New Approaches in Sensing and Targeting Bacterial rRNA A-site

2019 ◽  
Vol 15 ◽  
Author(s):  
Preethi Parameswaran ◽  
Nihar Ranjan ◽  
S.J.S. Flora
Keyword(s):  
Antibiotic Resistance ◽  
Life Cycle ◽  
High Throughput ◽  
Antibacterial Agents ◽  
Lead Compounds ◽  
New Class ◽  
Chemical Agents ◽  
Direct Sensing ◽  
A Site ◽  
Fluorescent Molecules

: New chemical agents that could combat increasing antibiotic resistance are urgently needed. In this mini-review, an old but highly relevant RNA sequence which is crucial for the continuation of bacterial life-cycle is covered. Some of the most significant advances of the last decade in sensing and targeting the bacterial rRNA A-site: a well-validated binding site of proverbially known aminoglycoside antibiotics is described. Some of the major advances in direct sensing of the bacterial decoding side (A-site) are described and also new fluorescent molecules that are capable of detecting lead compounds through high-throughput assays by displacement of fluorescent probe molecules are highlighted. Lastly, a focus on some of the recently discovered non-aminoglycoside small molecule binders of bacterial rRNA A-site as a new class of molecules that could provide future scaffolds and molecules for developing new antibacterial agents has been discussed.1

Large-scale High-throughput Screening Revealed 5'-(carbonylamino)-2,3'- bithiophene-4'-carboxylate as Novel Template for Antibacterial Agents

2020 ◽  
Vol 17 (5) ◽  
pp. 716-724
Author(s):  
Yan A. Ivanenkov ◽  
Renat S. Yamidanov ◽  
Ilya A. Osterman ◽  
Petr V. Sergiev ◽  
Vladimir A. Aladinskiy ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
High Throughput ◽  
High Throughput Screening ◽  
Large Scale ◽  
Antibacterial Agents ◽  
Sos Response ◽  
Luciferase Assay ◽  
Translational Machinery ◽  
E Coli ◽  
New Class

Background: The key issue in the development of novel antimicrobials is a rapid expansion of new bacterial strains resistant to current antibiotics. Indeed, World Health Organization has reported that bacteria commonly causing infections in hospitals and in the community, e.g. E. Coli, K. pneumoniae and S. aureus, have high resistance vs the last generations of cephalosporins, carbapenems and fluoroquinolones. During the past decades, only few successful efforts to develop and launch new antibacterial medications have been performed. This study aims to identify new class of antibacterial agents using novel high-throughput screening technique. Methods: We have designed library containing 125K compounds not similar in structure (Tanimoto coeff.< 0.7) to that published previously as antibiotics. The HTS platform based on double reporter system pDualrep2 was used to distinguish between molecules able to block translational machinery or induce SOS-response in a model E. coli system. MICs for most active chemicals in LB and M9 medium were determined using broth microdilution assay. Results: In an attempt to discover novel classes of antibacterials, we performed HTS of a large-scale small molecule library using our unique screening platform. This approach permitted us to quickly and robustly evaluate a lot of compounds as well as to determine the mechanism of action in the case of compounds being either translational machinery inhibitors or DNA-damaging agents/replication blockers. HTS has resulted in several new structural classes of molecules exhibiting an attractive antibacterial activity. Herein, we report as promising antibacterials. Two most active compounds from this series showed MIC value of 1.2 (5) and 1.8 μg/mL (6) and good selectivity index. Compound 6 caused RFP induction and low SOS response. In vitro luciferase assay has revealed that it is able to slightly inhibit protein biosynthesis. Compound 5 was tested on several archival strains and exhibited slight activity against gram-negative bacteria and outstanding activity against S. aureus. The key structural requirements for antibacterial potency were also explored. We found, that the unsubstituted carboxylic group is crucial for antibacterial activity as well as the presence of bulky hydrophobic substituents at phenyl fragment. Conclusion: The obtained results provide a solid background for further characterization of the 5'- (carbonylamino)-2,3'-bithiophene-4'-carboxylate derivatives discussed herein as new class of antibacterials and their optimization campaign.

