scholarly journals Simulation-guided engineering of antibiotics for improved bacterial uptake

2020 ◽  
Author(s):  
Ricardo J. Ferreira ◽  
Peter M. Kasson

AbstractThe Gram-negative bacterial outer membrane poses a major obstacle to the development of much-needed antibiotics against drug-resistant infections. Its chemical composition and porin proteins differ from Gram-positive bacteria and mammalian cells, and heuristics developed for mammalian cell uptake apply poorly. Recently, machine-learning methods have predicted small-molecule uptake into Gram-negative bacteria, offering the possibility to rationally optimize this aspect of antibiotic lead development. Here, we report physics-based methods to prospectively predict Gram-negative bacterial uptake, select, and synthesize promising chemical derivatives targeting E. coli DNA gyrase B. Our methods do not require empirical parameterization and are readily adaptable to new chemical scaffolds. These physics-based predictions well capture experimentally measured uptake (r > 0.95) and are indeed predictive of antimicrobial activity (r > 0.92). These methods can be used prospectively in combination with target-binding simulations to optimize both bacterial uptake and target binding, overcoming important barriers to antibiotic lead generation before small-molecule synthesis.

2017 ◽  
Vol 37 (1) ◽  
Author(s):  
Xuemin Liu ◽  
Xuwen Cao ◽  
Su Wang ◽  
Guangdong Ji ◽  
Shicui Zhang ◽  
...  

The emergence of multidrug-resistant (MDR) microbes caused by overuse of antibiotics leads to urgent demands for novel antibiotics exploration. Our recent data showed that Ly2.1–3 (a novel lymphocyte antigen 6 (Ly6) gene cluster) were proteins with cationic nature and rich in cysteine content, that are characteristic of antimicrobial peptides (AMPs) and their expression were all significantly up-regulated after challenge with lipopolysaccharide (LPS). These strongly suggested that Ly2.1–3 are potential AMPs, but firm evidence are lacking. Here, we clearly showed that the recombinant proteins of Ly2.1–3 were capable of killing Gram-negative bacteria Aeromonas hydrophila and Escherichia coli, while they had little bactericidal activity against the Gram-positive bacteria Staphylococcus aureus and Bacillus subtilis. We also showed that recombinant proteins Ly2.1–3 (rLy2.1–3) were able to bind to the Gram-negative bacteria A. hydrophila, E. coli and the microbial signature molecule LPS, but not to the Gram-positive bacteria S. aureus and B. subtilis as well as the microbial signature molecule LTA. Moreover, the Scatchard analysis revealed that rLy2.1–3 could specifically bind to LPS. Finally, we found that Ly2.1–3 were not cytotoxic to mammalian cells. All these together indicate that Ly2.1–3 can function as AMPs.


2021 ◽  
Vol 9 (3) ◽  
pp. 592
Author(s):  
Mohamed Belal Hamed ◽  
Ewa Burchacka ◽  
Liselotte Angus ◽  
Arnaud Marchand ◽  
Jozefien De Geyter ◽  
...  

The increasing problem of bacterial resistance to antibiotics underscores the urgent need for new antibacterials. Protein export pathways are attractive potential targets. The Sec pathway is essential for bacterial viability and includes components that are absent from eukaryotes. Here, we used a new high-throughput in vivo screen based on the secretion and activity of alkaline phosphatase (PhoA), a Sec-dependent secreted enzyme that becomes active in the periplasm. The assay was optimized for a luminescence-based substrate and was used to screen a ~240K small molecule compound library. After hit confirmation and analoging, 14 HTS secretion inhibitors (HSI), belonging to eight structural classes, were identified with IC50 < 60 µM. The inhibitors were evaluated as antibacterials against 19 Gram-negative and Gram-positive bacterial species (including those from the WHO’s top pathogens list). Seven of them—HSI#6, 9; HSI#1, 5, 10; and HSI#12, 14—representing three structural families, were bacteriocidal. HSI#6 was the most potent hit against 13 species of both Gram-negative and Gram-positive bacteria with IC50 of 0.4 to 8.7 μM. HSI#1, 5, 9 and 10 inhibited the viability of Gram-positive bacteria with IC50 ~6.9–77.8 μM. HSI#9, 12, and 14 inhibited the viability of E. coli strains with IC50 < 65 μM. Moreover, HSI#1, 5 and 10 inhibited the viability of an E. coli strain missing TolC to improve permeability with IC50 4 to 14 μM, indicating their inability to penetrate the outer membrane. The antimicrobial activity was not related to the inhibition of the SecA component of the translocase in vitro, and hence, HSI molecules may target new unknown components that directly or indirectly affect protein secretion. The results provided proof of the principle that the new broad HTS approach can yield attractive nanomolar inhibitors that have potential as new starting compounds for optimization to derive potential antibiotics.


