Kaempferol inhibits the activity of pancreatic lipase and its synergistic effect with orlistat

Mechanistic insights into the inhibition of pancreatic lipase by apigenin: Inhibitory interaction, conformational change and molecular docking studies

Mycoloyltransferases: A large and major family of enzymes shaping the cell envelope of Corynebacteriales.

Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer’s dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000 ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite () to AChE. Further, molecular dynamics simulations for 1000 ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential.

/pdf/identification-of-potential-herbal-inhibitor-of-55tix00ndc.pdf

Identification of potential herbal inhibitor of acetylcholinesterase associated Alzheimer's disorders using molecular docking and molecular dynamics simulation.

Lipases have been widely used as biocatalysts for numerous biotechnological applications. In an earlier paper, we presented experimental results showing significantly enhanced activity of the Lip2 lipase immobilized on carbon nanotubes (CNTs). In this work, to elucidate the activation mechanism of the lipase, we present an atomic resolution analysis of the lid domain motion of the Lip2 lipase upon immobilization by simulating the protein dynamics. The Lip2 lipase interacts with the CNT at a local site. However, the effects of that interaction are propagated to a remote lid subdomain. The chain of events initiated by the interaction provide the basis for a fundamental understanding of the lid opening mechanism. We identify the structural path followed by co-operative interactions that originate at the interaction site. In addition, salt bridge and hydrogen bonding interactions, which contribute to the propagation of interaction effects to distal regions, are also identified. The present study provides a plausible molecular model for understanding the mechanisms of lid opening of the immobilized lipase. The importance of the structural characteristics of the lipase upon immobilization on the CNT suggests that enzymes may be engineered to be site-specifically immobilized onto a hydrophobic support, such as carbon nanotubes, to achieve enhanced enzymatic activity.

Activation mechanism of Yarrowia lipolytica lipase immobilized on carbon nanotubes

Molecular dynamics simulations of lectin domain of FimH and immunoinformatics for the design of potential vaccine candidates

Antigen85 (Ag85) proteins of Mycobacterium tuberculosis are mycolyl transferases that aid in cell wall biosynthesis. MPT51 (Ag85D) is closely related to Ag85 proteins. We have performed a comparative molecular dynamics (MD) simulation study of Ag85 proteins (Ag85A, Ag85B, and Ag85C) and MPT51. We observe that helix α5, β7-α9 loop, and N-terminal region of helix α9 of Ag85 proteins are mobile, suggestive of lid like movement over the active site. Further, in Ag85B, we observe the proposed scooting mode of the hydrophobic gating residue Phe232. Our simulations also show a similar scooting mode for Phe232 of Ag85A and Trp158 of Ag85C. We also found aromatic residue clusters at the ends of the hydrophobic channel of Ag85 proteins, which may have functional significance. Although MPT51 lacks the tunnel, it has the aromatic clusters. The aromatic cluster region has the ability to bind trehalose. From an immunoinformatics study, a promiscuous linear epitope was identified in MPT51 which could be useful in subunit vaccine studies. Recent studies have shown that a mycobacterial protein HupB, interacts with Ag85 proteins and has a regulatory role in cell wall biogenesis, with implications in growth rate and latency. We performed molecular docking studies of HupB protein with Ag85 proteins and predicted potential sites of interaction in Ag85 proteins. The insights gained through the current study can potentially pave way for newer therapeutic interventions. Graphical Abstract Dynamics of antigen85 proteins and MPT51 from Mycobacterium tuberculosis.

Functional insights from a comparative study on the dynamics of Antigen85 proteins and MPT51 from Mycobacterium tuberculosis.

Cavities create a potential back door in epoxide hydrolase Rv1938 from Mycobacterium tuberculosis-A molecular dynamics simulation study

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2010.10.021

Molecular dynamics simulations of human and dog gastric lipases: Insights into domain movements

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Papers

Molecular dynamics simulations of lectin domain of FimH and immunoinformatics for the design of potential vaccine candidates

Functional insights from a comparative study on the dynamics of Antigen85 proteins and MPT51 from Mycobacterium tuberculosis.

Cavities create a potential back door in epoxide hydrolase Rv1938 from Mycobacterium tuberculosis-A molecular dynamics simulation study

Molecular dynamics simulations of human and dog gastric lipases: Insights into domain movements