mosquito-borne pathogen. Even though some anti-viral drugs are now available to reduce the disease severity. Still, there is a need of better drug compound to combat with dengue fever. The NS2B/NS3 protease is a major therapeutic drug target for Insilco drug discovery.

MATERIALS & METHODS

Previously, we have performed a pharmacophore features based virtual screening studies, which has led to the identification of ZINC92615064 compound as a potent NS2B/NS3 protease inhibitor and demonstrated its potential to act as anti-dengue drug-like compound using computational approaches. In this present study, the identified lead compound ZINC92615064 has been made to undergo scaffold hopping based novel library generation, and the resulted novel library of compounds has been virtually screened on to NS2B/NS3 protease towards identifying novel proprietary scaffold of compound which is acting as a potent inhibitor for the given drug target of NS2B/NS3.

RESULT & CONCLUSION

A total of 16,847 novel designed compounds library was generated using the scaffold hopping technology based on the structure of the lead compound ZINC92615064. Out of which, compound design no. 3718 has shown the best binding potential with a predicted IC50 value of 417.13 nM along with a permissible range of ADMET properties based on its descriptor values. This NS2B/NS3 protease in complex with compound 3718 was subjected to a rigorous molecular dynamic simulation study to further validate this complex thermodynamic stability, along with the aim to reveal the underlying molecular level interactions and potential mode of action.

Ameliorative effects of quercetin against bisphenol A-caused oxidative stress in human erythrocytes: an in vitro and in silico study

Bisphenol A (BPA) is an endocrine disruptor of xenobiotic type, mainly used for the production of polycarbonate plastic, epoxy resins and non-polymer additives. Because of its wide usages in the environment, the toxic effects of BPA have proved to be harmful to human health. However, its effects on human haemoglobin remain unclear. The affinity between BPA and haemoglobin, as well as erythrocytes, is an important factor in understanding the mechanism of the toxicity of BPA. Flavonoids are strong antioxidants that prevent oxidative stress and Quercetin is a flavonoid found in numerous vegetables and fruits. Therefore, the present investigation was undertaken to investigate whether Quercetin can be used to alleviate the toxic effects of BPA in vitro in human red blood cells (RBC). Venous blood samples were collected from healthy, well-nourished adult volunteers (25-30 years old) by phlebotomy. In a RBC suspension with a cell density of 2 × 104 cell per mL, the concentration of BPA (25-150 µg mL-1) was found to cause an increase in the lipid peroxidation (LPO) and a decrease in the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) in human RBC. However, the concurrent addition of BPA (150 µg mL-1) and quercetin (10-50 µg mL-1) lead to significant amelioration. In silico studies gave structural insight into BPA and quercetin to decipher the plausible binding mechanism and molecular level recognition.

Discovery of novel inhibitors of Mycobacterium tuberculosis MurG: homology modelling, structure based pharmacophore, molecular docking, and molecular dynamics simulations

MurG (Rv2153c) is a key player in the biosynthesis of the peptidoglycan layer in Mycobacterium tuberculosis (Mtb). This work is an attempt to highlight the structural and functional relationship of Mtb MurG, the three-dimensional (3D) structure of protein was constructed by homology modelling using Discovery Studio 3.5 software. The quality and consistency of generated model was assessed by PROCHECK, ProSA and ERRAT. Later, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with substrate Uridine-diphosphate-N-acetylglucosamine (UD1) facilitated us to employ structure-based virtual screening approach to obtain new hits from Asinex database using energy-optimized pharmacophore modelling (e-pharmacophore). The pharmacophore model was validated using enrichment calculations, and finally, validated model was employed for high-throughput virtual screening and molecular docking to identify novel Mtb MurG inhibitors. This study led to the identification of 10 potential compounds with good fitness, docking score, which make important interactions with the protein active site. The 25 ns MD simulations of three potential lead compounds with protein confirmed that the structure was stable and make several non-bonding interactions with amino acids, such as Leu290, Met310 and Asn167. Hence, we concluded that the identified compounds may act as new leads for the design of Mtb MurG inhibitors.

