Structural insights into the potential binding sites of Cathepsin D using molecular modelling techniques

Alzheimer's disease (AD) is the most prevalent type of dementia caused by the accumulation of amyloid beta (Aβ) peptides. The extracellular deposition of Aβ peptides in human AD brain causes neuronal death. Therefore, it has been found that Aβ peptide degradation is a possible therapeutic target for AD. CathD has been known to breakdown amyloid beta peptides. However, the structural role of CathD is not yet clear. Hence, for the purpose of gaining a deeper comprehension of the structure of CathD, the present computational investigation was performed using virtual screening technique to predict CathD's active site residues and substrate binding mode. Ligand-based virtual screening was implemented on small molecules from ZINC database against crystal structure of CathD. Further, molecular docking was utilised to investigate the binding mechanism of CathD with substrates and virtually screened inhibitors. Localised compounds obtained through screening performed by PyRx and AutoDock 4.2 with CathD receptor and the compounds having highest binding affinities were picked as; ZINC00601317, ZINC04214975 and ZINCC12500925 as our top choices. The hydrophobic residues Viz. Gly35, Val31, Thr34, Gly128, Ile124 and Ala13 help stabilising the CathD-ligand complexes, which in turn emphasises substrate and inhibitor selectivity. Further, MM-GBSA approach has been used to calculate binding free energy between CathD and selected compounds. Therefore, it would be beneficial to understand the active site pocket of CathD with the assistance of these discoveries. Thus, the present study would be helpful to identify active site pocket of CathD, which could be beneficial to develop novel therapeutic strategies for the AD.

Lipopolysaccharide induced neuroprotective effects of bacterial protease against Alzheimer's disease in male Wistar albino rats

Alzheimer's disease (AD) is a highly severe neurodegenerative condition that affects the hippocampus and is characterized by memory loss and dementia. This investigation aims to determine the potential of a bacterial protease enzyme produced by a new mutant strain of bacteria (Bacillus cereus S6-3/UM90) to influence the rat behavioural, biochemical, histological, and immuno-histochemical functions induced by lipopolysaccharides (LPS) experimentally. The administration of LPS exhibited a decline in memory performance via Morris' Water Maze test along with an elevation of IL-6, IL-17, amino acid neurotransmitters, Adenosine monophosphate (AMP), and 8-OHdG, whereas a decrease in ATP (Adenosine Triphosphate), monoamine transmitters, AChE (acetylcholinesterase) and PC (phosphatidylcholine). Additionally, there was a notable increase in GFAP (glial fibrillary acidic protein) and p-Tau protein immuno-expression levels along with obvious histological lesions in the hippocampal CA3 region. Moreover, the administration of protease or Donepezil restored the measured parameters to nearly normal levels and improved the histological architecture of the hippocampus and ameliorated memory impairments. In conclusion, the study provides evidence that the treatment with Bacterial protease can improve the memory and learning impairments of LPS-induced AD and may be used as a promising therapeutic agent to manage AD since it has anti-inflammatory and antioxidant effects.

Structural significance of Neprylysin from Streptococcus suis GZ1 in the degradation of Aβ peptides, a causative agent in Alzheimer's disease

Alzheimer's disease (AD) is a progressive brain disorder. The accumulation of amyloid beta (Aβ) peptides in the human brain leads to AD. The cleavage of Aβ peptides by several enzymes is being considered as an essential aspect in the treatment of AD. Neprilysin (NEP) is an important enzyme that clears the Aβ plaques in the human brain. The human NEP activity has been found reduced due to mutations in NEP and the presence of inhibitors. However, the role of NEP in the degradation of Aβ peptides in detail at the molecular level is not yet clear. Hence, in the present study, we have investigated the structural significance of NEP from the bacterial source Streptococcus suis GZ1 using various bioinformatics approaches. The homology modelling technique was used to predict the three-dimensional structure of NEP. Further, molecular dynamic (MD) simulated model of NEP was docked with Aβ peptide. Analysis of MD simulated docked complex showed that the wild-type NEP-Aβ-peptide complex is more stable as compared to mutant complex. Hydrogen bonding interactions between NEP with Zn²⁺and Aβ peptide confirm the degradation of the Aβ peptide. The molecular docking and MD simulation results revealed that the active site residue Glu-538 of bacterial NEP along with Zn²⁺ interact with His-13 of Aβ peptide. This stable interaction confirms the involvement of NEP with Glu-538 in the degradation of the Aβ peptide. The other residues such as Glu203, Ser537, Gly140, Val587, and Val536 could also play an important role in the cleavage of Aβ peptide in between Asp1-Ala2, Arg5-His6, Val18-Phe19, Gly9-Tyr10, and Arg5-His6. Hence, the predicted model of the NEP enzyme of Streptococcus suis GZ1could be useful to understand the Aβ peptide degradation in detail at the molecular level. The information obtained from this study would be helpful in designing new lead molecules for the effective treatment of AD.