Recent Advances in 1,3,5-Triazine Derivatives as Antibacterial Agents

2020 ◽  
Vol 17 (8) ◽  
pp. 991-1041
Author(s):  
Divya Utreja ◽  
Jagdish Kaur ◽  
Komalpreet Kaur ◽  
Palak Jain
Keyword(s):  
Antibacterial Activity ◽  
Heterocyclic Compounds ◽  
Antibacterial Agents ◽  
Rapid Development ◽  
Pharmacological Action ◽  
Biological Properties ◽  
Vast Array ◽  
Bacterial Diseases ◽  
New Class ◽  
Triazine Derivatives

Triazine, one of the nitrogen containing heterocyclic compounds has attracted the considerable interest of researchers due to the vast array of biological properties such as anti-viral, antitumor, anti-convulsant, analgesic, antioxidant, anti-depressant, herbicidal, insecticidal, fungicidal, antibacterial and anti-inflammatory activities offered by it. Various antibacterial agents have been synthesized by researchers to curb bacterial diseases but due to rapid development in drug resistance, tolerance and side effects, there had always been a need for the synthesis of a new class of antibacterial agents that would exhibit improved pharmacological action. Therefore, this review mainly focuses on the various methods for the synthesis of triazine derivatives and their antibacterial activity.

scholarly journals Thiazole Analogues of the Marine Alkaloid Nortopsentin as Inhibitors of Bacterial Biofilm Formation

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 81
Author(s):  
Anna Carbone ◽  
Stella Cascioferro ◽  
Barbara Parrino ◽  
Daniela Carbone ◽  
Camilla Pecoraro ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Bacterial Biofilm ◽  
Thiazole Derivatives ◽  
Gram Positive ◽  
Lead Compounds ◽  
New Class ◽  
Marked Selectivity ◽  
Global Threat ◽  
New Compounds ◽  
Reference Strains

Anti-virulence strategy is currently considered a promising approach to overcome the global threat of the antibiotic resistance. Among different bacterial virulence factors, the biofilm formation is recognized as one of the most relevant. Considering the high and growing percentage of multi-drug resistant infections that are biofilm-mediated, new therapeutic agents capable of counteracting the formation of biofilms are urgently required. In this scenario, a new series of 18 thiazole derivatives was efficiently synthesized and evaluated for its ability to inhibit biofilm formation against the Gram-positive bacterial reference strains Staphylococcus aureus ATCC 25923 and S. aureus ATCC 6538 and the Gram-negative strain Pseudomonas aeruginosa ATCC 15442. Most of the new compounds showed a marked selectivity against the Gram-positive strains. Remarkably, five compounds exhibited BIC50 values against S. aureus ATCC 25923 ranging from 1.0 to 9.1 µM. The new compounds, affecting the biofilm formation without any interference on microbial growth, can be considered promising lead compounds for the development of a new class of anti-virulence agents.

scholarly journals Novel Seleno- and Thio-Urea Containing Dihydropyrrol-2-One Analogues as Antibacterial Agents

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 321
Author(s):  
Shekh Sabir ◽  
Tsz Tin Yu ◽  
Rajesh Kuppusamy ◽  
Basmah Almohaywi ◽  
George Iskander ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Antibiotic Resistance ◽  
Quorum Sensing ◽  
Antibacterial Agents ◽  
Inhibitory Concentration ◽  
Resistant Bacteria ◽  
Drug Resistant ◽  
Positive Bacterium ◽  
Quorum Sensing Inhibition ◽  
Drug Resistant Bacteria

The quorum sensing (QS) system in multi-drug-resistant bacteria such as P. aeruginosa is primarily responsible for the development of antibiotic resistance and is considered an attractive target for antimicrobial drug discovery. In this study, we synthesised a series of novel selenourea and thiourea-containing dihydropyrrol-2-one (DHP) analogues as LasR antagonists. The selenium DHP derivatives displayed significantly better quorum-sensing inhibition (QSI) activities than the corresponding sulphur analogues. The most potent analogue 3e efficiently inhibited the las QS system by 81% at 125 µM and 53% at 31 µM. Additionally, all the compounds were screened for their minimum inhibitory concentration (MIC) against the Gram-positive bacterium S. aureus, and interestingly, only the selenium analogues showed antibacterial activity, with 3c and 3e being the most potent with a MIC of 15.6 µM.

