Computational insights into the stereo-selectivity of catechins for the inhibition of the cancer therapeutic target EGFR kinase

The epidermal growth factor receptor (EGFR) plays a crucial role in regulating cellular growth and survival, and its dysregulation is implicated in various cancers, making it a prime target for cancer therapy. Natural compounds known as catechins have garnered attention as promising anticancer agents. These compounds exert their anticancer effects through diverse mechanisms, primarily by inhibiting receptor tyrosine kinases (RTKs), a protein family that includes the notable member EGFR. Catechins, characterized by two chiral centers and stereoisomerism, demonstrate variations in chemical and physical properties due to differences in the spatial orientation of atoms. Although previous studies have explored the membrane fluidity effects and transport across cellular membranes, the stereo-selectivity of catechins concerning EGFR kinase inhibition remains unexplored. In this study, we investigated the stereo-selectivity of catechins in inhibiting EGFR kinase, both in its wild-type and in the prevalent L858R mutant. Computational analyses indicated that all stereoisomers, including the extensively studied catechin (-)-EGCG, effectively bound within the ATP-binding site, potentially inhibiting EGFR kinase activity. Notably, gallated catechins emerged as superior EGFR inhibitors to their non-gallated counterparts, revealing intriguing binding trends. The top four stereoisomers exhibiting high dock scores and binding energies with wild-type EGFR comprise (-)-CG (-)-GCG (+)-CG, and (-)-EGCG. To assess dynamic behavior and stability, molecular dynamics simulations over 100 ns were conducted for the top-ranked catechin (-)-CG and the widely investigated catechin (-)-EGCG with EGFR kinase. This study enhances our understanding of how the stereoisomeric nature of a drug influences inhibitory potential, providing insights that could guide the selection of specific stereoisomers for improved efficacy inexisting drugs.

Analysis of some flavonoids for inhibitory mechanism against cancer target phosphatidylinositol 3-kinase (PI3K) using computational tool

Cancer has been one of the leading causes of mortality worldwide over the past few years. Some progress has been made in the development of more effective cancer therapeutics, resulting in improved survival rates. However, the desired outcome in the form of successful treatment is yet to be achieved. There is high demand for the development of innovative, inexpensive, and effective anticancer treatments using natural resources. Natural compounds have been increasingly discovered and used for cancer therapy owing to their high molecular diversity, novel biofunctionality, and minimal side effects. These compounds can be utilized as chemopreventive agents because they can efficiently inhibit cell growth, control cell cycle progression, and block several tumor-promoting signaling pathways. PI3K is an important upstream protein of the PI3K-Akt-mTOR pathway and a well-established cancer therapeutic target. This study aimed to explore the small molecules, natural flavonoids, viz. quercetin, luteolin, kaempferol, genistein, wogonin, daidzein, and flavopiridol for PI3Kγ kinase activity inhibition. In this study, the binding pose, interacting residues, molecular interactions, binding energies, and dissociation constants were investigated. Our results showed that these flavonoids bound well with PI3Kγ with adequate binding strength scores and binding energy ranging from (-8.19 to -8.97 Kcal/mol). Among the explored ligands, flavopiridol showed the highest binding energy of -8.97 Kcal/mol, dock score (-44.40), and dissociation constant term, p K d of 6.58 against PI3Kγ. Based on the above results, the stability of the most promising ligand, flavopiridol, against PI3Kγ was evaluated by molecular dynamics simulations for 200 ns, confirming the stable flavopiridol and PI3Kγ complex. Our study suggests that among the selected flavonoids specifically flavopiridol may act as potential inhibitors of PI3Kγ and could be a therapeutic alternative to inhibit the PI3Kγ pathway, providing new insights into rational drug discovery research for cancer therapy.

In depth molecular interaction analyses of the complex of a proposed CTXM-inhibitor bound to the bacterial enzyme

A 'Thumb Rule for Antibiotic Design' against bacteria can be given as, 'The minimum pace of drug design ought to match the swiftness with which bacteria display cutting-edge resistance mechanisms; thereby outwitting the antibiotics and, in turn, the researchers'. Occurrence of drug resistance attributable to CXTM-variants in bacterial pathogens is widespread. In line with our above proposed thumb rule, the present article employed concatenation of virtual screening, docking and simulation to identify a potent in silico validated anti-CTXM-14 ligand. Specifically, this research used the 'MCULE' drug discovery platform to screen a total of 5 million candidate inhibitors to evaluate their binding efficacy with an antibiotic resistance enzyme, CTXM-14 found in bacterial pathogens. A new median approach between 'structure' and 'ligand'-based protocols was employed. Pharmacokinetic profiling was achieved by 'SWISS ADME'. Safety profile for humans was appraised by 'Toxicity Checker'. The complex consisting of the 'Top ligand' (obtained from the screen) harbored within the active pocket of the bacterial CTXM-14 was subjected to 60 ns molecular dynamics simulation with the aid of licensed YASARA STRUCTURE v.21.8.27. Complex tasks were performed by YANACONDA. Fine resolution figures (notably, plots generated from trajectory analyses) were constructed. Simulation snaps were acquired at every 250 picoseconds of the run. The ligand having the IUPAC name as 1-Amino-3-(4-hydroxyphenyl)pyrido[1,2-a]benzimidazole-2,4-dicarbonitrile demonstrated the overall best binding with CTXM-14. Fifteen amino acid residues were found to line the interacting pocket. Remarkably, all of these interacting residues were found to be present among the interacting residues displayed by the reference complex as well, i.e. CTXM-14:Vaborbactam complex (PDB ID 6V7H). A total of 240 simulation snaps were retrieved. The RMSD plot revealed that a plateau was achieved at 32 ns, after which the backbone RMSD fluctuations remained confined within 1.4-2 Å. Video recording of molecular actions was also achieved. In conclusion, this study provides a fresh lead molecule, 1-Amino-3-(4-hydroxyphenyl)pyrido[1,2-a]benzimidazole-2,4-dicarbonitrile against bacterial CTXM-14 protein. The study utilized a new median approach between 'structure' and 'ligand'-based drug design. The lead molecule passed ADMET conditions and an array of medicinal chemistry filters, and is further supported by a stable molecular dynamics. An acceptable skin permeation supports its probable use in antibiotic creams. Moreover, the study provides a clear 'Thumb Rule for Antibiotic Design' against bacteria, which although often assumed, can be clearly stated for the first time. Synthesis of the screening-proposed molecule followed by in-vitro and in-vivo validation is highly recommended.Communicated by Ramaswamy H. Sarma.

Nano-Formulating Besifloxacin and Employing Quercetin as a Synergizer to Enhance the Potency of Besifloxacin against Pathogenic Bacterial Strains: A Nano-Synergistic Approach

The present study applied a nano-synergistic approach to enhance besifloxacin's potency via nano-formulating besifloxacin on gold nanoparticles (Besi-AuNPs) and adding quercetin as a natural synergistic compound. In fact, a one-pot AuNP synthesis approach was applied for the generation of Besi-AuNPs, where besifloxacin itself acted as a reducing and capping agent. Characterization of Besi-AuNPs was performed by spectrophotometry, DLS, FTIR, and electron microscopy techniques. Moreover, antibacterial assessment of pure besifloxacin, Besi-AuNPs, and their combinations with quercetin were performed on Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. UV-spectra showed a peak of AuNPs at 526 nm, and the electron microscopy-based size was estimated to be 15 ± 3 nm. The effective MIC₅₀ concentrations of besifloxacin after loading on AuNPs were reduced by approximately 50% against the tested bacterial strains. Interestingly, adding quercetin to Besi-AuNPs further enhanced their antibacterial potency, and isobologram analysis showed synergistic potential (combination index below 1) for different quercetin and Besi-AuNP combinations. However, Besi-AuNPs and quercetin combinations were most effective against Gram-positive S. aureus in comparison to Gram-negative P. aeruginosa and E. coli. Their potent activity against S. aureus has its own clinical significance, as it is one the main causative agents of ocular infection, and besifloxacin is primarily used for treating infectious eye diseases. Thus, the outcomes of the present study could be explored further to provide better medication for eye infections caused by resistant pathogens.

