Bioactive components of different nasal spray solutions may defeat SARS-Cov2: repurposing and in silico studies

Khan, Mohammad Faheem; Ansari, Waseem Ahmad; Ahamad, Tanveer; Khan, Mohsin Ali; Khan, Zaw Ali; Sarfraz, Aqib; Khan, Mohd Aamish

doi:10.1007/s00894-022-05213-9

Cited by 13 publications

(18 citation statements)

References 55 publications

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“…The binding free energies of simulated complexes were evaluated by performing the Prime MM‐GBSA module of the Schrödinger 2020–4 LCC, New York, USA. We fragmented the simulation trajectory of complexes into 50 snapshots of 20 frames at every 2.0 ns and calculated binding energy by applying this command: thermal_mmgbsa.py, which was executed in terms of (ΔG) Gibbs‐free energy 9,44 …”

Section: Methodsmentioning

confidence: 99%

“…Death occurs in 90% of cases if proper treatment is not received, with an average case fatality rate of 7% 8 . In 2020, more than 90% of new cases reported to the WHO occurred in 10 countries: Brazil, China, Ethiopia, Eritrea, India, Kenya, Somalia, South Sudan, Sudan, and Yemen 9–11 …”

Section: Introductionmentioning

confidence: 99%

“…8 In 2020, more than 90% of new cases reported to the WHO occurred in 10 countries: Brazil, China, Ethiopia, Eritrea, India, Kenya, Somalia, South Sudan, Sudan, and Yemen. [9][10][11] Treatment responses to VL vary by region, and therefore the recommended treatments also differ. They have limited treatment options.…”

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confidence: 99%

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Drug repositioning to discover novel ornithine decarboxylase inhibitors against visceral leishmaniasis

Sheikh

Ansari²,

Hassan

et al. 2023

J of Molecular Recognition

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Visceral leishmaniasis (VL) is caused by Leishmania donovani (Ld), and most cases occur in Brazil, East Africa, and India. The treatment for VL is limited and has many adverse effects. The development of safer and more efficacious drugs is urgently needed. Drug repurposing is one of the best processes to repurpose existing drugs. Ornithine decarboxylase (ODC) is an important target against L. donovani in the polyamine biosynthesis pathway. In this study, we have modeled the 3D structure of ODC and performed high‐throughput virtual screening of 8630 ZINC database ligands against Leishmania donovani ornithine decarboxylase (Ld ODC), selecting 45 ligands based on their high binding score. It is further validated through molecular docking simulation and the selection of the top two lead molecules (ceftaroline fosamil and rimegepant) for Molecular Dynamics (MD) simulation, Density functional theory (DFT), and molecular mechanics generalized born surface area (MMGBSA) analysis. The results showed that the binding affinities of ceftaroline fosamil, and rimegepant are, respectively, −10.719 and 10.159 kcal/mol. The docking complexes of the two lead compounds, ceftaroline fosamil, and rimegepant, with the target ODC, were found stable during molecular dynamics simulations. Furthermore, the analysis of MMGBSA revealed that these compounds had a high binding free energy. The DFT analysis showed that the top lead molecules were more reactive than the standard drug (pentamidine). In‐silico findings demonstrated that ceftaroline fosamil, and rimegepant might be recognized as potent antagonists against ODC for the treatment of VL.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Drug repositioning to discover novel ornithine decarboxylase inhibitors against visceral leishmaniasis

Sheikh

Ansari²,

Hassan

et al. 2023

J of Molecular Recognition

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“…The RMSD value expresses the distance (Å) of the other binding points of the ligand from the reference point (the first site where the ligand binds). [56] The upper bound aligns every atom in one conformation with its counterpart in the other conformation, ignoring any symmetry. The lower one matches each atom in the conformation to its close atom in the other conformation.…”

Section: Molecular Docking Studies For Eo Content and B-dna Interactionmentioning

confidence: 99%

In vitro Genotoxicity and In silico Docking Analyses of the Essential Oils of Thuja orientalis

BOZARI

2024

Chemistry & Biodiversity

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Two main objectives were pursued to assess the reliability of Thuja orientalis essential oils (TOEO). The first objective was to extract TOEO, analyze them by GC‐MS, and determine their in vitro genotoxicity against selected plants using the RAPD‐PCR method. The second objective was to evaluate the in‐silico toxicity of TOEO. The binding sites and energies of each content was calculated against B‐DNA. In‐silico analyses were performed using a simulation program, AutoDock Vina, and Toxicity Estimation Software Tools. 3‐carene, cedrol, and 2‐pinene were identified as the predominant components. In vitro studies showed that the TOEO had a more significant impact on reducing genomic stability in wheat compared to the amaranth. The lowest stability was determined as 39.78% in wheat and 53.58% in amaranth. Cedrol (‐5,7 kcal/mol) and selinene (‐5,6 kcal/mol) exhibited the highest binding affinity. The toxicity test indicated that components other than cyclohexene may have toxic effects, none of them were predicted to be mutagenic, and LD50 (mol/kg) values could vary between 1.33 and 1.55.

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“…Figure 2 reports the possible mechanisms involved in the effectiveness of nanodrugs for prevention and treatment of COVID-19. The discovery and development of antiviral nanodrugs take enormous advantages from the employment of in silico and computational approaches, which are widely used today and strongly contribute to identification of the potential specific interactions between the virus’ macromolecules and the investigated antiviral systems [ 25 , 26 , 27 , 28 ]. There is also a growing interest in the design of coordination compounds to be used against COVID-19 infections [ 29 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

Nanoscale Technologies in the Fight against COVID-19: From Innovative Nanomaterials to Computer-Aided Discovery of Potential Antiviral Plant-Derived Drugs

et al. 2022

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The last few years have increasingly emphasized the need to develop new active antiviral products obtained from artificial synthesis processes using nanomaterials, but also derived from natural matrices. At the same time, advanced computational approaches have found themselves fundamental in the repurposing of active therapeutics or for reducing the very long developing phases of new drugs discovery, which represents a real limitation, especially in the case of pandemics. The first part of the review is focused on the most innovative nanomaterials promising both in the field of therapeutic agents, as well as measures to control virus spread (i.e., innovative antiviral textiles). The second part of the review aims to show how computer-aided technologies can allow us to identify, in a rapid and therefore constantly updated way, plant-derived molecules (i.e., those included in terpenoids) potentially able to efficiently interact with SARS-CoV-2 cell penetration pathways.

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Bioactive components of different nasal spray solutions may defeat SARS-Cov2: repurposing and in silico studies

Cited by 13 publications

References 55 publications

Drug repositioning to discover novel ornithine decarboxylase inhibitors against visceral leishmaniasis

Drug repositioning to discover novel ornithine decarboxylase inhibitors against visceral leishmaniasis

In vitro Genotoxicity and In silico Docking Analyses of the Essential Oils of Thuja orientalis

Nanoscale Technologies in the Fight against COVID-19: From Innovative Nanomaterials to Computer-Aided Discovery of Potential Antiviral Plant-Derived Drugs

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