Destabilization of Alzheimer's Aβ42 protofibrils with acyclovir, carmustine, curcumin, and tetracycline: insights from molecular dynamics simulations

Among the neurodegenerative diseases, one of the most common dementia is Alzheimer's disease (AD).

In silico and in vivo anti-malarial investigation on 1-(heteroaryl)-2-((5-nitroheteroaryl)methylene) hydrazine derivatives

Background

Resistance of Plasmodium falciparum against common anti-malarial drugs emphasizes the need of alternative and more effective drugs. Synthetic derivatives of 1-(heteroaryl)-2-((5-nitroheteroaryl)methylene) hydrazine have showed in vitro anti-plasmodial activities. The present study aimed to evaluate the molecular binding and anti-plasmodial activity of synthetic compounds in vivo.

Methods

The molecular docking was used to study the binding of compounds to haem and Plasmodium falciparum lactate dehydrogenase (PfLDH). Acute toxicity of the synthetic compounds was evaluated based on the modified up & down method. The anti-plasmodial activity of the compounds was conducted by the two standard tests of Peters’ and of Rane, using chloroquine-sensitive Plasmodium berghei in mice. Also, the toxicity to the internal organs of mice was evaluated on the seventh day after the treatment in addition to the histopathology of their liver. Compound 3 that showed high activity in the lowest dose was selected for further pharmacodynamic studies.

Results

According to the docking studies, the active site of PfLDH had at least four common residues, including Ala98, Ile54, Gly29, and Tyr97 to bind the compounds with the affinity, ranging from − 8.0 to − 8.4 kcal/mol. The binding mode of ligands to haem revealed an effective binding affinity, ranging from − 5.1 to − 5.5 kcal/mol. Compound 2 showed the highest  % suppression of parasitaemia (99.09%) at the dose of 125 mg/kg/day in Peters’ test. Compound 3, with 79.42% suppression, was the best in Rane’s test at the lowest dose (31 mg/kg/day). Compound 3 was confirmed by the pharmacodynamic study to have faster initial parasite elimination in the lowest concentration. The histopathology of the livers of mice did not reveal any focal necrosis of hepatocytes in the studied compounds.

Conclusions

The docking studies verified Pf LDH inhibition and the inhibitory effect on the haemozoin formation for the studied compounds. Accordingly, some compounds may provide new avenues for the development of anti-malarial drugs without liver toxicity, although further studies are required to optimize their anti-plasmodial activity.

Amyloid beta peptide-degrading microbial enzymes and its implication in drug design

Alzheimer's disease (AD) is a chronic and progressive neurological brain disorder. AD pathophysiology is mainly represented by formation of neuritic plaques and neurofibrillary tangles (NFTs). Neuritic plaques are made up of amyloid beta (Aβ) peptides, which play a central role in AD pathogenesis. In AD brain, Aβ peptide accumulates due to overproduction, insufficient clearance and defective proteolytic degradation. The degradation and cleavage mechanism of Aβ peptides by several human enzymes have been discussed previously. In the mean time, numerous experimental and bioinformatics reports indicated the significance of microbial enzymes having potential to degrade Aβ peptides. Thus, there is a need to shift the focus toward the substrate specificity and structure-function relationship of Aβ peptide-degrading microbial enzymes. Hence, in this review, we discussed in vitro and in silico studies of microbial enzymes viz. cysteine protease and zinc metallopeptidases having ability to degrade Aβ peptides. In silico study showed that cysteine protease can cleave Aβ peptide between Lys16-Cys17; similarly, several other enzymes also showed capability to degrade Aβ peptide at different sites. Thus, this review paves the way to explore the role of microbial enzymes in Aβ peptide degradation and to design new lead compounds for AD treatment.

Effects of tosyl-l-arginine methyl ester (TAME) on the APC/c subunits: An in silico investigation for inhibiting cell cycle

The anaphase-promoting complex/cyclosome (APC/c) is requisite for controlling mitosis, which is activated by Cdh1 and Cdc20 activators. Dysregulation of APC/c is observed in many cancers and is known as a targeted drug particularly in cancer drug resistance. It was shown that tosyl-l-arginine methyl ester (TAME), via mimicking isoleucine-arginine (IR) tail of co-activators, inhibits APC/c functions. However, structure details and interaction of TAME with APC/c are poorly defined. In the current study, a well-established set of computational methods was used to identify the best binding pocket in order to inhibit APC activity. Therefore, the interaction of IR tail and Cbox of co-activators, as well as TAME as an inhibitor, as an inhibitor, with APC3 and APC8 subunits of APC/c were analyzed, regarding structure, molecular docking, molecular dynamics, and free binding energy. The results indicated that TAME bound to APC3 with a higher binding affinity (∼-7.3 kcal/mol) than APC8 (∼-5.7 kcal/mol). Also, the binding free energy value obtained for the APC3-TAME was -22.25 ± 1.12 kcal/mol. According to binding free energies, van der Waals energy was the major favorable contributor to the ligand binding. These results offer that TAME had more affinity to interact with the APC3 subunit, at the IR binding pocket than the APC8 subunit at the Cbox binding pocket. In conclusion, IR binding pocket can serve as an appropriate potential target for TAME as an inhibitor of APC/c.