Molecular interaction of a putative inhibitor with bacterial SHV, an enzyme associated with antibiotic resistance

Tackling the ever-looming threat of antibiotic resistance remains a challenge for clinicians and microbiologists across the globe. Sulfhydryl variable (SHV) is a known bacterial enzyme associated with antibiotic resistance. The SHV enzyme has many variants. The present article describes identification and molecular interaction of a putative inhibitor with the bacterial SHV enzyme as a step towards novel antibacterial drug discovery. The MCULE-platform was used for screening a collection of 5 000 000 ligand molecules to evaluate their binding potential to the bacterial SHV-1 enzyme. Estimation of pharmacokinetic features was realized with the aid of the 'SWISS ADME' tool. Toxicity-checks were also performed. The docked complex of 'the top screened out ligand' and 'the bacterial SHV-1 protein' was subjected to molecular dynamics simulation of 101 ns. The obtained ligand molecule, 1,1'-(4H,8H-Bis[1,2,5]oxadiazolo[3,4-b:3',4'-e]pyrazine-4,8-diyl)diethanone, displayed the most favourable binding interactions with bacterial SHV-1. A total of 15 amino acid residues were found to hold the ligand in the binding site of SHV-1. Noticeably, 12 of the 15 residues were found as common to the binding residues of the reference (PDB ID: 4ZAM). The RMSD values plotted against the simulation time showed that nearby 11 ns, equilibrium was reached and, thenceforth, the 'SHV-1-Top ligand' complex remained typically stable. Starting from around 11 ns and straight to 101 ns, the backbone RMSD fluctuations were found to be confined inside a range of 1.0-1.6 Å. The ligand, 1,1'-(4H,8H-Bis[1,2,5]oxadiazolo[3,4-b:3',4'-e]pyrazine-4,8-diyl)diethanone, satisfied ADMET criteria. Furthermore, the practicability of the described 'SHV-1-Top ligand' complex was reinforced by a comprehensive molecular dynamics simulation of 101 ns. This ligand hence can be considered a promising lead for antibiotic design against SHV-1 producing resistant bacteria, and thus warrants wet laboratory evaluation.

Concatenation of molecular docking and molecular simulation of BACE-1, γ-secretase targeted ligands: in pursuit of Alzheimer's treatment

INTRODUCTION

Alzheimer's disease (AD), the most predominant cause of dementia, has evolved tremendously with an escalating frequency, mainly affecting the elderly population. An effective means of delaying, preventing, or treating AD is yet to be achieved. The failure rate of dementia drug trials has been relatively higher than in other disease-related clinical trials. Hence, multi-targeted therapeutic approaches are gaining attention in pharmacological developments.

AIMS

As an extension of our earlier reports, we have performed docking and molecular dynamic (MD) simulation studies for the same 13 potential ligands against beta-site APP cleaving enzyme 1 (BACE-1) and γ-secretase as a therapeutic target for AD. The In-silico screening of these ligands as potential inhibitors of BACE-1 and γ-secretase was performed using AutoDock enabled PyRx v-0.8. The protein-ligand interactions were analyzed in Discovery Studio 2020 (BIOVIA). The stability of the most promising ligand against BACE-1 and γ-secretase was evaluated by MD simulation using Desmond-2018 (Schrodinger, LLC, NY, USA).

RESULTS

The computational screening revealed that the docking energy values for each of the ligands against both the target enzymes were in the range of -7.0 to -10.1 kcal/mol. Among the 13 ligands, 8 (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed binding energies of ≤-8 kcal/mol against BACE-1 and γ-secretase. For the selected enzyme targets, BACE-1 and γ-secretase, 6Z5 displayed the lowest binding energy of -10.1 and -9.8 kcal/mol, respectively. The MD simulation study confirmed the stability of BACE-6Z5 and γ-secretase-6Z5 complexes and highlighted the formation of a stable complex between 6Z5 and target enzymes.

CONCLUSION

The virtual screening, molecular docking, and molecular dynamics simulation studies revealed the potential of these multi-enzyme targeted ligands. Among the studied ligands, 6Z5 seems to have the best binding potential and forms a stable complex with BACE-1 and γ-secretase. We recommend the synthesis of 6Z5 for future in-vitro and in-vivo studies.

Molecular interaction of inhibitors with human brain butyrylcholinesterase

Alzheimer's disease is a topic of deep research interest across the global scientific community. Butyrylcholinesterase (BuChE) is an important enzyme, and an interesting anti-Alzheimer's target. Identification or fresh design of promising BuChE-inhibitors is warranted. Virtual screening supported by molecular dynamics simulations has emerged as a key component of present drug-discovery cascades. The research piece aimed at identification of a putative BuChE-inhibitor as a fresh molecular frame that might aid drug design in the context of Alzheimer's disease. The study utilized 'MCULE' to screen a set of 5 million ligands to test their ability to bind to human BuChE. Pharmacokinetic profiling was achieved by the 'SWISS ADME' program. Toxicities were duly assessed. YASARA STRUCTURE version 20.10.4.W.64 was employed to run 133 ns molecular dynamics (MD) simulation for the complex of 'the top screened out inhibitor' and 'the human BuChE enzyme'. The simulation was executed for approx. 4 days (~93 hrs) on an HP ZR30w workstation. YANACONDA, a special language contained in YASARA STRUCTURE was employed to perform complex tasks. Fine resolution figures (notably the RMSD vs time plot) were created. Snapshots were extracted at every 250 ps. The selected ligand, (3-Bromophenyl)[5-(4-chlorophenyl)-5-hydroxy-3-(trifluoromethyl)-4,5-dihydro-1H-pyrazol-1-yl]methanone, exhibited the best overall binding with human BuChE. It interacted with human BuChE through 19 residues. Markedly, 9 of the 19 residues were confirmed to be matching to those of the reference complex (PDB ID 5DYW). Trajectory analysis returned 533 snapshots. The RMSD versus time plot indicated that around 22 ns, equilibrium was achieved and, from then on, the 'BuChE-Top inhibitor' complex remained predominantly stable. From 22 ns and onwards till 133 ns, the backbone RMSD fluctuations were observed to remain limited within a range of 1.2-1.9 Å. The molecule, (3-Bromophenyl)[5-(4-chlorophenyl)-5-hydroxy-3-(trifluoromethyl)-4,5-dihydro-1H-pyrazol-1-yl]methanone, satisfied ADMET requirements. Additionally, the feasibility of the proposed enzyme-inhibitor complex was supported by an adequately extended MD simulation of 133 ns. Hence, the proposed molecule could be a likely lead for designing inhibitor(s) against human BuChE. Scope remains for validatory wet laboratory investigation.

Can manipulation of gut microbiota really be transformed into an intervention strategy for cardiovascular disease management?

Recent advancement in manipulation techniques of gut microbiota either ex vivo or in situ has broadened its plausible applicability for treating various diseases including cardiovascular disease. Several reports suggested that altering gut microbiota composition is an effective way to deal with issues associated with managing cardiovascular diseases. However, actual translation of gut microbiota manipulation-based techniques into cardiovascular-therapeutic approach is still questionable. This review summarized the evidence on challenges, opportunities, recent development, and future prospects of gut microbiota manipulation for targeting cardiovascular diseases. Initially, issues associated with current cardiovascular diseases treatment strategy, association of gut microbiota with cardiovascular disease, and its influence on cardiovascular drugs were discussed, followed by applicability of gut microbiota manipulation as a cardiovascular disease intervention strategy along with its challenges and future prospects. Despite the fact that the gut microbiota is rugged, interventions like probiotics, prebiotics, synbiotics, fecal microbiota transplantation, fecal virome transplantation, antibiotics, diet changes, and exercises could manipulate it. Advanced techniques like administration of engineered bacteriophages and bacteria could also be employed. Intensive exploration revealed that if sufficiently controlled approach and proper monitoring were applied, gut microbiota could provide a compelling answer for cardiovascular therapy.