scholarly journals High-Throughput Virtual Screening for a New Class of Antagonist Targeting LasR of Pseudomonas aeruginosa

ACS Omega ◽  
2021 ◽  
Author(s):  
Aishwarya Vetrivel ◽  
Santhi Natchimuthu ◽  
Vidyalakshmi Subramanian ◽  
Rajeswari Murugesan
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Virtual Screening ◽  
High Throughput ◽  
New Class ◽  
High Throughput Virtual Screening

scholarly journals Development of NS3/4A Protease-Based Reporter Assay Suitable for Efficiently Assessing Hepatitis C Virus Infection

2009 ◽  
Vol 53 (11) ◽  
pp. 4825-4834 ◽  
Author(s):  
Kao-Lu Pan ◽  
Jin-Ching Lee ◽  
Hsing-Wen Sung ◽  
Teng-Yuang Chang ◽  
John T.-A. Hsu
Keyword(s):  
Cell Culture ◽  
Life Cycle ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Virus Infection ◽  
High Throughput ◽  
High Throughput Screening ◽  
Reporter System ◽  
Viral Protease ◽  
Peptide Cleavage

ABSTRACT A cell culture system for the production of hepatitis C virus (HCV) whole virions has greatly accelerated studies of the virus life cycle and the discovery of anti-HCV agents. However, the quantification of the HCV titers in a whole-virus infection/replication system currently relies mostly on reverse transcription-PCR or immunofluorescence assay, which would be cumbersome for high-throughput drug screening. To overcome this problem, this study has generated a novel cell line, Huh7.5-EG(Δ4B5A)SEAP, that carries a dual reporter, EG(Δ4B5A)SEAP. The EG(Δ4B5A)SEAP reporter is a viral protease-cleavable fusion protein in which the enhanced green fluorescence protein is linked to secreted alkaline phosphatase (SEAP) in frame via Δ4B5A, a short peptide cleavage substrate for NS3/4A viral protease. This study demonstrates that virus replication/infection in the Huh7.5-EG(Δ4B5A)SEAP cells can be quantitatively indicated by measuring the SEAP activity in cell culture medium. The levels of SEAP released from HCV-infected Huh7.5-EG(Δ4B5A)SEAP cells correlated closely with the amounts of HCV in the inocula. The Huh7.5-EG(Δ4B5A)SEAP cells were also shown to be a suitable host for the discovery of anti-HCV inhibitors by using known compounds that target multiple stages of the HCV life cycle. The Z′-factor of this assay ranged from 0.64 to 0.74 in 96-well plates, indicating that this reporter system is suitable for high-throughput screening of prospective anti-HCV agents.

scholarly journals Synthesis and biological evaluation of triphenyl-imidazoles as a new class of antimicrobial agents

2018 ◽  
Vol 9 (4) ◽  
pp. 369-374 ◽  
Author(s):  
Anupam Anupam ◽  
Mohammed Al-Bratty ◽  
Hassan Ahmad Alhazmi ◽  
Shamim Ahmad ◽  
Supriya Maity ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Biological Evaluation ◽  
Fungal Strain ◽  
Dilution Method ◽  
Serum Glutamic Oxaloacetic Transaminase ◽  
Active Compounds ◽  
Lead Compounds ◽  
New Class ◽  
Diffusion Technique ◽  
Ft Ir

Newer triphenyl-imidazole derivatives (4a-h) were synthesized in good yields by the reaction of benzil and substituted benzaldehydes in equimolar quantities and refluxing the product with acetyl chloride thereafter. Structures were confirmed by using FT-IR, 1H NMR and 13C NMR spectroscopic methods. All the synthesized compounds were tested for their antimicrobial activity using agar diffusion technique against Gram positive (Staphhylococcus aureus and Bacillus subtilis), Gram negative (Escherichia coli and Pseudomonas aureginosa) as well as Fungal strain (Candida albicans). Interestingly compounds 4a, 4b, 4f and 4h showed significant antibacterial activity, whereas compound 4b was found to have remarkable activity against the fungal strain. The Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) of most active compounds were determined by broth dilution method and compound 4b emerged to have potent activities against most of the strains having MIC in the range of 25-200 µg/mL. To check the possible toxicities of the most active compounds, they were orally administered in rats and the concentration of liver enzymes serum glutamic-oxaloacetic transaminase (SGOT), serum glutamic pyruvic transaminase (SGPT) and alkaline phosphatase (ALKP) were determined. Compound 4h showed significant increase in the enzymes level depicting the hepatotoxicity. The structure-activity relationship studies showed the importance of electron withdrawing groups at the distant phenyl ring at ortho and para positions as the compounds having chloro or nitro at these positions tend to be more active than the compounds with electron releasing groups such as methoxy. These compounds may act as lead compounds for further studies and appropriate modification in their structure may lead to agents having high efficacy with lesser toxicity.