2020 ◽  
Vol 15 (6) ◽  
pp. 665-679
Author(s):  
Alok K. Srivastava ◽  
Lokesh K. Pandey

Background: [1, 3, 4]oxadiazolenone core containing chalcones and nucleosides were synthesized by Claisen-Schmidt condensation of a variety of benzaldehyde derivatives, obtained from oxidation of substituted 5-(3/6 substituted-4-Methylphenyl)-1, 3, 4-oxadiazole-2(3H)-one and various substituted acetophenone. The resultant chalcones were coupled with penta-O-acetylglucopyranose followed by deacetylation to get [1, 3, 4] oxadiazolenone core containing chalcones and nucleosides. Various analytical techniques viz IR, NMR, LC-MS and elemental analysis were used to confirm the structure of the synthesised compounds.The compounds were targeted against Bacillus subtilis, Staphylococcus aureus and Escherichia coli for antibacterial activity and Aspergillus flavus, Aspergillus niger and Fusarium oxysporum for antifungal activity. Methods: A mixture of Acid hydrazides (3.0 mmol) and N, Nʹ- carbonyl diimidazole (3.3 mmol) in 15 mL of dioxane was refluxed to afford substituted [1, 3, 4]-oxadiazole-2(3H)-one. The resulted [1, 3, 4]- oxadiazole-2(3H)-one (1.42 mmol) was oxidized with Chromyl chloride (1.5 mL) in 20 mL of carbon tetra chloride and condensed with acetophenones (1.42 mmol) to get chalcones 4. The equimolar ratio of obtained chalcones 4 and β -D-1,2,3,4,6- penta-O-acetylglucopyranose in presence of iodine was refluxed to get nucleosides 5. The [1, 3, 4] oxadiazolenone core containing chalcones 4 and nucleosides 5 were tested to determined minimum inhibitory concentration (MIC) value with the experimental procedure of Benson using disc-diffusion method. All compounds were tested at concentration of 5 mg/mL, 2.5 mg/mL, 1.25 mg/mL, 0.62 mg/mL, 0.31 mg/mL and 0.15 mg/mL for antifungal activity against three strains of pathogenic fungi Aspergillus flavus (A. flavus), Aspergillus niger (A. niger) and Fusarium oxysporum (F. oxysporum) and for antibacterial activity against Gram-negative bacterium: Escherichia coli (E. coli), and two Gram-positive bacteria: Staphylococcus aureus (S. aureus) and Bacillus subtilis(B. subtilis). Result: The chalcones 4 and nucleosides 5 were screened for antibacterial activity against E. coli, S. aureus and B. subtilis whereas antifungal activity against A. flavus, A. niger and F. oxysporum. Compounds 4a-t showed good antibacterial activity whereas compounds 5a-t containing glucose moiety showed better activity against fungi. The glucose moiety of compounds 5 helps to enter into the cell wall of fungi and control the cell growth. Conclusion: Chalcones 4 and nucleosides 5 incorporating [1, 3, 4] oxadiazolenone core were synthesized and characterized by various spectral techniques and elemental analysis. These compounds were evaluated for their antifungal activity against three fungi; viz. A. flavus, A. niger and F. oxysporum. In addition to this, synthesized compounds were evaluated for their antibacterial activity against gram negative bacteria E. Coli and gram positive bacteria S. aureus, B. subtilis. Compounds 4a-t showed good antibacterial activity whereas 5a-t showed better activity against fungi.


2020 ◽  
Vol 7 (8) ◽  
pp. 1290
Author(s):  
Saswat Subhankar ◽  
K. Madhuri ◽  
Vivek D. Alone

Osteomyelitis is an infection of the bones caused by pyogenic organisms. The ribs are an extremely uncommon site for osteomyelitis, occurring in less than 1% cases. The main causative organisms are Gram-positive bacteria, such as Staphylococcus aureus and Hemophilus influenzae. Gram-negative bacteria like E. coli have been rarely reported. Authors hereby present a case of an immune-competent patient who presented with an osteomyelitis of the ribs caused by the latter. In developing countries, tuberculosis is considered as the primary cause of osteomyelitis and pleural effusions. However, other organisms should also be considered in patients who present with fulminant infections.


