Structure-based drug designing for N-methyl-D-aspartate receptor: Link between neurodegenerative disease and glioblastoma

Response regulator GacA and transcriptional activator RhlR proteins involved in biofilm formation of Pseudomonas aeruginosa are prospective targets for natural lead molecules: Computational modelling, molecular docking and dynamic simulation studies

A Long Shot? Could neurodegenerative disease be caused by a cyanobacterial toxin?

Background Triple-negative breast cancers are defined as tumors that lack the expression of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). It exhibits unique clinical and pathological features, is highly aggressive, and has a relatively poor prognosis and poor clinical outcome. Objective To identify a novel drug target protein against triple-negative breast cancer (TNBC) and potential phytochemical lead molecules against novel drug targets. Methods In this study, we retrieved TNBC samples from NGS and microarray datasets in the Gene Expression Omnibus database and employed a combination of differential gene expression studies, protein-protein interaction analysis, and network topology investigation to identify the target protein. Using molecular docking and molecular dynamics simulation studies, followed by Molecular Mechanics with Generalised Born Surface Area solvation, a potential lead molecule was identified. Result The androgen receptor (AR) was found to be the target protein, and 2-hydroxynaringenin was discovered to be a possible phytochemical lead molecule to combat TNBC. Upregulated genes with LogFC > 1.25 and P-value < 0.05 from the TNBC gene expression dataset were given to STRING tool to investigate the network topology, and androgen receptor (AR) was found to be an appropriate hub gene in the protein-protein interaction network. Phytochemicals that inhibit breast cancer were retrieved from the PubChem database and virtual screening was performed using PyRx against the AR protein. Based on Lipinski’s rule and ADMET properties, molecular interaction studies were analyzed using induced fit docking, wherein significant binding interactions were displayed by 2-hydroxynaringenin. Molecular dynamics studies and MM-GBSA of AR and the 2-hydroxynaringenin complex revealed strong and stable interactions. Conclusion AR was identified as a hub protein that is highly expressed in breast cancer and 2-hydroxynaringenin efficacy of counter TNBC needs to be investigated further in vitro and in vivo.

One of the significant therapeutic targets for Alzheimer’s disease (AD) is Glycogen Synthase Kinase-3β (GSK-3β). Inhibition of GSK-3β can prevent hyperphosphorylation of tau, and thus prevent formation and accumulation of neurofibrillary tangles and neuropil threads that block intracellular transport, trigger unfolded protein response, and increase oxidative stress, cumulatively leading to neurodegeneration. In this study, we have performed structure-based virtual screening of two small-molecule libraries from ChemDiv CNS databases using AutoDock Vina to identify hit molecules based on their binding affinities compared to that of an established GSK-3β inhibitor, indirubin-3’-monoxime (IMO). Pharmacoinformatic screening on SwissADME and pkCSM servers enabled identification of lead molecules with favorable pharmacoinformatic properties for drug likeliness, including blood brain barrier (BBB) permeability. Further, molecular dynamic simulations identified six candidate lead molecules that show stable complex formation with GSK-3β in dynamic state under physiological conditions. Principal component analysis of the dynamic state was used to plot Free Energy Landscapes (FELs) of GSK-3β-ligand complexes. STRIDE secondary structure analysis of the lowest energy conformations identified from FEL plots, and binding free energy calculations by Molecular Mechanics Poisson-Boltzmann Surface Area ((ΔGbind )MM-PBSA) of the simulation trajectories led to the identification of two ligands as potential lead molecules having favorable free energy landscape profiles as well as significantly lower (ΔGbind )MM-PBSA in dynamic state compared to that of reference inhibitor IMO. Hence, this study identifies two novel brain penetrant GSK-3β inhibitors that are likely to have therapeutic potential against Alzheimer’s disease.

Aberrant Protein S-Nitrosylation in Neurodegenerative Diseases

This study aimed to screen putative drug targets associated with biofilm formation of multidrug-resistant Acinetobacter baumannii and Pseudomonas areugenosa and prioritize carbon nano-fullerene as potential lead molecule by structure-based virtual screening. Based on the functional role, 36 and 83 genes that are involved in biofilm formation of A. baumannii and P. areugenosa respectively were selected and metabolic network was computationally constructed. The genes that lack three-dimensional structures were predicted and validated. Carbon nano-fullerene selected as lead molecule and their drug-likeliness and pharmacokinetics properties were computationally predicted. The binding potential of carbon nano-fullerene toward selected drug targets was modeled and compared with the binding of conventional drugs, doripenem, and polymyxin-B with their usual targets. The stabilities of four best-docked complexes were confirmed by molecular dynamic (MD) simulation. This study suggested that selected genes demonstrated relevant interactions in the constructed metabolic pathways. Carbon fullerene exhibited significant binding abilities to most of the prioritized targets in comparison with the binding of last-resort antibiotics and their usual target. The four best ligand–receptor interactions predicted by molecular docking revealed that stability throughout MD simulation. Notably, carbon fullerene exhibited profound binding with outer membrane protein (OmpA) and ribonuclease-HII (rnhB) of A. baumannii and 2-heptyl-4(1H)-quinolone synthase (pqsBC) and chemotaxis protein (wspA) of P. aeruginosa. Thus, the current study suggested that carbon fullerene was probably used as potential lead molecules toward selected targets of A. baumannii and P. aeruginosa and the applied aspects probably scaled up to design promising lead molecules toward these pathogens. Communicated by Ramaswamy H. Sarma.

