Development of the computational antibiotic screening platform (CLASP) to aid in the discovery of new antibiotics

Soft Matter ◽  
2021 ◽  
Author(s):  
Yinghui Dai ◽  
Huilin Ma ◽  
Meishan Wu ◽  
Tory Alane Welsch ◽  
Soor Rajiv Vora ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Potential Drug ◽  
Clock Time ◽  
Output Data ◽  
Drug Molecules ◽  
Outer Membrane Porins ◽  
Antibiotic Screening ◽  
New Antibiotics ◽  
Bacterial Outer Membrane ◽  
Screening Platform

The CLASP is a freely-distributed script for screening potential drug molecules through bacterial outer membrane porins. The automated scripts provide comprehensive thermodynamic and kinetic output data within a few hours of wall-clock time.

Role of lysines in ion selectivity of bacterial outer membrane porins

1986 ◽  
Vol 860 (2) ◽  
pp. 263-267 ◽  
Author(s):  
Robert E.W. Hancock ◽  
Angela Schmidt ◽  
Katherina Bauer ◽  
Roland Benz
Keyword(s):  
Outer Membrane ◽  
Ion Selectivity ◽  
Outer Membrane Porins ◽  
Bacterial Outer Membrane

scholarly journals Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules

ACS Nano ◽  
2017 ◽  
Vol 11 (6) ◽  
pp. 5465-5473 ◽  
Author(s):  
Harsha Bajaj ◽  
Silvia Acosta Gutierrez ◽  
Igor Bodrenko ◽  
Giuliano Malloci ◽  
Mariano Andrea Scorciapino ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Polar Molecules ◽  
Outer Membrane Porins ◽  
Bacterial Outer Membrane

Clinically Relevant Bacterial Outer Membrane Models for Antibiotic Screening Applications

2021 ◽  
Author(s):  
Zeinab Mohamed ◽  
Jung-Ho Shin ◽  
Surajit Ghosh ◽  
Abhishek K. Sharma ◽  
Ferra Pinnock ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Antibiotic Screening ◽  
Bacterial Outer Membrane ◽  
Membrane Models

Combinatorial Design of Molecule using Activity-Linked Substructural Topological Information as Applied to Antitubercular Compounds

2018 ◽  
Vol 15 (1) ◽  
pp. 67-81 ◽  
Author(s):  
Chandan Raychaudhury ◽  
Md. Imbesat Hassan Rizvi ◽  
Debnath Pal
Keyword(s):  
Biological Activities ◽  
Combinatorial Design ◽  
Combinatorial Structure ◽  
Potential Drug ◽  
Structure Generation ◽  
Topological Information ◽  
Active Compounds ◽  
Antitubercular Drugs ◽  
Topological Distance ◽  
Drug Molecules

Background: Generating a large number of compounds using combinatorial methods increases the possibility of finding novel bioactive compounds. Although some combinatorial structure generation algorithms are available, any method for generating structures from activity-linked substructural topological information is not yet reported. Objective: To develop a method using graph-theoretical techniques for generating structures of antitubercular compounds combinatorially from activity-linked substructural topological information, predict activity and prioritize and screen potential drug candidates. </P><P> Methods: Activity related vertices are identified from datasets composed of both active and inactive or, differently active compounds and structures are generated combinatorially using the topological distance distribution associated with those vertices. Biological activities are predicted using topological distance based vertex indices and a rule based method. Generated structures are prioritized using a newly defined Molecular Priority Score (MPS). Results: Studies considering a series of Acid Alkyl Ester (AAE) compounds and three known antitubercular drugs show that active compounds can be generated from substructural information of other active compounds for all these classes of compounds. Activity predictions show high level of success rate and a number of highly active AAE compounds produced high MPS score indicating that MPS score may help prioritize and screen potential drug molecules. A possible relation of this work with scaffold hopping and inverse Quantitative Structure-Activity Relationship (iQSAR) problem has also been discussed. The proposed method seems to hold promise for discovering novel therapeutic candidates for combating Tuberculosis and may be useful for discovering novel drug molecules for the treatment of other diseases as well.

scholarly journals Bacterial Outer Membrane Vesicles as Nano‐Scale Bioreactors: A Fatty Acid Conversion Case Study

ChemCatChem ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 4080-4086
Author(s):  
Ji‐Won Song ◽  
Yoonjin Baeg ◽  
Ha‐Yeon Jeong ◽  
Jinwon Lee ◽  
Deok‐Kun Oh ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Outer Membrane ◽  
Membrane Vesicles ◽  
Outer Membrane Vesicles ◽  
Nano Scale ◽  
Bacterial Outer Membrane
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