Author(s):  
Yoshimitsu Masuda ◽  
Shun Kawabata ◽  
Tatsuya Uedoi ◽  
Ken-ichi Honjoh ◽  
Takahisa Miyamoto

We demonstrated that we could combine LLB and phage to construct promising novel antimicrobial agents, LLB-phage. The first LLB-phage, lnqQ -T7 phage, can control the growth of both the Gram-negative host strain and neighboring Gram-positive bacteria while preventing the emergence of phage resistance in the host strain.


1996 ◽  
Vol 34 (10) ◽  
pp. 89-95 ◽  
Author(s):  
Hu Tai-Lee

The use of biomass for the removal of reactive dyes from an aqueous solution with different bacterial genera has been investigated. Three Gram-negative bacteria: Aeromonas sp., P. luteola and E. coli, and two Gram-positive bacteria: B. subtilis and S. aureus and a mixed biomass of activated sludge are the tested biosorbents. Dead cells of Gram-negative bacteria have a higher specific adsorption capacity than the living cells. The dye removal is in the order of Aeromonoas sp. &gt; P. luteola &gt; E. coli. The adsorption equilibrium can be reached within one hour. Due to the positively charged cells at acidic pH, the removal of reactive dyes increases with decreasing pH. Evaluating the adsorption parameters, bacterial biomass exhibits stable adsorption characteristics, which makes it a suitable adsorbent for different dye compounds.


2019 ◽  
Vol 18 (5) ◽  
pp. 1147-1155 ◽  
Author(s):  
Rehan Khan ◽  
Melis Özkan ◽  
Aisan Khaligh ◽  
Dönüs Tuncel

Water-dispersible glycosylated poly(2,5′-thienylene)porphyrin-based nanoparticles have the ability to generate singlet oxygen in high yields and exhibit light-triggered antibacterial activity against Gram negative bacteria, E. coli as well as Gram positive bacteria, B. subtilis.


2020 ◽  
Vol 840 ◽  
pp. 265-269
Author(s):  
Nurjanah Nurjanah ◽  
Endang Saepudin

Curcumin, a diarylheptanoids compound which isolated primary from Curcuma longa, exhibits a variety of exciting biological activities, including as an antibacterial agent. In the present study, a sulfanilamide-contained curcumin compound was synthesized and characterized to investigate the antibacterial activity against gram-positive bacteria S. aureus, B. subtilis and gram-negative bacteria E. coli. The characterization of the synthesized compound was determined by analysing peak absorbance, functional group, and molecular weight using mass spectroscopy, UV/Vis and FTIR spectrophotometry. Curcumin-sulfanilamide compound exhibited the best antibacterial activity against gram-negative bacteria compared to curcumin and the curcumin-derived compound containing isoxazole with inhibitory zone of 11 mm.


2005 ◽  
Vol 2 (2) ◽  
pp. 109-112
Author(s):  
A. K. Parekh ◽  
K. K. Desai

Some new chalcones have been prepared by Claisen-schmidt condensation of ketone and different aromatic aldehydes. These chalcones on condensation with urea in presence of acid gave Pyrimidine-2-ones. The synthesized compounds have been characterized by elemental analysis, IR and1H NMR spectral data. They have been screened for their antibacterial activity against Gram positive bacteria B. subtillis & S. aureus and Gram negative bacteria E. coli & S. typhi.


Author(s):  
Chinyere Benardette Chinaka Ikpa ◽  
Uchechukwu C. Okoro ◽  
Collins I. Ubochi ◽  
Kieran O. Nwanorh

The 2-phenylsulphonamide derivatives of amino acids were synthesis by simple substitution of benzenesulphonylchloride (6) with amino acids (1-5) containing pharmacological active functionalities. Structures of the synthesised compounds (7a-7e) were characterised using FT-IR, NMR(1H,13C) and elemental analysis. The anti bacterial activities of the synthesised compounds were evaluated against gram positive bacteria: Staph and Streptococcus, gram negative bacteria: E-coli, Klebsiella, Proteus, and pseudomonas using 200 µl of 10 mg/ml and minimum inhibitory concentration (MIC) were also determined. The compounds exhibited effective anti bacterial properties though some are not more active than the standard drug ciprofloxacin.


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