Insight into the screening of potential beta-lactamase inhibitors as anti-bacterial chemical agents through pharmacoinformatics study.
11 Feb 2021-Journal of Biomolecular Structure & Dynamics (Taylor & Francis)-Vol. 39, Iss: 3, pp 923-942
TL;DR: Observations from the multiple pharmacoinformatics approach explained without any doubt that selected molecules are potential enough being promising anti-bacterial compounds.
Abstract: Drug resistance is an unsolved and major concern in the bacterial infection. Continuous development of drug-resistance to the antibiotics exponentially rises the danger of bacterial infections. Che...
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TL;DR: Glyasperin A and glycyrrhizic acid could be considered as the best molecule from liquorice, which could find useful against COVID-19, a pandemic caused by SARS-CoV-2.
Abstract: At present, the world is facing a pandemic named as COVID-19, caused by SARS-CoV-2 Traditional Chinese medicine has recommended the use of liquorice (Glycyrrhiza species) in the treatment of infec
99 citations
Cites methods from "Insight into the screening of poten..."
...Theory and details of this method have been given in our previous publication (Bhowmick et al., 2019; Parida et al., 2020)....
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TL;DR: An insight is given into the amoxicillin detection, development of resistance along with its impact and ecotoxicity on living beings and in-depth studies are important for the development of better and sustainable technology for cleaner environment.
Abstract: Increased use of antibiotics has led to the contamination of the water bodies. Pharmaceutically active compounds can lead to severe effects including the production of antibiotic-resistant microbes, endocrine disruption, toxicity to aquatic organisms, and genotoxicity. Though the antibiotics are found in the aquatic environment at a very low concentration ranging from nanogram to microgram per liter, but exert adverse effects and contribute to pollution. A global medical crisis is unfolding as antibiotics lose effectiveness against a growing number of bacterial pathogens. Among the antibiotics, amoxicillin is one of the frequently used antibiotics for the treatment of both gram-positive and negative bacteria including the infections of the middle ear. It is most commonly used in human and veterinary medicine around the world. Amoxicillin's impact on human health and the environment is uncertain hence it is regarded as an emerging contaminant. Wastewater treatment plants (WWTPs) do not efficiently remove amoxicillin which contributes to its presence in drinking water and water bodies. Various physicochemical processes and bioremediation are used for the removal of amoxicillin, but antibiotics, being hydrophobic and lipophilic are recalcitrant to degradation and cannot be completely removed from the environment, but in-depth studies are important for the development of better and sustainable technology for cleaner environment. The present review gives an insight into the amoxicillin detection, development of resistance along with its impact and ecotoxicity on living beings. Amoxicillin removal using physicochemical parameters, nanoparticles, phytoremediation, and via the use of bacteria and algae have been discussed in the paper.
32 citations
TL;DR: In this paper, a virtual screening protocol was implemented on three anti-viral specific chemical libraries against SARS-CoV-2 main protease (Mpro) for the treatment of COVID-19.
Abstract: Worldwide coronavirus disease 2019 (COVID-19) outbreak is still threatening global health since its outbreak first reported in the late 2019. The causative novel virus has been designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although COVID-19 emergent with significant mortality, there is no availability of definite treatment measures. It is now extremely desirable to identify potential chemical entities against SARS-CoV-2 for the treatment of COVID-19. In the present study, a state-of-art virtual screening protocol was implemented on three anti-viral specific chemical libraries against SARS-CoV-2 main protease (Mpro). Particularly, viewing the large-scale biological role of Mpro in the viral replication process it has been considered as a prospective anti-viral drug target. Herein, on collected 79,892 compounds, hierarchical multistep docking followed by relative binding free energy estimation has been performed. Thereafter, implying a user-defined XP-dock and MM-GBSA cut-off scores as -8.00 and -45.00 kcal/mol, chemical space has been further reduced. Exhaustive molecular binding interactions analyses and various pharmacokinetics profiles assessment suggested four compounds (ChemDiv_D658-0159, ChemDiv_F431-0433, Enamine_Z3019991843 and Asinex_LAS_51389260) as potent inhibitors/modulators of SARS-CoV-2 Mpro. In-depth protein-ligand interactions stability in the dynamic state has been evaluated by 100 ns molecular dynamics (MD) simulation studies along with MM-GBSA-based binding free energy estimations of entire simulation trajectories that have revealed strong binding affinity of all identified compounds towards Mpro. Hence, all four identified compounds might be considered as promising candidates for future drug development specifically targeting the SARS-CoV-2 Mpro; however, they also need experimental assessment for a better understanding of molecular interaction mechanisms.
16 citations
TL;DR: In this article, the authors present a review of the recent strategies that are in line for development as potential alternatives to conventional antibiotics, including the development of plant-based drugs, antimicrobial peptides, nano-formulations, bacteriophage therapy, use of CRISPR-Cas9, RNA silencing and antibiotic conjugates with nanoparticles of antimacterial peptides.
14 citations
References
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TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
46,130 citations
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
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19,213 citations
"Insight into the screening of poten..." refers methods in this paper
...Finally, for better visualization of the docked complex analyses, the PyMol (Delano, 2002) and Visual Molecular Dynamics (VMD) (Humphrey, Dalke, & Schulten, 1996) were used....
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TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less
17,897 citations
"Insight into the screening of poten..." refers methods in this paper
...A coulombic interaction cutoff radius of 9 Å was used for evaluating short-range interactions during minimization, while smooth particle mesh Ewald method (PME) (Essmann et al., 1995) used for evaluating long-range coulombic interactions....
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TL;DR: It is argued that certain duties of patients counterbalance an otherwise unfair captivity of doctors as helpers and that vulnerability does not exclude obligation.
Abstract: There has been a shift from the general presumption that “doctor knows best” to a heightened respect for patient autonomy. Medical ethics remains one-sided, however. It tends (incorrectly) to interpret patient autonomy as mere participation in decisions, rather than a willingness to take the consequences. In this respect, medical ethics remains largely paternalistic, requiring doctors to protect patients from the consequences of their decisions. This is reflected in a one-sided account of duties in medical ethics. Medical ethics may exempt patients from obligations because they are the weaker or more vulnerable party in the doctor-patient relationship. We argue that vulnerability does not exclude obligation. We also look at others ways in which patients’ responsibilities flow from general ethics: for instance, from responsibilities to others and to the self, from duties of citizens, and from the responsibilities of those who solicit advice. Finally, we argue that certain duties of patients counterbalance an otherwise unfair captivity of doctors as helpers.
17,373 citations