Memory processes have been widely studied in recent decades. Unfortunately, although several intriguing hypotheses about the possibility of modulating cognition have been developed, no conclusive result has been obtained (69). Two different neurotransmission models are of major interest in understanding how the brain can acquire and store a single cognitive event (3,23). The main neuronal agents involved in transferring this kind of information seem to be acetylcholine and glutamic acid. These two neurotransmitters are present in all the cerebral areas involved in the memory processes and both are responsible for the stimulation currents linked to the propagation of neuronal signals (1,4). The cholinergic hypothesis of memory ( 3 ) is based on the observation that a marked degeneration of the cholinergic neuronal pathway is often associated with the development of cognitive disorders ( 12). Moreover, it has been reported that one distinctive feature of Alzheimer’s disease (AD) consists of a progressive loss of either cholinergic or adrenergic neurons’ ability to transmit stimuli received from the limbic areas to the cerebral cortex (10,12,21,75). To help preserve high levels of acetylcholine in the synaptic cleft, several antiacetylcholinesterase agents have been synthesized and tested on both biochemical and behavioral models of learning (32,46). Tacrine is certainly the most studied among these agents ( 13). Clinical trials with tacrine revealed some interesting pro-mnemic properties of this compound (42,68), but tacrine exhibits major hepatotoxicity that strongly restricts its use ( 13,73). Donepezil (E2020) is another interesting compound of this family. Two recently published clinical studies (25,63) demonstrate both the efficacy of donepezil in patients with mild-to-moderate Alzheimer’s disease and its relative liver safety. Other potent acetylcholinesterase inhibitors, such as metrifonate and SDZ ENA 7 13, are currently under clinical evaluation (28,62,65). The glutamatergic hypothesis of memory is based on a particular characteristic of the glutamatergic neuronal pathway: long-term potentiation (LTP). LTP was first defined by Bliss and Collingridge (8) as a synaptic memory model expressed as a persistent increase in the size of the synaptic component of the evoked response. The

Gonorrhea, one of the sexually transmitted disease caused by a gram negative diplococcus bacteria Neisseria gonorrhoeae. Rho protein is indispensable for bacterial viability due to its versatile functions in physiology apart from RNA dependent transcription termination. Based on conserved function and wider role in several cellular processes, inhibitors specifically targeting Rho proteins are largely in use these days to treat various bacterial infections. In this study, three dimensional structure of Rho protein was modeled using the template protein from E. coli and further the optimized model was simulated for 100 ns to understand the structural stability and compactness. Owing to the therapeutic potential of Rho, traditional structure-based virtual screening was applied to identify potential inhibitors for the selected target. Based on empirical glide scoring functions two potent lead molecules (ChemBridge_6121956 and ChemBridge_5232688) were selected from ChemBridge database. The pharmacokinetic properties of these lead molecules are within the permissible range. DFT descriptor revealed that the lead molecules are more reactive, which also supports the molecular docking studies. The stability of Rho and Rho-inhibitor complexes was studied using molecular dynamics simulation. Parameters include binding free energy calculation, RMSD, RMSF and hydrogen bond analysis depicts the stability of Rho and Rho-inhibitors throughout the simulation. Altogether, the identified lead molecules require further optimization towards the design and development of new antibiotics against N. gonorrhoeae. Communicated by Ramaswamy H. Sarma

Amyloid beta 42 oligomers induce neuronal and synaptic receptor dysfunctions.

Molecular docking simulations were conducted to analyze the interactions between eight lead molecules with AR and PSA proteins.The lead molecules included Enzalutamide, Abiraterone, Docetaxel, Apalutamide, Cabazitaxel, Bicalutamide, Curcumin, Galeterone, Resveratrol, and Darolutamide.For the Androgen Receptor (AR), Enzalutamide displayed the most favorable docking energy of -10.96Kcal/mol, followed by Galeterone (-10.52Kcal/mol) and Darolutamide .The binding affinities of these compounds to AR suggest potential inhibitors.On the other hand, resveratrol exhibited the strongest interaction with the AR protein (-8.02Kcal.mol)among the natural compounds studied (Resveratrol and Curcumin).In the case of Prostate Specific Antigen (PSA), Abiraterone showed a docking energy of -9.14 kcal/mol, indicating a potential interaction with PSA.The docking results suggest that Enzalutamide, Galeterone, and Darolutamide, hold promise as potential inhibitors for the Androgen Receptor in prostate cancer treatment.Abiraterone, Enzalutamide, Apalutamide ligands shown a significant interaction on Prostate Specific Antigen, hinting at its potential as a dual-target agent.