Characterization, molecular docking, dynamics simulation and metadynamics of kisspeptin receptor with kisspeptin

We report molecular characterization of the kisspeptin receptor (kiss1r), an essential gatekeeper for reproduction and onset of puberty in vertebrates. The full-length cDNA sequence of kiss1r is 1786bp which consist of 5' UTR (untranslated region) 261bp, 3' UTR of 424bp and open reading frame of 1101 encoding a putative protein of 366 amino acids. Basal tissue expression pattern of kiss1r mRNA revealed that it is mainly expressed in the brain and testis. We also report the structure of the kiss1r, along with plausible activation mechanism of this receptor by kisspeptin using computational modelling and dynamic simulation approach of multiple 100ns of timescale. A present modelling and simulations studies shed light on the molecular level of interaction, suggesting that direct hydrogen bonds between ASN4, SER5, GLY7, ARG9 and PHE10 of kisspeptin and TRP7, ASN8, GLU11, ILE17, ASN19 and TYR183 of kiss1r could be crucial role players in initial binding of receptor and the kisspeptin towards allosteric modulatory effects of kisspeptin on the receptor. To the best our knowledge, this is the first report on computational modelling and molecular dynamic simulations of kiss1r in animals shedding light on its possible mode of activation.

Insights from molecular modeling, docking and simulation of imidazole nucleus containing chalcones with EGFR kinase domain for improved binding function

EGFR Kinase domain is a crucial role player cell surface receptor protein activated by specific binding of its ligand like EGFR. Importance of this protein as a therapeutically important drug target towards treating various cancer types has been proven elsewhere in previous literature. In this present study, we have designed a novel series of five compounds and computationally evaluated their potential to act as inhibitors of EGFR kinase domain towards anti-cancer activity. Our docking study shows compounds have the potential to dock into the active site of the EGFR Kinase domain with a binding energy in a range of -5.46 to - 7.32 Kcal/mol, Among all the compounds, compound 2 was found to be the lead like molecule with the binding energy of -7.32 kcal/mol with predicted IC50 value of 4.33 micro molar level. Molecular dynamic simulation studies for this compound 2 in complex with EGFR kinase domain has revealed several interesting molecular interactions with some of the important residues present at the active binding site of EGFR Kinase domain. Conclusively, novel designed compound 2 of the present study have shown promising anti-cancer potential worth considering for further evaluations.

Pharmacophore feature-based virtual screening for finding potent GSK-3 inhibitors using molecular docking and dynamics simulations

Glycogen synthase kinase-3 (GSK-3) is a multitasking serine/threonine protein kinase, which is associated with the pathophysiology of several diseases such as diabetes, cancer, psychiatric and neurodegenerative diseases. Tideglusib is a potent, selective, and irreversible GSK-3 inhibitor that has been investigated in phase II clinical trials for the treatment of progressive supranuclear palsy and Alzheimer's disease. In the present study, we performed pharmacophore feature-based virtual screening for identifying potent targetspecific GSK-3 inhibitors. We found 64 compounds that show better GSK-3 binding potentials compared with those of Tideglusib. We further validated the obtained binding potentials by performing 20-ns molecular dynamics simulations for GSK-3 complexed with Tideglusib and with the best compound found via virtual screening in this study. Several interesting molecular-level interactions were identified, including a covalent interaction with Cys199 residue at the entrance of the GSK-3 active site. These findings are expected to play a crucial role in the binding of target-specific GSK-3 inhibitors.

In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions

Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported. Here, we have attempted an in silico elucidation of the uncrystallized dehydratase (DH) catalytic domain of human FASN. This theoretical model for DH domain was predicted using comparative modeling methods. Different stand-alone tools and servers were used to validate and check the reliability of the predicted models, which suggested it to be a highly plausible model. The stereochemical analysis showed 92.0% residues in favorable region of Ramachandran plot. The initial physiological substrate β-hydroxybutyryl group was docked into active site of DH domain using Glide. The molecular dynamics simulations carried out for 20 ns in apo and holo states indicated the stability and accuracy of the predicted structure in solvated condition. The predicted model provided useful biochemical insights into the substrate–active site binding mechanisms. This model was then used for identifying potential FASN inhibitors using high-throughput virtual screening of the National Cancer Institute database of chemical ligands. The inhibitory efficacy of the top hit ligands was validated by performing molecular dynamics simulation for 20 ns, where in the ligand NSC71039 exhibited good enzyme inhibition characteristics and exhibited dose-dependent anticancer cytotoxicity in retinoblastoma cancer cells in vitro.

