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 (Aß) peptides. The extracellular deposition of Aß peptides in human AD brain causes neuronal death. Therefore, it has been found that Aß 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.

Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study.

CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native catalytic activity and non-reusability. Enzyme immobilization is a necessary step for enabling its reuse, and it provides methods for regulating the biocatalyst's functional efficacy in a synthetic setting. MOFs represent a novel category of porous materials possessing distinct superlative features that make MOFs an optimal host matrix for developing enzyme-MOF composites. In this study, we employed molecular modeling approaches, for instance, molecular docking and MD simulation, to explore the interactions between CRL and a specific MOF, ZIF-8. The present study involved conducting secondary structural analysis and homology modeling of CRL, followed by docking ZIF-8 with CRL. The results of the molecular docking analysis indicate that ZIF-8 was situated within the active site pocket of CRL, where it formed hydrogen bonds with Val-81, Phe-87, Ser-91, Asp-231, Thr-132, Lue-297, Phe-296, Phe-344, Thr-347, and Ser-450. The MD simulation analysis revealed that the CRL and ZIF-8 docked complex exhibited stability over the entire simulation period, and all interactions presented in the initial docked complex were maintained throughout the simulation. The findings derived from this investigation could promote comprehension of the molecular mechanisms underlying the interaction between CRL and ZIF-8 as well as the development of immobilized CRL for diverse industrial purposes.

Molecular insights into the inhibition of early stages of Aß peptide aggregation and destabilization of Alzheimer's Aß protofibril by dipeptide D-Trp-Aib: A molecular modelling approach.

Amyloid beta (Aß) peptide aggregates rapidly into the soluble oligomers, protofibrils and fibrils to form senile plaques, a neurotoxic component and pathological hallmark of Alzheimer's disease (AD). Experimentally, it has been demonstrated the inhibition of an early stages of Aß aggregation by a dipeptide D-Trp-Aib inhibitor, but its molecular mechanism is still unclear. Hence, in the present study, we used molecular docking and molecular dynamics (MD) simulations to explore the molecular mechanism of inhibition of an early oligomerization and destabilization of preformed Aß protofibril by D-Trp-Aib. Molecular docking study showed that the D-Trp-Aib binds at the aromatic (Phe19, Phe20) region of Aß monomer, Aß fibril and hydrophobic core of Aß protofibril. MD simulations revealed the binding of D-Trp-Aib at the aggregation prone region (Lys16-Glu22) resulted in the stabilization of Aß monomer by π-π stacking interactions between Tyr10 and indol ring of D-Trp-Aib, which decreases the ß-sheet content and increases the α-helices. The interaction between Lys28 of Aß monomer to D-Trp-Aib could be responsible to block the initial nucleation and may impede the fibril growth and elongation. The loss of hydrophobic contacts between two ß-sheets of Aß protofibril upon binding of D-Trp-Aib at the hydrophobic cavity resulted in the partial opening of ß-sheets. This also disrupts a salt bridge (Asp23-Lys28) leading to the destabilization of Aß protofibril. Binding energy calculations revealed that van der Waals and electrostatic interactions maximally favours the binding of D-Trp-Aib to Aß monomer and Aß protofibril respectively. The residues Tyr10, Phe19, Phe20, Ala21, Glu22, Lys28 of Aß monomer, whereas Leu17, Val18, Phe19, Val40, Ala42 of protofibril contributing for the interactions with D-Trp-Aib. Thus, the present study provides structural insights into the inhibition of an early oligomerization of Aß peptides and destabilization of Aß protofibril, which could be useful to design novel inhibitors for the treatment of AD.

Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation.

In the landscape of epigenetic regulation, histone deacetylase 3 (HDAC3) has emerged as a prominent therapeutic target for the design and development of candidate drugs against various types of cancers and other human disorders. Herein, we have performed ligand-based pharmacophore modeling, virtual screening, molecular docking, and MD simulations to design potent and selective inhibitors against HDAC3. The predicted best pharmacophore model 'Hypo 1' showed excellent correlation (R2 = 0.994), lowest RMSD (0.373), lowest total cost value (102.519), and highest cost difference (124.08). Hypo 1 consists of four salient pharmacophore features viz. one hydrogen bond acceptor (HBA), one ring aromatic (RA), and two hydrophobic (HYP). Hypo 1 was validated by Fischer's randomization with a 95% of confidence level and the external test set of 60 compounds with a good correlation coefficient (R2 = 0.970). The virtual screening of chemical databases, drug-like properties calculations followed by molecular docking resulted in identifying 22 representative hit compounds. Performed 50 ns of MD simulations on top three hits were retained the salient π-stacking, Zn2+ coordination, hydrogen bonding, and hydrophobic interactions with catalytic residues from the active site pocket of HDAC3. Total binding energy calculated by MM-PBSA showed that the Hit 1 and Hit 2 formed stable complexes with HDAC3 as compared to reference TSA. Further, the PLIP analysis showed a close resemblance between the salient pharmacophore features of Hypo 1 and the presence of molecular interactions in co-crystallized FDA-approved drugs. We conclude that the screened hit compounds may act as potent inhibitors of HDAC3 and further preclinical and clinical studies may pave the way for developing them as effective therapeutic agents for the treatment of different cancers and neurodegenerative disorders.