The prevalence of multi-drug resistance S. aureus is one of the most challenging tasks for the treatment of nosocomial infections. Proteins and enzymes of peptidoglycan biosynthesis pathway are one among the well-studied targets, but many of the enzymes are unexplored as targets. MurE is one such enzyme featured to be a promising target. As MurE plays an important role in ligating the L-lys to stem peptide at third position that is crucial for peptidoglycan synthesis. To screen the potential MurE inhibitor by in silico approach and evaluate the best potential lead molecule by in vitro methods. In the current study, we have employed structure based virtual screening targeting the active site of MurE, followed by Molecular dynamics and in vitro studies. Virtual screening resulted in successful screening of potential lead molecule ((2R)-2-[[1-[(2R)- 2-(benzyloxycarbonylamino) propanoyl] piperidine-4-carbonyl]amino]-5-guanidino-pentan). The molecular dynamics of the MurE and Lead molecule complex emphasizes that lead molecule has shown stable interactions with active site residues Asp 406 and with Glu 460. In vitro studies demonstrate that the lead molecule shows antibacterial activity close to standard antibiotic Vancomycin and higher than that of Ampicillin, Streptomycin and Rifampicin. The MIC of lead molecule at 50μg/mL was observed to be 3.75 μg/mL, MBC being bactericidal with value of 6.25 μg/mL, cytotoxicity showing 34.44% and IC50 of 40.06μg/mL. These results suggest ((2R)-2-[[1-[(2R)-2-(benzyloxycarbonylamino) propanoyl] piperidine-4-carbonyl]amino]-5-guanidino-pentan) as a promising lead molecule for developing a MurE inhibitor against treatment of S. aureus infections.

Triple-negative breast cancers (TNBC) are defined as tumors that lack the expression of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). It exhibits unique clinical and pathological features, demonstrates high aggressiveness, and has a relatively poor prognosis and clinical outcome. To identify a novel drug target protein against TNBC and potential phytochemical lead molecules against the identified target. In this study, we retrieved TNBC samples from NGS and microarray datasets in the Gene Expression Omnibus database. We employed a combination of differential gene expression studies, protein-protein interaction analysis, and network topology investigation to identify the target protein. Additionally, the molecular docking and molecular dynamics (MD) simulation studies followed by Molecular Mechanics with Generalised Born Surface Area salvation was used to identify potential lead molecule. The upregulated genes with LogFC > 1.25 and P-value < 0.05 from the TNBC gene expression dataset were identified. Androgen receptor (AR) was found to be an appropriate hub target in the protein-protein interaction network. Phytochemicals that inhibit breast cancer target were retrieved from the PubChem database and virtual screening was performed using PyRx against the AR protein. Thereby, the AR was found to be the target protein and 2-hydroxynaringenin was discovered to be a possible phytochemical lead molecule for combating TNBC. Moreover, the AR and the 2-hydroxynaringenin complex showed structural stability and higher binding affinity through molecular dynamics and MM-GBSA studies. AR was identified as a hub protein that is highly expressed in breast cancer and 2-hydroxynaringenin efficacy of counter TNBC requires further investigation both in vitro and in vivo.

Ligand-based pharmacophore filtering, atom based 3D-QSAR, virtual screening and ADME studies for the discovery of potential ck2 inhibitors

Disease-associated oligodendrocyte signatures in neurodegenerative disease: the known and unknown.

The excessive activation of N-methyl-D-aspartate (NMDA) receptors by glutamate results in neuronal excitotoxicity. cAMP is a key second messenger and contributes to NMDA receptor-dependent synaptic plasticity. Adenylyl cyclases 1 (AC1) and 8 (AC8) are the two major calcium-stimulated ACs in the central nervous system. Previous studies demonstrate AC1 and AC8 play important roles in synaptic plasticity, memory, and persistent pain. However, little is known about the possible roles of these two ACs in glutamate-induced neuronal excitotoxicity. Here, we report that genetic deletion of AC1 significantly attenuated neuronal death induced by glutamate in primary cultures of cortical neurons, whereas AC8 deletion did not produce a significant effect. AC1, but not AC8, contributes to intracellular cAMP production following NMDA receptor activation by glutamate in cultured cortical neurons. AC1 is involved in the dynamic modulation of cAMP-response element-binding protein activity in neuronal excitotoxicity. To explore the possible roles of AC1 in cell death in vivo, we studied neuronal excitotoxicity induced by an intracortical injection of NMDA. Cortical lesions induced by NMDA were significantly reduced in AC1 but not in AC8 knock-out mice. Our findings provide direct evidence that AC1 plays an important role in neuronal excitotoxicity and may serve as a therapeutic target for preventing excitotoxicity in stroke and neurodegenerative diseases.