Serine 106 preserves the tertiary structure, function, and stability of a cyclophilin from Staphylococcus aureus

Author(s):  
Soham Seal ◽  
Nilanjan Banerjee ◽  
Rohit Mahato ◽  
Tanmoy Kundu ◽  
Debabrata Sinha ◽  
...  
2012 ◽  
Vol 12 (1) ◽  
pp. 20-33 ◽  
Author(s):  
Takeru Hayashi ◽  
Miki Senda ◽  
Hiroko Morohashi ◽  
Hideaki Higashi ◽  
Masafumi Horio ◽  
...  

2021 ◽  
Vol 17 (3) ◽  
pp. 393-403
Author(s):  
V Lakshmi Ranganatha ◽  

It is of interest to document the design, synthesis, docking, Hirshfeld surface analysis and DFT calculations of 2-methylxanthen-9-with the FtsZ protein (PDB ID: 3VOB) from Staphylococcus aureus for antimicrobial applications. We report the quantitative structure function data in this context.


2021 ◽  
Author(s):  
Margaret Deming ◽  
Alatheia King ◽  
Robert A Coover ◽  
Cale D Fahrenholtz ◽  
Aurijit Sarkar

We have ascertained that phenylindolylmethyldiaminopyrimidines (PIDAPs), stop the growth of USA300 MRSA at low micromolar concentrations. The controls, penicillin G and vancomycin, are able to stop the growth of MRSA at ~765 μM (256 μg/mL) and ~1.38 μM (2 μg/mL) respectively. We have also found out that PIDAPs are bactericidal at or close to the MIC. No activity was observed against Gram-negative pathogens. Other Gram-positive pathogens have not yet been tested. Based on a search through the ChEMBL database, PIDAPs are a novel class of chemicals with antimicrobial properties. A limited structure-function study suggests that the diaminopyrimidine is part of the pharmacophore. Unfortunately, we also detected potential dose-limiting toxicity on human cell lines. Further, detailed studies are needed.


2015 ◽  
Vol 89 (6) ◽  
pp. 3285-3294 ◽  
Author(s):  
Cindy Buffone ◽  
Bianca Schulte ◽  
Silvana Opp ◽  
Felipe Diaz-Griffero

ABSTRACTThe alpha interferon (IFN-α)-inducible restriction factor myxovirus B (MxB) blocks HIV-1 infection after reverse transcription but prior to integration. MxB binds to the HIV-1 core, which is composed of capsid protein, and this interaction leads to inhibition of the uncoating process of HIV-1. Previous studies suggested that HIV-1 restriction by MxB requires binding to capsid. This work tests the hypothesis that MxB oligomerization is important for the ability of MxB to bind to the HIV-1 core. For this purpose, we modeled the structure of MxB using the published tertiary structure of MxA. The modeled structure of MxB guided our mutagenic studies and led to the discovery of several MxB variants that lose the capacity to oligomerize. In agreement with our hypothesis, MxB variants that lost the oligomerization capacity also lost the ability to bind to the HIV-1 core. MxB variants deficient for oligomerization were not able to block HIV-1 infection. Overall, our work showed that oligomerization is required for the ability of MxB to bind to the HIV-1 core and block HIV-1 infection.IMPORTANCEMxB is a novel restriction factor that blocks infection of HIV-1. MxB is inducible by IFN-α, particularly in T cells. The current work studies the oligomerization determinants of MxB and carefully explores the contribution of oligomerization to capsid binding and restriction. This work takes advantage of the current structure of MxA and models the structure of MxB, which is used to guide structure-function studies. This work leads to the conclusion that MxB oligomerization is important for HIV-1 capsid binding and restriction.