Genotyping of interleukins-18 promoters and their correlation with coronary artery stenosis in Saudi population

BACKGROUND

Complex coronary atherosclerotic lesions often lead to coronary occlusion, clinically represented as a single-vessel disease (SVD) and multivessel disease (MVD). These occlusions could hinder the blood flow in coronary arteries that affects appropriate management of the CVD. The current study intended to genotype interleukin (IL)-18 promoter's hotspots (rs187238, rs1946518, and rs1946519) and their possible association with coronary artery stenosis.

MATERIAL AND METHODS

The IL-18 promoter genotyping was performed by the Sanger method along with the examination of biochemical parameters in 125 study subjects categorized into three groups, viz. controls, SVD and MVD.

RESULTS

The current study observed a significant association of diabetes, hypertension, and dyslipidemia between the studied group's viz. healthy controls, SVD, and MVD. Fasting blood sugar and glycosylated hemoglobin (HBA1C) were also significantly enhanced from 4.82 vs. 8.01 and 4.33 vs. 8.27, in SVD, and MVD respectively. Despite the visible differences in the pattern of genotypic and allelic expressions, the current study did not show any statistically significant correlation with IL-18 promoter polymorphism at its hotspots with controls, SVD, and MVD subjects. The only exception of the above results was the distribution of allelic frequency at the rs1946519 hotspot, where a significant change (P < 0.05) was observed.

CONCLUSION

This study is of additional value to our previous reports, revealing the pattern of genotypes and allelic frequency of IL-18 promoters in a small cohort of Saudi ethnicity. Further investigations on larger sample size are recommended to envisage the presence of functional mutations in the IL-18 gene that could establish or rule out the possible association of IL-18 polymorphism with SVD and MVD.

High Throughput Virtual Screening and Molecular Dynamics Simulation for Identifying a Putative Inhibitor of Bacterial CTX-M-15

Background: Multidrug resistant bacteria are a major therapeutic challenge. CTX-M-type enzymes are an important group of class A extended-spectrum β-lactamases (ESBLs). ESBLs are the enzymes that arm bacterial pathogens with drug resistance to an array of antibiotics, notably the advanced-generation cephalosporins. The current need for an effective CTX-M-inhibitor is high. Objective: The aim of the current study was to identify a promising anti-CTX-M-15 ligand whose chemical skeleton could be used as a ‘seed-molecule’ for future drug design against resistant bacteria. Methods: Virtual screening of 5,000,000 test molecules was performed by ‘MCULE Drug Discovery Platform’. ‘ADME analyses’ was performed by ‘SWISS ADME’. TOXICITY CHECKER of MCULE was employed to predict the safety profile of the test molecules. The complex of the ‘Top inhibitor’ with the ‘bacterial CTX-M-15 enzyme’ was subjected to 102.25 ns molecular dynamics simulation. This simulation was run for 3 days on a HP ZR30w workstation. Trajectory analyses were performed by employing the macro ‘md_analyze.mcr’ of YASARA STRUCTURE version 20.12.24.W.64 using AMBER14 force field. YANACONDA macro language was used for complex tasks. Figures, including RMSD and RMSF plots, were generated. Snapshots were acquired after every 250 ps. Finally, two short videos of ‘41 s’ and ‘1 min and 22 s’ duration were recorded. Results: 5-Amino-1-(2H-[1,2,4]triazino[5,6-b]indol-3-yl)-1H-pyrazole-4-carbonitrile, denoted by the MCULE-1352214421-0-56, displayed the most efficient binding with bacterial CTX-M-15 enzyme. This screened molecule significantly interacted with CTX-M-15 via 13 amino acid residues. Notably, nine amino acid residues were found common to avibactam binding (the reference ligand). Trajectory analysis yielded 410 snapshots. The RMSD plot revealed that around 26 ns, equilibrium was achieved and, thereafter, the complex remained reasonably stable. After a duration of 26 ns and onwards until 102.25 ns, the backbone RMSD fluctuations were found to be confined within a range of 0.8–1.4 Å. Conclusion: 5-Amino-1-(2H-[1,2,4]triazino[5,6-b]indol-3-yl)-1H-pyrazole-4-carbonitrile could emerge as a promising seed molecule for CTX-M-15-inhibitor design. It satisfied ADMET features and displayed encouraging ‘simulation results’. Advanced plots obtained by trajectory analyses predicted the stability of the proposed protein-ligand complex. ‘Hands on’ wet laboratory validation is warranted.

Identification of a putative anti-rheumatoid arthritis molecule by virtual screening

Purpose: To propose an improved chemical skeleton whose scaffolds could be used for the design of future thymidylate synthase (TS)-inhibitors against rheumatoid arthritis. Methods: The drug discovery platform, ‘MCULE’, was employed for inhibitor-screening. The ‘methotrexate-interaction site’ in the crystal (PDB ID 5X66) was used as a target. One ‘RO5 violation’ was permitted. A maximum of ‘10 rotatable bonds’ and ‘100 diverse molecules’ were also allowed in the protocol. The ‘threshold similarity cut off’ was 0.7. The input values describing the remaining parameters were kept as ‘default’. The ‘Open Babel Linear Fingerprint’ was used for the analyses of molecular descriptors, followed by ADME-check. Results: 4-(4-Methyl-1-piperazinyl)-2-phenyl[1]benzofuro[3,2-d]pyrimidine corresponding to the MCULE ID-7590816301-0-93 exhibited the overall best binding with TS. The free energy of binding was -8.6 kcal/mol. A total of 17 amino acid residues were significant for the binding interactions. Importantly, 9 residues were common to methotrexate binding. It satisfied pertinent ADME conditions. Conclusion: 4-(4-Methyl-1-piperazinyl)-2-phenyl[1]benzofuro[3,2-d]pyrimidinemay emerge as a potent seed molecule for TS-inhibitor design in the context of rheumatoid arthritis. It has satisfied pertinent ADME features. However, there is need for further wet laboratory validation. Keywords: Anti-rheumatoid arthritis, Inhibitor design, Methotrexate, Seed molecule, Thymidylate synthase, Virtual screening

Molecular interaction of anti-cancer ligands with human brain acetylcholinesterase

There are a significant number of cases whereby cancer patients belonging to the old age group additionally suffer from cognition decline (a hallmark feature of Alzheimer's disease). Hence, it is understandable that it would be a boon if certain drug molecules could provide health benefits to a patient suffering from cancer as well as Alzheimer's disease. The objective of the work was to identify anticancer molecule(s) whose chemical-skeleton could be used as 'seed' for future design of dual-acting drugs against Alzheimer's disease and cancer. The study employed criterion-based search, docking, SWISS-ADME-profiling, ▵ASA-calculations, molecular-overlay and 'MoMA'-simulation to query possible binding of selected anticancer molecules with human brain acetylcholinesterase (AChE). Molecular interactions of all of the top ranking ligands were analyzed. 'BOILED-egg' model was employed to query brain-penetration of the ligands. A detailed molecular-simulation-analysis was performed. Snapshots of different stages of dynamic molecular interactions (selected from 254 pdb files) were captured by MoMA LigPath, a robotics inspired simulation algorithm. The study concluded that chemical skeletons of 'Niraparib' and 'Ponatinib' might be used as 'seed(s)' for design of such drugs. If successfully materialized in future, this approach could decrease the total number of daily pills that an old patient needs to take. Furthermore, novel anticancer drugs could be synthesized that do not inhibit AChE (e.g. by removal/modification of moieties that are crucial to binding of anticancer drug to AChE) even if those happen to be 'Blood Brain Barrier'-permeable. Alternatively, fresh AChE-inhibitors could be designed based on the scaffolds of the aforementioned anticancer drugs.Communicated by Ramaswamy H. Sarma.