Biofilm inhibition mechanism from extract of Hymenocallis littoralis leaves

ETHNOPHARMACOLOGICAL RELEVANCE

Hymenocallis littoralis (Jacq.) Salisb. has been referred as beach spider lily and commonly known for its rich phytochemical diversity. Phytochemicals such as alkaloids, volatile constituents, phenols, flavonoids, flavonols extracted from different parts of these plants like bulbs, flowers, leaf, stem and root had been used in folk medicines from ancient times because of their excellent antimicrobial and antioxidant properties. The leaf and bulb extract of H. littoralis plant was traditionally used for wound healing. Alkaloids extracted from bulb of this plant possess anti-viral, anti-neoplastic and cytotoxic properties. However, these phytochemicals have also shown antibiofilm activity, which is considered as one of the important factor accountable for the drug resistance in microorganisms. Thus, the investigation of medicinal properties of H. littoralis could be useful to control biofilm producing pathogens.

AIM OF THE STUDY

Explore antimicrobial, antibiofilm and antioxidant potentials of H. littoralis against pathogenic microorganisms using experimental and computational biology approach.

MATERIALS AND METHODS

Phytochemical extraction from dried powder of H. littoralis leaves was done by solvent extraction using methanol. Antimicrobial and antibiofilm activities of leaves extract were carried out using agar well diffusion method, growth curve, minimum inhibitory concentration (MIC) and Scanning Electron Microscopy (SEM). Liquid Chromatography and Mass Spectroscopy (LCMS) technique was used for the identification of phytochemicals. Molecular docking studies of antibiofilm agents with adhesin proteins were performed using Autodock 4.2. Antioxidant activity of extract was carried out by FRAP assay. The noxious effect of extract was investigated by histological studies on rat skin.

RESULTS

The preliminary phytochemical analysis of methanolic leaves extract revealed the presence of alkaloids, flavonoids, terpenoid, glycosides, terpene, terpenoids and phenolics. The various phytochemicals such as Apigenin 7-(4'', 6'' diacetylalloside)-4'- alloside, Catechin 7-O- apiofuranoside, Emodic acid, Epicatechin 3-O- β-D-glucopyranoside, 4 - Methylesculetin, Methylisoeugenol, Quercetin 5,7,3',4'-tetramethyl ether 3-rutinoside, 4 - Methylumbelliferyl β-D- glucuronide were extracted, characterized and recognized from the leaves extract of H. littoralis. The identification of these phytochemicals was performed using LC-MS. The antimicrobial property of H. littoralis leaf extract was investigated against different pathogenic microorganisms. Out of these tested microorganisms, promising antibiofilm and antimicrobial activities were confirmed against S. aureus NCIM 2654 and C. albicans NCIM 3466 by using growth curve and SEM analysis. MIC of this leaf extract was identified as 45 µg/ml and 70 µg/ml for S. aureus NCIM 2654 and C. albicans NCIM 3466 respectively. The leaves extract also showed good antioxidant activity due to presence of phenols and flavonoids. Molecular docking of these identified antibiofilm components interacts with the active site residues of adhesin proteins, Sortase A and Als3 from S. aureus and C. albicans respectively. Histological studies of extracted phytochemicals revealed non-noxious effects on rat skin.

CONCLUSION

Thus, the present study revealed that the leaves extract of H. littoralis contains various phytochemicals having good extent of antimicrobial, antibiofilm and antioxidant properties. The in-vitro and in-silico results would be useful to design new lead compounds against biofilm producing pathogenic microorganisms.

Preferences of AAA/AAG codon recognition by modified nucleosides, τm5s2U34 and t6A37 present in tRNALys