scholarly journals High throughput functional variant screens via in-vivo production of single-stranded DNA

2020 ◽  
Author(s):  
Max G. Schubert ◽  
Daniel B. Goodman ◽  
Timothy M. Wannier ◽  
Divjot Kaur ◽  
Fahim Farzadfard ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
High Throughput ◽  
Entire Genome ◽  
Single Stranded Dna ◽  
Functional Variant ◽  
Continuous Generation ◽  
Sources Of Variation ◽  
Targeted Deep Sequencing ◽  
High Throughput Screens

AbstractTremendous genetic variation exists in nature, but our ability to create and characterize individual genetic variants remains far more limited in scale. Likewise, engineering proteins and phenotypes requires the introduction of synthetic variants, but design of variants outpaces experimental measurement of variant effect. Here, we optimize efficient and continuous generation of precise genomic edits in Escherichia coli, via in-vivo production of single-stranded DNA by the targeted reverse-transcription activity of retrons. Greater than 90% editing efficiency can be obtained using this method, enabling multiplexed applications. We introduce Retron Library Recombineering (RLR), a system for high-throughput screens of variants, wherein the association of introduced edits with their retron elements enables a targeted deep sequencing phenotypic output. We use RLR for pooled, quantitative phenotyping of synthesized variants, characterizing antibiotic resistance alleles. We also perform RLR using sheared genomic DNA of an evolved bacterium, experimentally querying millions of sequences for antibiotic resistance variants. In doing so, we demonstrate that RLR is uniquely suited to utilize non-designed sources of variation. Pooled experiments using ssDNA produced in vivo thus present new avenues for exploring variation, both designed and not, across the entire genome.

scholarly journals Application of Life Cycle Assessment and Machine Learning for High-Throughput Screening of Green Chemical Substitutes

2020 ◽  
Author(s):  
Xinzhe Zhu ◽  
Chi-Hung Ho ◽  
Xiaonan Wang
Keyword(s):  
Machine Learning ◽  
Life Cycle Assessment ◽  
Life Cycle ◽  
Production Process ◽  
Environmental Impacts ◽  
High Throughput ◽  
High Throughput Screening ◽  
Molecular Descriptors ◽  
Trifluoroacetic Anhydride ◽  
Chemical Materials

<p><a></a><a>The production process of many active pharmaceutical ingredients such as sitagliptin could cause severe environmental problems due to the use of toxic chemical materials and production infrastructure, energy consumption and wastes treatment. The environmental impacts of sitagliptin production process were estimated with life cycle assessment (LCA) method, which suggested that the use of chemical materials provided the major environmental impacts. Both methods of Eco-indicator 99 and ReCiPe endpoints confirmed that chemical feedstock accounted 83% and 70% of life-cycle impact, respectively. Among all the chemical materials used in the sitagliptin production process, </a><a>trifluoroacetic anhydride </a>was identified as the largest influential factor in most impact categories according to the results of ReCiPe midpoints method. Therefore, high-throughput screening was performed to seek for green chemical substitutes to replace the target chemical (i.e. trifluoroacetic anhydride) by the following three steps. Firstly, thirty most similar chemicals were obtained from two million candidate alternatives in PubChem database based on their molecular descriptors. Thereafter, deep learning neural network models were developed to predict life-cycle impact according to the chemicals in Ecoinvent v3.5 database with known LCA values and corresponding molecular descriptors. Finally, 1,2-ethanediyl ester was proved to be one of the potential greener substitutes after the LCA data of these similar chemicals were predicted using the well-trained machine learning models. The case study demonstrated the applicability of the novel framework to screen green chemical substitutes and optimize the pharmaceutical manufacturing process.</p>

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