In silico screening of glycogen synthase kinase-3β targeted ligands against acetylcholinesterase and its probable relevance to Alzheimer's disease

Alzheimer's disease (AD) is a growing global health concern that affects 10% of the population aged above 65 years. A growing body of evidence indicates that multi-targeted drugs might be useful therapeutic options owing to the heterogeneity of AD pathology. The current study exploited advanced computational biology tools to identify ligands that might display effective binding to two protein targets in the context of AD. The present study used in silico virtual screening of small molecules library to identify effectiveness against two AD targets viz. acetyl cholinesterase (AChE) and glycogen synthase kinase-3β (GSK-3β). PyRX-Python prescription with AutodockVina was used to generate binding energy profiles. Further screening was accomplished using SwissADME and molecular interaction studies. The present study obtained 48 ligands (absolute binding energy >8 kcal/mol), by virtual screening of 100 ligands. Among those, 13 ligands (BRW, 6VK, 6Z5, SMH, X37, 55E, 65 A, IQ6, 6VL, 6VM, F1B, 6Z2 and GVP) were selected based on blood brain barrier (BBB) permeability, acceptable ADME properties as well as their molecular interaction profiles with the aforementioned AD-targets. The present study has predicted certain molecules that appear worthy to be tested for effectiveness against two AD targets, namely AChE and GSK-3β. However, the results warrant further wet laboratory validation, as computational studies are merely predictive in nature. This approach might be useful for future treatment of AD.Communicated by Ramaswamy H. Sarma.

Molecular interaction of 4-amino-N’-(benzoyloxy)-N-(2,4- dimethylphenyl)-1,2,5-oxadiazole-3-carboximidamide with the methotrexate binding site of human DHFR, and its implication in rheumatoid arthritis

Purpose: To identify an improved lead molecule for the human dihydrofolate reductase (DHFR) inhibition that ‘sits’ in the same binding cavity as methotrexate by high throughput computationalscreening.Methods: The 3-D structure of the DHFR binding site was examined using ‘CASTp3.0’. Structure based in silico screening of about 5 million drug candidates housed in the MCULE database was performed. The obtained molecule-hits were ranked in accordance with their VINA scores, made to pass through drug-likeness filters, ΔG cut-off criterion, toxicity-checker and finally ‘zero RO5 criterion’.Results: The ‘top molecule’, namely, 4-amino-N'-(benzoyloxy)-N-(2,4-dimethylphenyl)-1,2,5-oxadiazole- 3-carboximidamide, displayed robust binding with human DHFR through 21 amino acid residues (ΔG = - 9.6 kcal/mol) while 10 of these residues were the same as those displayed by ‘methotrexate binding interactions’. It passed through relevant drug screening filters including the ‘Toxicity Checker’.Conclusion: This research work describes the molecular interaction of human DHFR with an improved lead molecule named, 4-amino- N’-(benzoyloxy)-N-(2,4-dimethylphenyl)-1,2,5-oxadiazole-3- carboximidamide, with a ΔG of -9.6 kcal/mol, thus satisfying adequate ADME features for further in vitro and in vivo validation in the context of rheumatoid arthritis. Keywords: Dihydrofolate reductase, In silico screening, Methotrexate, Rheumatoid arthritis, DHFR

Association of Plasma Fibrinogen Level with Insulin Resistance in Angiographically Confirmed Coronary Artery Disease Patients

Fibrinogen is an important coagulation factor that plays a key role in thrombus formation. The co-existence of CAD, insulin resistance (IR) and coagulation incongruity are believed to exacerbate the existing condition towards more lethal pathological events.The purpose of current study was to find out a possible association between fibrinogen and IR in CAD patients. The study population consist of 135 participants; 82 angiographically confirmed CAD patients who visited the outpatient department at King Abdulaziz University Hospital (KAUH), Jeddah and 53 healthy control individuals. Peripheral blood samples were collected from CAD patients and healthy control individuals. Various biochemical parameters such as complete blood count, C-reactive protein (CRP), glycosylated hemoglobin (HbA1c), insulin, C-peptide, lipid profile, platelet, partial thromboplastin time (PTT), fibrinogen and D-dimer levels were measured by the use of different analytical methods. Calculation of homeostasis model assessment (HOMA) and non-HDL were done by using online tools. Among the studied parameters, majority of the conventional risk factors were found to be significantly increased in CAD patients compared with control individuals. Different coagulation components such as fibrinogen (223.8 vs. 394 mg/dL), D-dimer (0.25 vs. 0.63 mg/L), platelet (222.9 vs. 245.9 K/uL) and PTT (27.6 vs. 29.6 seconds) were also found to be significantly enhanced in CAD patients. Based on the severity of IR [HOMA index up to 3 and ≥ 3], comparison with different parameters such as fibrinogen, D-dimer, C-peptide and insulin in CAD groups were also made. As per HOMA index, fibrinogen level was found to be significantly increased in below and above 3 categories. Moreover, C-peptide (P < 0.01) and insulin (P < 0.001) levels also showed significant association with both HOMA groups. Our study provides an insight towards the association of fibrinogen and IR in CAD patients with respect to severity.

Molecular interaction of investigational ligands with human brain acetylcholinesterase

Alzheimer's disease, a neurodegenerative disorder continues to be an area of investigation by the international researchers' fraternity. Despite all the ongoing efforts, the effective set of promising cholinesterase inhibitors available in the market for patients' use is limited. Furthermore, the currently available drugs could provide only a palliative type of treatment instead of providing a complete cure or foolproof prevention. Hence, design/discovery of fresh drug molecules as acetylcholinesterase (AChE) inhibitors still remains an urgent requirement. The drug discovery platform, MCULE in the "structure-based virtual screening" (SBVS) mode was used for high throughput ligand screening of over five million structures targeted against the AChE catalytic site. A stepwise query was made for the SBVS input. The number of hits was narrowed down in consecutive succession via varied filtration criteria as AutoDock-Vina rankings, MCULE toxicity filtration, exclusion of ligands having less than four H-bond acceptors, filtration by ΔG cutoff, rule-of-five violation and SWISS ADME profiling. This was followed by holistic analysis of all the results, thereby leading to one promising ligand. The screened out drug molecule, MCULE-5872671137-0-1 exhibited a robust interaction with the AChE catalytic site involving 20 amino acid residues, an acceptable binding free energy of -10.2 kcal/mol in addition to a favorable SWISS ADME-profie showing no harmful effects on the human body. It can be carefully stated that the molecule, MCULE-5872671137-0-1, which is chemically (3S)-N-{4-[(4-chlorophenyl)sulfanyl]phenyl}-3-hydroxypyrrolidine-1-carboxamide could function as a significant "seed" ligand for future design of potent AChE inhibitors and/or novel neuro drugs built upon the seed-scaffold.