Deficiency of 5-taurinomethyl-2-thiouridine, τm⁵s²U at the 34th 'wobble' position in tRNA^Lys causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNA^Lys, recognizes AAA/AAG codons during protein biosynthesis process. Its preference to identify cognate codons has not been studied at the atomic level. Hence, multiple MD simulations of various molecular models of anticodon stem loop (ASL) of mt tRNA^Lys in presence and absence of τm⁵s²U₃₄ and N⁶-threonylcarbamoyl adenosine (t⁶A₃₇) along with AAA and AAG codons have been accomplished. Additional four MD simulations of multiple ASL mt tRNA^Lys models in the context of ribosomal A-site residues have also been performed to investigate the role of A-site in recognition of AAA/AAG codons. MD simulation results show that, ASL models in presence of τm⁵s²U₃₄ and t⁶A₃₇ with codons AAA/AAG are more stable than the ASL lacking these modified bases. MD trajectories suggest that τm⁵s²U recognizes the codons initially by 'wobble' hydrogen bonding interactions, and then tRNA^Lys might leave the explicit codon by a novel 'single' hydrogen bonding interaction in order to run the protein biosynthesis process smoothly. We propose this model as the 'Foot-Step Model' for codon recognition, in which the single hydrogen bond plays a crucial role. MD simulation results suggest that, tRNA^Lys with τm⁵s²U and t⁶A recognizes AAA codon more preferably than AAG. Thus, these results reveal the consequences of τm⁵s²U and t⁶A in recognition of AAA/AAG codons in mitochondrial disease, MERRF.

Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β42 monomer: insights from molecular dynamics simulations

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β₄₂ (Aβ₄₂) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ₄₂ aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ₄₂. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ₄₂ by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ₄₂ monomer. Overall, MD simulations reveal that C1 inhibits Aβ₄₂ aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ₄₂.

Molecular Docking Technique to Understand Enzyme-Ligand Interactions

Molecular docking has advanced to such an extent that one can rapidly and accurately identify pharmaceutically useful lead compounds. It is being used routinely to understand molecular interactions between enzyme and ligand molecules. Several computational approaches are combined with experimental work to investigate molecular mechanisms in detail at the atomic level. Molecular docking method is also useful to investigate proper orientation and interactions between receptor and ligand. In this chapter we have discussed protein-protein approach to understand interactions between enzyme and amyloid beta (Aß) peptide. The Aß peptide is a causative agent of Alzheimer's disease. The Aß peptides can be cleaved specifically by several enzymes. Their interactions with Aß peptide and specific enzyme can be investigated using molecular docking. Thus, the molecular information obtained from docking studies might be useful to design new therapeutic approaches in treatment of Alzheimer's as well as several other diseases.

The influence of hypermodified nucleosides lysidine and t(6)A to recognize the AUA codon instead of AUG: a molecular dynamics simulation study

Hypermodified nucleosides lysidine (L) and N(6)-threonylcarbamoyladenosine (t(6)A) influence codon-anticodon interactions during the protein biosynthesis process. Lysidine prevents the misrecognition of the AUG codon as isoleucine and that of AUA as methionine. The structural significance of these modified bases has not been studied in detail at the atomic level. Hence, in the present study we performed multiple molecular dynamics (MD) simulations of anticodon stem loop (ASL) of tRNA(Ile) in the presence and absence of modified bases 'L' and 't(6)A' at the 34th and 37th positions respectively along with trinucleotide 'AUA' and 'AUG' codons. Hydrogen bonding interactions formed by the tautomeric form of lysidine may assist in reading the third base adenine of the 'AUA' codon, unlike the guanine of the 'AUG' codon. Such interactions might be useful to restrict codon specificity to recognize isoleucine tRNA instead of methionine tRNA. The t(6)A side chain interacts with the purine ring of the first codon nucleotide adenine, which might provide base stacking interactions and could be responsible for restricting extended codon-anticodon recognition. We found that ASL tRNA(Ile) in the absence of modifications at the 34th and 37th positions cannot establish proper hydrogen bonding interactions to recognize the isoleucine codon 'AUA' and subsequently disturbs the anticodon loop structure. The binding free energy calculations revealed that tRNA(Ile) ASL with modified nucleosides prefers the codon AUA over AUG. Thus, these findings might be useful to understand the role of modified bases L and t(6)A to recognize the AUA codon instead of AUG.

Amyloid cascade hypothesis: Pathogenesis and therapeutic strategies in Alzheimer's disease

Alzheimer's disease is an irreversible, progressive neurodegenerative disorder. Various therapeutic approaches are being used to improve the cholinergic neurotransmission, but their role in AD pathogenesis is still unknown. Although, an increase in tau protein concentration in CSF has been described in AD, but several issues remains unclear. Extensive and accurate analysis of CSF could be helpful to define presence of tau proteins in physiological conditions, or released during the progression of neurodegenerative disease. The amyloid cascade hypothesis postulates that the neurodegeneration in AD caused by abnormal accumulation of amyloid beta (Aβ) plaques in various areas of the brain. The amyloid hypothesis has continued to gain support over the last two decades, particularly from genetic studies. Therefore, current research progress in several areas of therapies shall provide an effective treatment to cure this devastating disease. This review critically evaluates general biochemical and physiological functions of Aβ directed therapeutics and their relevance.

Molecular basis of laccase bound to lignin: insight from comparative studies on the interaction of Trametes versicolor laccase with various lignin model compounds

Binding orientation of lignin model compounds in laccase.