A Comprehensive In Silico Analysis on the Structural and Functional Impact of SNPs in the Congenital Heart Defects Associated with NKX2-5 Gene-A Molecular Dynamic Simulation Approach

Congenital heart defects (CHD) presented as structural defects in the heart and blood vessels during birth contribute an important cause of childhood morbidity and mortality worldwide. Many Single nucletotide polymorphisms (SNPs) in different genes have been associated with various types of congenital heart defects. NKX 2–5 gene is one among them, which encodes a homeobox-containing transcription factor that plays a crucial role during the initial phases of heart formation and development. Mutations in this gene could cause different types of congenital heart defects, including Atrial septal defect (ASD), Atrial ventricular block (AVB), Tetralogy of fallot and ventricular septal defect. This highlights the importance of studying the impact of different SNPs found within this gene that might cause structural and functional modification of its encoded protein. In this study, we retrieved SNPs from the database (dbSNP), followed by identification of potentially deleterious Non-synonymous single nucleotide polymorphisms (nsSNPs) and prediction of their effect on proteins by computational screening using SIFT and Polyphen. Furthermore, we have carried out molecular dynamic simulation (MDS) in order to uncover the SNPs that would cause the most structural damage to the protein altering its biological function. The most important SNP that was found using our approach was rs137852685 R161P, which was predicted to cause the most damage to the structural features of the protein. Mapping nsSNPs in genes such as NKX 2–5 would provide valuable information about individuals carrying these polymorphisms, where such variations could be used as diagnostic markers.

Molecular docking based screening of G6PS with 1, 5 Benzothiazepine derivates for a potential inhibitor

Glucosamine-6-phosphate synthase (G6PS) (EC 2.6.1.16) is a known target for anti-bacterial and anti-fungal infections. Therefore, it is of interest to design potential inhibitors using 1, 5 benzo-thiazepine skeleton with appropriate modifications. We report the binding data for 20 derivatives of the skeleton molecule to G6PS having binding energy from -7.35 to -9.99 Kcal/mol with predicted IC50 value range of 4.11 to 47.68 nano-molar. It should be noted that this data should be further evaluated using in vitro and in vivo studies for safety, activity, efficacy and toxicity.

Molecular docking based screening of novel designed chalcone series of compounds for their anti-cancer activity targeting EGFR kinase domain

Epidermal growth factor receptors (EGFR) are critical for the growth of many tumors and expressed at high levels in about one third of epithelial cancers. Hence, blockade of the binding sites for EGFR has been hypothesized as an effective anti-cancer therapy. Chalcone derivative compounds have been shown to be highly effective anti-cancer agents, however there are still so many novel derivatives possible, one of which might get us the best targeted EGFR inhibitor. In this effort directed towards the discovery of novel, potent anti-tumor agents for the treatment of cancer, in the present study a library of novel chalcone series of compounds has been designed and evaluated for their anti-cancer activity targeting EGFR kinase domain using various computational approaches. Among the twenty five novel designed chalcone series of compounds, all of them have found to be successfully docking inside the active binding domain of EGFR receptor target with a binding energy in a range of -6.10 to -9.25 Kcal/mol with predicted IC50 value range of 33.50 micor molar to 164.66 nano molar respectively. On the other hand, calculated 2DQSAR molecular descriptor properties of the compounds showed promising ADME parameters and found to be well in compliance with Lipinski׳s rule of five. Among all the twenty five compounds tested, compound 21 ((2E)-3-(anthracen-9-yl)-1-phenylprop-2-2n-1- one) was found to be the best lead like molecule with a binding energy of -9.25 kcal/mol with predicted IC50 value of 164.66 nano molar. Conclusively, novel designed compound 21 of the present study have shown promising anti-cancer potential worth considering for further evaluations.

Potential Anticancer Properties and Mechanisms of Action of Withanolides

Plant-based Ayurvedic medicine has been practiced in India for thousands of years for the treatment of a variety of disorders. They are rich sources of bioactive compounds potentially useful for prevention and treatment of cancer. Withania somnifera (commonly known as Ashwagandha in Ayurvedic medicine) is a widely used medicinal plant whose anticancer value was recognized after isolation of steroidal compounds withanolides from the leaves of this shrub. Withaferin A is the first member of withanolides to be isolated, and it is the most abundant withanolide present in W. somnifera. Its cancer-protective role has now been established using chemically induced and oncogene-driven rodent cancer models. The present review summarizes the key preclinical studies demonstrating anticancer effects of withaferin along with its molecular targets and mechanisms related to its anticancer effects. Anticancer potential of other withanolides is also discussed.