Molecular and enzoinformatics perspectives of targeting Polo-like kinase 1 in cancer therapy

Cancer is a disease that has been the focus of scientific research and discovery and continues to remain so. Polo-like kinases (PLKs) are basically serine/threonine kinase enzymes that control cell cycle from yeast to humans. PLK-1 stands for 'Polo-like kinase-1'. It is the most investigated protein among PLKs. It is crucial for intracellular processes, hence a 'hot' anticancer drug-target. Accelerating innovations in Enzoinformatics and associated molecular visualization tools have made it possible to literally perform a 'molecular level walk' traversing through and observing the minutest contours of the active site of relevant enzymes. PLK-1 as a protein consists of a kinase domain at the protein N-terminal and a Polo Box Domain (PBD) at the C-terminal connected by a short inter-domain linking region. PBD has two Polo-Boxes. PBD of PLK-1 gives the impression of "a small clamp sandwiched between two clips", where the two Polo Boxes are the 'clips' and the 'phosphopeptide' is the small 'clamp'. Broadly, two major sites of PLK-1 can be potential targets: one is the adenosine-5'-triphosphate (ATP)-binding site in the kinase domain and the other is PBD (more preferred due to specificity). Targeting PLK-1 RNA and the interaction of PLK-1 with a key binding partner can also be approached. However, the list of potent small molecule inhibitors targeting the PBD site of PLK-1 is still not long enough and needs due input from the scientific community. Recently, eminent scientists have proposed targeting the 'Y'-shaped pocket of PLK-1-PBD and encouraged design of ligands that should be able to concurrently bind to two or more modules of the 'Y' pocket. Hence, it is suggested that during molecular interaction analyses, particular focus should be kept on the moiety in each ligand/drug candidate which directly interacts with the amino acid residue(s) that belong(s) to one of the three binding modules which together create this Y-shaped cavity. This obviously includes (but it is not limited to) the 'shallow cleft'-forming residues i.e. Trp414, H538 and K540, as significance of these binding residues has been consistently highlighted by many studies. The present article attempts to give a concise yet critically updated overview of targeting PLK-1 for cancer therapy.

Association of autoimmunity and cancer: An emphasis on proteolytic enzymes

Cancer and autoimmune diseases are the two devastating conditions that together constitute a leading health problem worldwide. The rising burden of these disorders in the developing world demands a multifaceted approach to address the challenges it poses. Understanding the root causes and specific molecular mechanisms by which the progression of the diseases takes place is need of the hour. A strong inflammatory background and common developmental pathways, such as activation of immune cells, proliferation, increased cell survival and migration which are controlled by growth factors and inflammatory cytokines have been considered as the critical culprits in the progression and complications of these disorders. Enzymes are the potential immune modulators which regulate various inflammatory events and can break the circulating immune complexes via macrophages production. In the current manuscript, we have uncovered the possible role of proteolytic enzymes in the pathogenesis and progression of cancer and autoimmune diseases. In the light of the available scientific literature, we advocate in-depth comprehensive studies which will shed light towards the role of proteolytic enzymes in the modulation of inflammatory responses in cancer and autoimmune diseases together.

Therapeutic Targeting of Amyloid Precursor Protein and its Processing Enzymes for Breast Cancer Treatment

Breast cancer cases in women are increasing at an alarming rate globally and extensive research is being conducted to identify a breakthrough medicine against this dreadful disease. In fact, researchers are looking for fresh targets to develop novel treatment strategies for cancer of the breasts. In this article, 'amyloid precursor protein' or (APP) and its processing enzymes are deeply studied so as to explore the same as prospective targets for breast cancer treatment. Even though most of the studies on APP and its processing enzymes have been performed on neuronal cells owing to their linkage with Alzheimer's disease, they are omnipresent on various non-neuronal cells also. Interestingly, APP and its processing enzymes have a role in the proliferation of cancer cells as well as in their growth, adherence and movement. Over-synthesis of APP and its processing enzymes are emerging as important hallmark features in breast cancer. It has been found that APP and its processing enzymes, i.e., γ-secretase and α- secretase are strongly linked with breast cancer via Akt phosporylation and Notch signaling pathways. Thus, targeting APP or γ-secretase or α-secretase could be considered as an effective strategy to treat breast cancer and even metastasis. There are various clinical trials which are in progress to explore the potential of γ-secretase inhibitor against breast cancer. Hence, the present review is composed of two sections, one section deals with all the possible linkages of APP and APP processing enzymes (α- secretase, β-secretase and γ-secretase) with breast cancer. However, the other section provides recent information on breast cancer treatment strategy using APP and APP processing enzymes as targets. We strongly believe that compilation of these studies would be beneficial to the scientist working in the field of 'breast cancer-treatment'.

Hepato-protective effect of Allium sativum against immobilization stress in rats

The purpose of the current study was to examine immobilization stress-induced antioxidant defense changes and estimation of the antioxidant potential of pre and post stress treatment of aqueous garlic extract in rat's liver. For this purpose, male Albino Wistar rats were treated with aqueous garlic extract both pre and after 6 h of immobilization stress. Pro-oxidant status of rat liver was evaluated by determining the levels of reduced glutathione (GSH), thiobarbituric acid reactive substances (TBARS), aspartate aminotransferase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), glucose, uric acid and the activities of super oxide dismutase (SOD), catalase (CAT) and glutathione-S-transferase (GST). In response to 6 h of immobilization stress a significant rise in the level of above mentioned liver enzymes were recorded. However, SOD, CAT and GST enzymatic activities showed a sharp decline. The extract treatment before and after stress, almost reverted the activities of studied biochemical parameters towards their control values. Current study highlighted the antioxidant potential of garlic extracts. Based on our study, we recommend the use of garlic extract as nutritional supplement for combating oxidative stress induced damage.

Interfering PLD1-PED/PEA15 interaction using self-inhibitory peptides: An in silico study to discover novel therapeutic candidates against type 2 diabetes

Diabetes type 2 (T2D) is a very complex disorder with a large number of cases reported worldwide. There are several reported molecular targets which are being used towards drug design. In spite of extensive research efforts, there is no sure shot treatment available. One of the major reasons for this failure or restricted success in T2D research is the identification of a major/breakthrough therapeutic target responsible for the progression of T2D. It has been well documented that one of the major causes mediating the insulin resistance is the interaction of PLD1 with PED/PEA15. Herein, we have performed in silico experiments to investigate the interaction between PLD1 with PED/PEA15. Furthermore, this study has explored pertinent molecular interactions involving the self-derived peptides. The peptides identified in this study are found to be capable of restricting the interaction of these two proteins. Accordingly, the study suggests that the “self-derived peptides” could be used as promising therapeutic candidate(s) against T2D.

Putative Anti-Cancer Drug Candidate Targeting the 'PLK-1-Polo-Box Domain' by High Throughput Virtual Screening: A Computational Drug Design Study

Cancer continues to remain a disease of scientific concern. Significant interest in targeting the Polo-Box-Domain (PBD) of Polo-like-kinase-1 (PLK-1) by novel ligands has arisen. The 'cleft' constituted by amino acid residues W414, H538, and K540 is the traditional target of PLK-1-PBD-inhibitors. However, this 'cleft' is merely a small part of the larger 'Y'-shaped cavity present therein. The objective of this study was to discover inhibitors of the PLK-1-PBD precisely directed against its trimodular 'Y'-pocket. High-throughput structure-based virtual screening (SBVS) of more than 5 million ligands against the aforementioned PLK-1 'Y'-pocket was performed. The SBVS hits were successively subjected to pass through various filters: VINA score ranking, toxicity checker, 'Special Criteria'-filtration, holistic tri-modular 'Y'-pocket interaction check, drug-likeness filters, and medicinal chemistry filters. Accordingly, we arrived at a single top ligand, 'SHAZ-i.' The top ligand, 3-{2-[(2-Methyl-2-propanyl)sulfonyl]phenyl}-5-phenyl-1,2-oxazole-4-carboxamide, displayed a robust interaction with the target crevice through 15 amino acid residues, an acceptable ΔG value of -7.8 kcal/mol, and a favorable pharmacokinetic profile with no adverse effects on humans. Hence, 3-{2-[(2-Methyl-2-propanyl)sulfonyl]phenyl}-5-phenyl-1,2-oxazole-4-carboxamide could emerge as a potent PLK-1-PBD inhibitor or might act as a 'seed' molecule for design of future inhibitors with a closely related backbone structure.

