Toward Selective Histone Deacetylase Inhibitor Design:  Homology Modeling, Docking Studies, and Molecular Dynamics Simulations of Human Class I Histone Deacetylases

2005 ◽  
Vol 48 (22) ◽  
pp. 6936-6947 ◽  
Author(s):  
Di-Fei Wang ◽  
Paul Helquist ◽  
Norbert L. Wiech ◽  
Olaf Wiest
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Molecular Dynamics Simulations ◽  
Histone Deacetylase ◽  
Histone Deacetylase Inhibitor ◽  
Histone Deacetylases ◽  
Docking Studies ◽  
Human Class ◽  
Deacetylase Inhibitor ◽  
Dynamics Simulations

scholarly journals Multidrug Resistance in Neisseria gonorrhoeae: Identification of Functionally Important Residues in the MtrD Efflux Protein

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Mohsen Chitsaz ◽  
Lauren Booth ◽  
Mitchell T. Blyth ◽  
Megan L. O’Mara ◽  
Melissa H. Brown
Keyword(s):  
Molecular Dynamics ◽  
Multidrug Resistance ◽  
Neisseria Gonorrhoeae ◽  
Molecular Dynamics Simulations ◽  
Docking Studies ◽  
Drug Binding ◽  
Multidrug Efflux ◽  
Content Type ◽  
Binding Pockets ◽  
Dynamics Simulations

ABSTRACT A key mechanism that Neisseria gonorrhoeae uses to achieve multidrug resistance is the expulsion of structurally different antimicrobials by the MtrD multidrug efflux protein. MtrD resembles the homologous Escherichia coli AcrB efflux protein with several common structural features, including an open cleft containing putative access and deep binding pockets proposed to interact with substrates. A highly discriminating N. gonorrhoeae strain, with the MtrD and NorM multidrug efflux pumps inactivated, was constructed and used to confirm and extend the substrate profile of MtrD to include 14 new compounds. The structural basis of substrate interactions with MtrD was interrogated by a combination of long-timescale molecular dynamics simulations and docking studies together with site-directed mutagenesis of selected residues. Of the MtrD mutants generated, only one (S611A) retained a wild-type (WT) resistance profile, while others (F136A, F176A, I605A, F610A, F612C, and F623C) showed reduced resistance to different antimicrobial compounds. Docking studies of eight MtrD substrates confirmed that many of the mutated residues play important nonspecific roles in binding to these substrates. Long-timescale molecular dynamics simulations of MtrD with its substrate progesterone showed the spontaneous binding of the substrate to the access pocket of the binding cleft and its subsequent penetration into the deep binding pocket, allowing the permeation pathway for a substrate through this important resistance mechanism to be identified. These findings provide a detailed picture of the interaction of MtrD with substrates that can be used as a basis for rational antibiotic and inhibitor design. IMPORTANCE With over 78 million new infections globally each year, gonorrhea remains a frustratingly common infection. Continuous development and spread of antimicrobial-resistant strains of Neisseria gonorrhoeae, the causative agent of gonorrhea, have posed a serious threat to public health. One of the mechanisms in N. gonorrhoeae involved in resistance to multiple drugs is performed by the MtrD multidrug resistance efflux pump. This study demonstrated that the MtrD pump has a broader substrate specificity than previously proposed and identified a cluster of residues important for drug binding and translocation. Additionally, a permeation pathway for the MtrD substrate progesterone actively moving through the protein was determined, revealing key interactions within the putative MtrD drug binding pockets. Identification of functionally important residues and substrate-protein interactions of the MtrD protein is crucial to develop future strategies for the treatment of multidrug-resistant gonorrhea.

Homology Modeling and Molecular Dynamics Simulations of the Mu Opioid Receptor in a Membrane-Aqueous System

ChemBioChem ◽  
2005 ◽  
Vol 6 (5) ◽  
pp. 853-859 ◽  
Author(s):  
Yan Zhang ◽  
Yuk Y. Sham ◽  
Ramkumar Rajamani ◽  
Jiali Gao ◽  
Philip S. Portoghese
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Molecular Dynamics Simulations ◽  
Opioid Receptor ◽  
Mu Opioid Receptor ◽  
Aqueous System ◽  
Mu Opioid ◽  
Dynamics Simulations
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