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

Alzheimer's disease (AD) is a progressive brain disorder. The accumulation of amyloid beta (Aß) peptides in the human brain leads to AD. The cleavage of Aß 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 Aß 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 Aß 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 Aß peptide. Analysis of MD simulated docked complex showed that the wild-type NEP-Aß-peptide complex is more stable as compared to mutant complex. Hydrogen bonding interactions between NEP with Zn2+and Aß peptide confirm the degradation of the Aß 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 Aß peptide. This stable interaction confirms the involvement of NEP with Glu-538 in the degradation of the Aß peptide. The other residues such as Glu203, Ser537, Gly140, Val587, and Val536 could also play an important role in the cleavage of Aß 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 Aß 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.

Structural insights and inhibition mechanism of TMPRSS2 by experimentally known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride to control SARS-coronavirus-2: A molecular modeling approach.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been responsible for the cause of global pandemic Covid-19 and to date, there is no effective treatment available. The spike 'S' protein of SARS-CoV-2 and ACE2 of the host cell are being targeted to design new drugs to control Covid-19. Similarly, a transmembrane serine protease, TMPRSS2 of the host cell plays a significant role in the proteolytic cleavage of viral 'S' protein helpful for the priming of ACE2 receptors and viral entry into human cells. However, three-dimensional structural information and the inhibition mechanism of TMPRSS2 is yet to be explored experimentally. Hence, we have used a molecular dynamics (MD) simulated homology model of TMPRSS2 to study the inhibition mechanism of experimentally known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride (BHH) using molecular modeling techniques. Prior to docking, all three inhibitors were geometry optimized by semi-empirical quantum chemical RM1 method. Molecular docking analysis revealed that Camostat mesylate and its structural analogue Nafamostat interact strongly with residues His296 and Ser441 present in the catalytic triad of TMPRSS2, whereas BHH binds with Ala386 along with other residues. Comparative molecular dynamics simulations revealed the stable behavior of all the docked complexes. MM-PBSA calculations also revealed the stronger binding of Camostat mesylate to TMPRSS2 active site residues as compared to Nafamostat and BHH. Thus, this structural information could be useful to understand the mechanistic approach of TMPRSS2 inhibition, which may be helpful to design new lead compounds to prevent the entry of SARS-Coronavirus 2 in human cells.

Evaluation of drug candidature: In silico ADMET, binding interactions with CDK7 and normal cell line studies of potentially anti-breast cancer enamidines.

We have recently explored novel class of potentially anti-breast cancer active enamidines in which four molecules 4a-c and 4h showed higher anticancer activity compared to standard drug doxorubicin. As a part of extension of this work, we have further evaluated in silico cheminformatic studies on bioactivity prediction of synthesized series of enamidines using mole information. The normal cell line study of four lead compounds 4a-c and 4h against African green monkey kidney vero strain further revealed that the compounds complemented good selectivity in inhibition of cancer cells. The in silico bioactivity and molecular docking studies also revealed that the compounds have significant interactions with the drug targets. The results reveal that enamidine moieties are vital for anti-breast cancer activity as they possess excellent drug-like characteristics, being potentially good inhibitors of cyclin dependent kinases7 (CDK7).

Molecular modeling approach to explore the role of cathepsin B from Hordeum vulgare in the degradation of Aß peptides.

The pathological hallmark of Alzheimer's disease is the accumulation of Aß peptides in human brains. These Aß peptides can be degraded by several enzymes such as hACE, hECE, hIDE and cathepsin B. Out of which cathepsin B also belongs to the papain super family and has been found in human brains, it has a role in Aß peptide degradation through limited proteolysis. The Aß concentrations are maintained properly by its production and clearance via receptor-mediated cellular uptake and direct enzymatic degradation. However, the reduced production of Aß degrading enzymes as well as their Aß degrading activity in human brains initiate the process of accumulation of Aß peptides. So it becomes essential to investigate the molecular interactions involved in the process of Aß degradation in detail at the atomic level. Hence, homology modeling, molecular docking and molecular dynamics simulation techniques have been used to explore the possible role of cathepsin B from Hordeum vulgare in the degradation of amyloid beta (Aß) peptides. The homology model of cathepsin B from Hordeum vulgare shows good similarity with human cathepsin B. Molecular docking and MD simulation results revealed that the active site residues Cys32, HIS112, HIS113 are involved in the catalytic activity of cathepsin B. The sulfhydryl group of the Cys32 residue of cathepsin B from Hordeum vulgare cleaves the Aß peptide from the carboxylic end of Glu11. Hence, this structural study might be helpful in designing alternative strategies for the treatment of AD.