Mutagenic, antioxidant and wound healing properties of Aloe vera

ETHNOPHARMACOLOGICAL RELEVANCE

Aloe vera is a widely used medicinal plant for its various biological activities. This study evaluate possible mutagenic and healing effects of the aqueous extract of A. vera (AEAV) in mice and its oxidant/antioxidant potential in different proficient and deficient Saccharomyces cerevisiae strains.

MATERIAL AND METHODS

The AEAV was topically treated on the wounded skin surface of male albino mice at doses of 10 and 50 mg/kg for seven successive days. The control group was similarly treated with 0.9% NaCl solution. For oxidative/anti-oxidative evaluation, both proficient and deficient strains of S. cerevisiae [cytoplasmic and mitochondrial superoxide dismutase mutant (SOD: Sod1Δ and Sod2Δ), cytoplasmic catalase mutant (CAT: Cat1Δ)], two double defective mutants of Sod1 and Sod2 and Sod1 and Cat1 genes along with a wild-type strains were used.

RESULTS

The healing property of AEAV was observed at the dose of 50 mg/kg but at the same dose it showed mutagenic and cytotoxic effects in peripheral blood. AEAV did not produce the oxidizing effect, except in the mutated CAT strain at highest concentration (50 mg/kg).

CONCLUSION

The high concentration of AEAV showed mutagenicity and cytotoxicity. Beside, the healing capacity is believed to be due to its anti-oxidative defense mechanism.

ADNCD: a compendious database on anti-diabetic natural compounds focusing on mechanism of action

Diabetes is a deteriorating metabolic ailment which negatively affects different organs; however, its prime target is insulin secreting pancreatic β-cells. Although, different medications have been affirmed for diabetes management and numerous drugs are undergoing clinical trials, no significant breakthrough has yet been achieved. Available drugs either show some side effects or provide only short-term alleviation. The rationales behind the failure of current anti-diabetic treatment strategy are association of complex patho-physiologies and participation of various organs. Consequently, there is a critical need to search for multi-effect drugs that might impede various patho-physiological mechanisms related to diabetes. Fortunately, one natural compound could act on several diabetes linked targets. Thus, natural compounds might be regarded as a viable alternative choice to improve the progression as well as side effects of diabetes. Despite the fact that immense literatures are available on natural compounds indicating promising outcomes against diabetes, more systematic studies are still needed to establish them as effective anti-diabetic agents. Till date, we are unable to access all the information regarding modes of action, toxicity risks and physicochemical properties of anti-diabetic natural compounds on one platform. Hence, anti-diabetic natural compounds database (ADNCD) has been created to categorize each anti-diabetic natural compound on the basis of their mode of action and to provide compendious information of their physicochemical properties and toxicity risks. In short, ADNCD has imperative information for the researchers working in the field of diabetes drug development.

Inhibition of Butyrylcholinesterase with Fluorobenzylcymserine, An Experimental Alzheimer's Drug Candidate: Validation of Enzoinformatics Results by Classical and Innovative Enzyme Kinetic Analyses

BACKGROUND

Selective butyrylcholinesterase (BuChE)-inhibition, increases acetylcholine (ACh) levels. In rodents, this inhibition is known to boost cognition. Also, this occurs without the typical unwanted adverse effects of acetylcholinesterase-inhibitors or AChE-Is. The novel compound, fluorobenzylcymserine (FBC), is derived from our effort to design a selective BuChE-inhibitor. Also, we wanted to check whether butyrylcholinesterase-inhibitors (BuChE-Is) possessed an edge over AChE-Is in Alzheimer's disease (AD) in terms of efficacy and/or tolerance.

METHOD

FBC was synthesized as reported earlier while enzymatic activity of BuChE was calculated by Ellman-technique. Molecular docking was performed using Autodock4.2. We applied classical as well as innovative analyses of enzyme-kinetics for exploring "FBC:human BuChE-interaction". The mode of inhibition and kinetic parameters were also determined.

RESULTS

Docking results displayed two strong interacting sites for FBC. One of these binding sites was previously identified as a deep narrow groove having polar aromatic residues while a second site was identified during this study which displayed better interaction and was lined with aliphatic and sulphur containing residues. At low concentrations of BuChE, the IC50 was found to be very low i.e. 4.79 and 6.10 nM for 12 and 36 µg, respectively, whereas it increased exponentially by increasing the units of BuChE.

CONCLUSION

These analyses indicate that FBC is an interesting AD drug candidate that could provide a potent and partial mixed type of inhibition of human BuChE.

Molecular Interaction of Anti-Diabetic Drugs With Acetylcholinesterase and Sodium Glucose Co-Transporter 2

Type 2 Diabetes Mellitus (T2DM) and Alzheimer's disease (AD) are the two disorders which are known to share pertinent pathological and therapeutic links. Sodium glucose co-transporter-2 (SGLT2) and Acetylcholinesterase (AChE) are established inhibition targets for T2DM and AD treatments, respectively. Reports suggest that anti-diabetic drugs could be used for AD treatment also. The present study used molecular docking by Autodock4.2 using our "Click-By-Click"-protocol, Ligplot1.4.3 and "change in accessible surface area (ΔASA)-calculations" to investigate the binding of two investigational anti-diabetic drugs, Ertugliflozin and Sotagliflozin to an established target (SGLT2) and a research target (human brain AChE). Sotagliflozin appeared more promising for SGLT2 as well as AChE-inhibition with reference to ΔG and Ki values in comparison to Ertugliflozin. The ΔG and Ki values for "Sotagliflozin:AChE-binding" were -7.16 kcal/mol and 5.6 μM, respectively while the same were found to be -8.47 kcal/mol and 0.62 μM, respectively for its interaction with SGLT2. Furthermore, "Sotagliflozin:SGLT2-interaction" was subjected to (un)binding simulation analyses by "Molecular-Motion-Algorithms." This information is significant as the exact binding mode, interacting amino acid residues and simulation results for the said interaction have not been described yet. Also no X-ray crystal is available for the same. Finally, the results described herein indicate that Sotagliflozin could have an edge over Ertugliflozin for treatment of Type 2 diabetes. Future design of drugs based on Sotagliflozin scaffolds for treatment of Type 2 and/or Type 3 diabetes are highly recommended. As these drugs are still in late phases of clinical trials, the results described herein appear timely. J. Cell. Biochem. 118: 3855-3865, 2017. © 2017 Wiley Periodicals, Inc.

Linkage of Stress with Neuromuscular Disorders

Aging is associated with a progressive loss of muscle strength and mass, and a decline in neurophysiologic functions, which are characteristic features of neuromuscular disorders (NMDs). Understanding aging induced neuromuscular junction (NMJ) dysfunction is very crucial to understand the mechanism underlying NMDs. Morphological and physiological changes result in remodelling of the motor unit and a decline in the number of motor neuron muscle fibres. These alterations lead to excitation-contraction uncoupling and a loss of communication between the neuromuscular system, causing a decline in skeletal muscle strength and muscle mass. Understanding the molecular basis of NMJ dysfunction is essential in search for new treatment options. Besides structural and molecular studies, search for animal models to establish connection between brain and muscle is needed. Among various factors it has been observed that stress is one of the leading causes of NMDs. In the present review, we aim to explore various factors linking stress and NMDs neuromuscular disorders which gets aggravated by aging, with a special emphasis on mitochondrial connection. This in turn will help us gain new insights in the treatment of NMDs by aiding in improved symptoms, increased mobility and prolonged life.