Plasmid ◽  
2012 ◽  
Vol 67 (2) ◽  
pp. 183-190 ◽  
Author(s):  
Carles Ubeda ◽  
María Ángeles Tormo-Más ◽  
José R. Penadés ◽  
Richard P. Novick

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Thanh Nguyen ◽  
Truc Kim ◽  
Hai Minh Ta ◽  
Won Sik Yeo ◽  
Jongkeun Choi ◽  
...  

ABSTRACTMannitol-1-phosphate dehydrogenase (M1PDH) is a key enzyme inStaphylococcus aureusmannitol metabolism, but its roles in pathophysiological settings have not been established. We performed comprehensive structure-function analysis of M1PDH fromS. aureusUSA300, a strain of community-associated methicillin-resistantS. aureus, to evaluate its roles in cell viability and virulence under pathophysiological conditions. On the basis of our results, we propose M1PDH as a potential antibacterial target.In vitrocell viability assessment of ΔmtlDknockout and complemented strains confirmed that M1PDH is essential to endure pH, high-salt, and oxidative stress and thus that M1PDH is required for preventing osmotic burst by regulating pressure potential imposed by mannitol. The mouse infection model also verified that M1PDH is essential for bacterial survival during infection. To further support the use of M1PDH as an antibacterial target, we identified dihydrocelastrol (DHCL) as a competitive inhibitor ofS. aureusM1PDH (SaM1PDH) and confirmed that DHCL effectively reduces bacterial cell viability during host infection. To explain physiological functions ofSaM1PDH at the atomic level, the crystal structure ofSaM1PDH was determined at 1.7-Å resolution. Structure-based mutation analyses and DHCL molecular docking to theSaM1PDH active site followed by functional assay identified key residues in the active site and provided the action mechanism of DHCL. Collectively, we proposeSaM1PDH as a target for antibiotic development based on its physiological roles with the goals of expanding the repertory of antibiotic targets to fight antimicrobial resistance and providing essential knowledge for developing potent inhibitors ofSaM1PDH based on structure-function studies.IMPORTANCEDue to the shortage of effective antibiotics against drug-resistantStaphylococcus aureus, new targets are urgently required to develop next-generation antibiotics. We investigated mannitol-1-phosphate dehydrogenase ofS. aureusUSA300 (SaM1PDH), a key enzyme regulating intracellular mannitol levels, and explored the possibility of usingSaM1PDH as a target for developing antibiotic. Since mannitol is necessary for maintaining the cellular redox and osmotic potential, the homeostatic imbalance caused by treatment with aSaM1PDH inhibitor or knockout of the gene encodingSaM1PDH results in bacterial cell death through oxidative and/or mannitol-dependent cytolysis. We elucidated the molecular mechanism ofSaM1PDH and the structural basis of substrate and inhibitor recognition by enzymatic and structural analyses ofSaM1PDH. Our results strongly support the concept that targeting ofSaM1PDH represents an alternative strategy for developing a new class of antibiotics that cause bacterial cell death not by blocking key cellular machinery but by inducing cytolysis and reducing stress tolerance through inhibition of the mannitol pathway.


2021 ◽  
Author(s):  
Margaret Deming ◽  
Alatheia King ◽  
Robert A Coover ◽  
Cale D Fahrenholtz ◽  
Aurijit Sarkar

We have ascertained that phenylindolylmethyldiaminopyrimidines (PIDAPs), stop the growth of USA300 MRSA at low micromolar concentrations. The controls, penicillin G and vancomycin, are able to stop the growth of MRSA at ~765 μM (256 μg/mL) and ~1.38 μM (2 μg/mL) respectively. We have also found out that PIDAPs are bactericidal at or close to the MIC. No activity was observed against Gram-negative pathogens. Other Gram-positive pathogens have not yet been tested. Based on a search through the ChEMBL database, PIDAPs are a novel class of chemicals with antimicrobial properties. A limited structure-function study suggests that the diaminopyrimidine is part of the pharmacophore. Unfortunately, we also detected potential dose-limiting toxicity on human cell lines. Further, detailed studies are needed.


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