Effect of an SNP in SCAP gene on lipid-lowering response to rosuvastatin in Indian patients with metabolic syndrome

AIM

Statins treat dyslipidemia associated with metabolic syndrome. Genetic factors contribute to variable response. Sterol regulatory element-binding factors cleavage-activating protein (SCAP) pathway regulates lipid homeostasis, so effect of SNP in SCAP gene on rosuvastatin response was studied.

MATERIALS & METHODS

Metabolic syndrome patients with low-density lipoprotein-cholesterol ≥130 mg/dl, were prescribed rosuvastatin 5 mg for 3 months. Lipids were measured initially and finally, and genotyping done.

RESULTS & CONCLUSION

Sixty-three patients completed the study. Twenty-three were homozygous for AA while 40 were heterozygous. Significant association was found between post-treatment lipid values and SCAP genotypes but not with baseline values. Cholesterol (p = 0.002) and low-density lipoprotein-cholesterol (p = 0.008) were significantly reduced in patients carrying G allele as compared with AA. There was a significant effect of G allele on cholesterol reduction (p = 0.043). Out of total responders (achieving >23.58% total cholesterol reduction), 80.5% were 2386G carriers (GG+GA) and only 19.5% were homozygous for A allele (p = 0.0048). SCAP 2386A>G gene polymorphism is a significant predictor of hypolipidemic response.

Prediction of Anti-Diabetic Drugs as Dual Inhibitors Against Acetylcholinesterase and Beta-Secretase: A Neuroinformatics Study

An increasing number of research evidences indicate linkage between type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD); the two most common diseases of aging. In addition, T2DM and AD also share some common pathophysiological features. Therefore, dual therapy that targets both the diseases can be regarded as a beneficial approach. Acetylcholinesterase (AChE) and beta-secretase (BACE) have been considered as potential therapeutic targets for AD. Accordingly, the piece of work presented here describes the binding of anti-diabetic drugs (Jardiance, Suiny and Nesina) with AChE and BACE so as to further investigate connecting bridges concerning the treatment of these two diseases. We have used "Autodock 4.2" for docking experiments. Both, hydrogen bond and hydrophobic interactions were found to be involved in the proper positioning of these diabetic drugs within the catalytic site (CAS) of AChE and BACE enzymes to permit docking. Free energy of binding (ΔG) for 'Jardiance-AChE', 'uiny-AChE' and 'Nesina-AChE' CAS interactions were found to be -9.21, -7.32 and -10.66 kcal/mol, respectively; while for 'Jardiance-BACE', 'Suiny -BACE' and 'Nesina-BACE' CAS interactions the same were determined to be -8.91, -8.58 and -10.40 kcal/mol, respectively. Hence, these diabetic drugs might act as potent dual inhibitors for the treatment of diabetes-associated neurological disorders. Consequently, the results described herein may form the basis of future dual therapy against the same.

A Synopsis of Nano-Technological Approaches Toward Anti-Epilepsy Therapy: Present and Future Research Implications

Epilepsy is a non-communicable central nervous system disorder that affects over 60 million people worldwide. The developments in epilepsy treatment face major hurdles due to drug resistance and disease recurrence after reduction in medication. Nano-technological anti-epileptic drug (AED) delivery systems have recently garnered attention due to their ability to cross the blood brain barrier, improved selectivity and potential for sustained drug delivery to the brain. This review focuses on several nano-based AED delivery systems, including liposomes, nano-emulsions, polymeric nanoparticles, solid-lipid nanoparticles and magnetic nanoparticles. Their limitations and future prospects in terms of AED delivery to the brain are also highlighted. It is hoped that the present communication will be helpful in the identification of potential AED delivery systems based on their advantages and disadvantages.

Kinetics and Molecular Docking Study of an Anti-diabetic Drug Glimepiride as Acetylcholinesterase Inhibitor: Implication for Alzheimer's Disease-Diabetes Dual Therapy

At the present time, treatment of two most common degenerative disorders of elderly population i.e., Type 2 Diabetes Mellitus (T2DM) and Alzheimer's disease (AD) is a major concern worldwide. As there are several evidences that proved strong linkages between these two disorders, the idea of using dual therapeutic agent for both the diseases might be considered as a good initiative. Earlier reports have revealed that oral anti-diabetic drugs such as peroxisome proliferator activated receptor γ (PPARγ) agonists (thiazolidinediones) when used in T2DM patients suffering from AD showed improved memory and cognition. However, the underlying mechanism still needs to be deciphered. Therefore, the present study was carried out to find whether glimepiride, an oral antidiabetic drug which is a PPARγ agonist could inhibit the activity of acetylcholine esterase (AChE) enzyme. Actually, AChE inhibitors seize the breakdown of acetylcholine which forms the main therapeutic strategy for AD. Here, glimepiride showed dose dependent inhibitory activity against AChE enzyme with IC50 value of 235 μM. Kinetic analysis showed competitive inhibition, which was verified by in silico docking studies. Glimepiride was found to interact with AChE enzyme at the same locus as that of substrate acetylcholine iodide (AChI). Interestingly, amino acid residues, Q71, Y72, V73, D74, W86, N87, Y124, S125, W286, F295, F297, Y337, F338 and Y341 of AChE were found to be common for 'glimepiride-AChE interaction' as well as 'AChI-AChE interaction'. Thus the present computational and kinetics study concludes that glimepiride and other thiazolidinediones derivatives could form the basis of future dual therapy against diabetes associated neurological disorders.

Forxiga (dapagliflozin): Plausible role in the treatment of diabetes-associated neurological disorders

Numerous clinical and epidemiological studies have provided direct evidence to strengthen the link between type 2 diabetes (T2D) and Alzheimer's disease (AD). The possibility that T2D patients might be at increased risk in developing AD has serious societal implications. Sodium glucose co-transporter 2 (SGLT2) is one of the best targets in the treatment of diabetes, whereas acetylcholinesterase (AChE) has long been regarded as a therapeutic target for AD. This study explores the molecular interactions between AChE and SGLT2 with a new US Food and Drug Administration approved antidiabetic drug Forxiga (dapagliflozin) to explore a possible link between the treatments of AD and diabetes. Docking study was performed using "Autodock4.2." Hydrophobic and cation-π interactions play an important role in the correct positioning of dapagliflozin within the catalytic site (CAS) of SGLT2 and AChE enzymes to permit docking. Free energy of binding (ΔG) of "dapagliflozin-SGLT2" and "dapagliflozin-CAS domain of AChE" interactions was found to be -6.25 and -6.28 kcal/mol, respectively. Hence, dapagliflozin might act as a potent dual inhibitor of SGLT2 and AChE. The results described herein may form the basis of future dual therapy against diabetes-associated neurological disorders.

Integrating Qualitative and Quantitative Tools for the Detection and Identification of Lectins in Major Human Diseases

Lectins are the (glyco)proteins that recognize and bind to specific sugar moieties without altering their structure. Galectins are mammalian lectins characterized by the presence of conserved 134 amino acids carbohydrate recognition domain and specificity for β-galactosides. The involvement of lectins in diverse biological spectrum, especially some deadly human diseases like cancer, neurological disorders and cardiovascular disorders has proclaimed them as one of the important components of glycobiology, thereby seeking the methods of their detection and identification heavily desirable. In the present manuscript, we have provided a comprehensive outline of various methods of detection and identification of lectins employed till date, with their needs and usage varying according to the level of infrastructure of laboratories and around the world. In addition, a vision for some quick, highly sensitive and advanced methods for lectin detection and identification for diagnostic and therapeutic of various diseases is also provided.

Protein misfolding and aggregation in Alzheimer's disease and type 2 diabetes mellitus

In general, proteins can only execute their various biological functions when they are appropriately folded. Their amino acid sequence encodes the relevant information required for correct three-dimensional folding, with or without the assistance of chaperones. The challenge associated with understanding protein folding is currently one of the most important aspects of the biological sciences. Misfolded protein intermediates form large polymers of unwanted aggregates and are involved in the pathogenesis of many human diseases, including Alzheimer's disease (AD) and Type 2 diabetes mellitus (T2DM). AD is one of the most prevalent neurological disorders and has worldwide impact; whereas T2DM is considered a metabolic disease that detrementally influences numerous organs, afflicts some 8% of the adult population, and shares many risk factors with AD. Research data indicates that there is a widespread conformational change in the proteins involved in AD and T2DM that form β-sheet like motifs. Although conformation of these β-sheets is common to many functional proteins, the transition from α-helix to β-sheet is a typical characteristic of amyloid deposits. Any abnormality in this transition results in protein aggregation and generation of insoluble fibrils. The abnormal and toxic proteins can interact with other native proteins and consequently catalyze their transition into the toxic state. Both AD and T2DM are prevalent in the aged population. AD is characterized by the accumulation of amyloid-β (Aβ) in brain, while T2DM is characterized by the deposition of islet amyloid polypeptide (IAPP, also known as amylin) within beta-cells of the pancreas. T2DM increases pathological angiogenesis and immature vascularisation. This also leads to chronic cerebral hypoperfusion, which results in dysfunction and degeneration of neuroglial cells. With an abundance of common mechanisms underpinning both disorders, a significant question that can be posed is whether T2DM leads to AD in aged individuals and the associations between other protein misfolding diseases.

Fetzima (levomilnacipran), a drug for major depressive disorder as a dual inhibitor for human serotonin transporters and beta-site amyloid precursor protein cleaving enzyme-1

Pharmacological management of Major Depressive Disorder includes the use of serotonin reuptake inhibitors which targets serotonin transporters (SERT) to increase the synaptic concentrations of serotonin. Beta-site amyloid precursor protein cleaving enzyme-1 (BACE-1) is responsible for amyloid β plaque formation. Hence it is an interesting target for Alzheimer's disease (AD) therapy. This study describes molecular interactions of a new Food and Drug Administration approved antidepressant drug named 'Fetzima' with BACE-1 and SERT. Fetzima is chemically known as levomilnacipran. The study has explored a possible link between the treatment of Depression and AD. 'Autodock 4.2' was used for docking study. The free energy of binding (ΔG) values for 'levomilnacipran-SERT' interaction and 'levomilnacipran-BACE1' interaction were found to be -7.47 and -8.25 kcal/mol, respectively. Levomilnacipran was found to interact with S438, known to be the most important amino acid residue of serotonin binding site of SERT during 'levomilnacipran-SERT' interaction. In the case of 'levomilnacipran-BACE1' interaction, levomilnacipran interacted with two very crucial aspartic acid residues of BACE-1, namely, D32 and D228. These residues are accountable for the cleavage of amyloid precursor protein and the subsequent formation of amyloid β plaques in AD brain. Hence, Fetzima (levomilnacipran) might act as a potent dual inhibitor of SERT and BACE-1 and expected to form the basis of a future dual therapy against depression and AD. It is an established fact that development of AD is associated with Major Depressive Disorder. Therefore, the design of new BACE-1 inhibitors based on antidepressant drug scaffolds would be particularly beneficial.

Role of anti-diabetic drugs as therapeutic agents in Alzheimer's disease

Recent data have suggested a strong possible link between Type 2 Diabetes Mellitus and Alzheimer's disease (AD), although exact mechanisms linking the two are still a matter of research and debate. Interestingly, both are diseases with high incidence and prevalence in later years of life. The link appears so strong that some scientists use Alzheimer's and Type 3 Diabetes interchangeably. In depth study of recent data suggests that the anti diabetic drugs not only have possible role in treatment of Alzheimer's but may also arrest the declining cognitive functions associated with it. The present review gives an insight into the possible links, existing therapeutics and clinical trials of anti diabetic drugs in patients suffering from AD primarily or as co-morbidity. It may be concluded that the possible beneficial effects and usefulness of the current anti diabetic drugs in AD cannot be neglected and further research is required to achieve positive results. Currently, several drug trials are in progress to give conclusive evidence based data.

Crystal structure and interaction of phycocyanin with β-secretase: A putative therapy for Alzheimer's disease

Alzheimer's disease (AD) represents a neurological disorder, which is caused by enzymatic degradation of an amyloid precursor protein into short peptide fragments that undergo association to form insoluble plaques. Preliminary studies suggest that cyanobacterial extracts, especially the light-harvesting protein phycocyanin, may provide a means to control the progression of the disease. However, the molecular mechanism of disease control remains elusive. In the present study, intact hexameric phycocyanin was isolated and crystallized from the cyanobacterium Leptolyngbya sp. N62DM, and the structure was solved to a resolution of 2.6 A. Molecular docking studies show that the phycocyanin αβ-dimer interacts with the enzyme β-secretase, which catalyzes the proteolysis of the amyloid precursor protein to form plaques. The molecular docking studies suggest that the interaction between phycocyanin and β-secretase is energetically more favorable than previously reported inhibitor-β-secretase interactions. Transgenic Caenorhabditis elegans worms, with a genotype to serve as an AD-model, were significantly protected by phycocyanin. Therefore, the present study provides a novel structure-based molecular mechanism of phycocyanin-mediated therapy against AD.

A neuroinformatics study to compare inhibition efficiency of three natural ligands (Fawcettimine, Cernuine and Lycodine) against human brain acetylcholinesterase

Enzyme-inhibition is considered as a potent therapeutic approach to the treatment of diseases associated with acetylcholinesterase (AChE). The present study elucidates molecular interactions of human brain AChE, with three natural ligands Lycodine, Cernuine and Fawcettimine for comparison. Docking between these ligands and enzyme was performed using 'Autodock 4.2'. It was determined that polar and hydrophobic interactions play an important role in the correct positioning of Lycodine, Cernuine and Fawcettimine within the 'catalytic site' of AChE to permit docking. This approach would be helpful to understand the selectivity of the given drug molecule in the treatment of neurological disorder. Moreover, the present study confirms that Lycodine is a more efficient inhibitor of human brain AChE compared to Cernuine and Fawcettimine with reference to ΔG and Ki values.

Prediction of comparative inhibition efficiency for a novel natural ligand, galangin against human brain acetylcholinesterase, butyrylcholinesterase and 5-lipoxygenase: a neuroinformatics study

The present study elucidates molecular interactions of human acetylcholinesterase (AChE), butyrylcholinesterase (BuChE) and 5-lipoxygenase (5-LPO) with a novel natural ligand Galangin (GAL); and also with the well-known ligands Bisnorcymserine (BNC) and Cymserine for comparison. Docking between these ligands and enzymes were performed using 'Autodock4.2'. It was found that hydrophobic interactions play an important role in the correct positioning of BNC within the 'catalytic site' of AChE, BuChE and 5-LPO to permit docking while hydrogen bonds are significant in case of cymserine for the same. However, only polar interactions are significant in the correct positioning of GAL within the 'catalytic site' of AChE, BuChE and 5-LPO to permit docking. Such information may aid in the design of versatile AChE, BuChE and 5 LPO-inhibitors, and is expected to aid in safe clinical use of above ligands. Scope still remains in the determination of the three-dimensional structure of AChE-GAL, BuChE-GAL and 5-LPO-GAL complex by X-ray crystallography to certify the described data. Moreover, the present study confirms that GAL is a more efficient inhibitor of human brain AChE compared to BNC and cymserine, while in case of 5-LPO and human brain BuChE, BNC is a more efficient inhibitor compared to GAL and cymserine with reference to ΔG and Ki values.