Docking and molecular dynamics simulation for therapeutic repurposing in small cell lung cancer (SCLC) patients infected with COVID-19

Pingali, M. Shivapriya; Singh, Anirudh; Singh, Vishal; Sahoo, Amaresh Kumar; Varadwaj, Pritish Kumar; Samanta, Sintu Kumar

doi:10.1080/07391102.2021.2002719

Cited by 13 publications

(5 citation statements)

References 34 publications

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“…Due to the lack of a standard therapeutic option, medication repurposing is now viable for COVID-19 patients with GC. Patients with GC infected with SARS-CoV-2 may take advantage of these medications [39].…”

Section: Discussionmentioning

confidence: 99%

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A review on in silico virtual screening methods in COVID-19 using anticancer drugs and other natural/chemical inhibitors

Sokouti

2023

Exploration of Targeted Anti-Tumor Therapy

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The present coronavirus disease 2019 (COVID-19) pandemic scenario has posed a difficulty for cancer treatment. Even under ideal conditions, malignancies like small cell lung cancer (SCLC) are challenging to treat because of their fast development and early metastases. The treatment of these patients must not be jeopardized, and they must be protected as much as possible from the continuous spread of the COVID-19 infection. Initially identified in December 2019 in Wuhan, China, the contagious coronavirus illness 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Finding inhibitors against the druggable targets of SARS-CoV-2 has been a significant focus of research efforts across the globe. The primary motivation for using molecular modeling tools against SARS-CoV-2 was to identify candidates for use as therapeutic targets from a pharmacological database. In the published study, scientists used a combination of medication repurposing and virtual drug screening methodologies to target many structures of SARS-CoV-2. This virus plays an essential part in the maturation and replication of other viruses. In addition, the total binding free energy and molecular dynamics (MD) modeling findings showed that the dynamics of various medications and substances were stable; some of them have been tested experimentally against SARS-CoV-2. Different virtual screening (VS) methods have been discussed as potential means by which the evaluated medications that show strong binding to the active site might be repurposed for use against SARS-CoV-2.

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Section: Discussionmentioning

confidence: 99%

“…Molecular mechanics with generalised born and surface area (MM-GBSA) solvation was applied to the compounds that had the most incredible docking findings. Using a default configuration of molecular dynamics (MD) software (i.e., Desmond), the authors simulated the stability of the SARS-CoV-2-RdRp-NiRAN domain-ligand complex [39].…”

Section: Cancer and Covid-19mentioning

confidence: 99%

A review on in silico virtual screening methods in COVID-19 using anticancer drugs and other natural/chemical inhibitors

Sokouti

2023

Exploration of Targeted Anti-Tumor Therapy

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“…All the system was equilibrated for 100 ps in the NVT and NPT equilibration processes. The Nose–Hoover thermostat and the Parrinello–Rahman barostat were used to control the temperature and pressure of the system, respectively. , Finally, molecular dynamics simulations were run for 100 ns, and all trajectories were saved at each 10 ps under periodic boundary condition (PBC) …”

Section: Methodsmentioning

confidence: 99%

“…28,29 Finally, molecular dynamics simulations were run for 100 ns, and all trajectories were saved at each 10 ps under periodic boundary condition (PBC). 30 2.7. In Vitro Analysis for Interaction of DNA with AMPs.…”

Section: Steered MDmentioning

confidence: 99%

Finding Novel AMPs Secreted from the Human Microbiome as Potent Antibacterial and Antibiofilm Agents and Studying Their Synergistic Activity with Ag NCs

Singh,

Amod,

Mulpuru

et al. 2023

ACS Appl. Bio Mater.

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Due to the enhanced resistance of bacteria to antibiotics, researchers always try to find effective alternatives to treat drug-resistant bacterial infections. In this context, we have explored antimicrobial peptides (AMPs), which are a broad class of small peptide molecules, and investigated their efficacy as potent antibacterial and antibiofilm agents. AMPs can cause cell death either through disruption of the cell membrane or by inhibiting vital intracellular functions, by binding to RNA, DNA, or intracellular components upon transversion through the cell membrane. We attempted to find potent intracellular cationic AMPs that can demonstrate antibacterial activity through interaction with DNA. As a source of AMPs, we have utilized those that are secreted from the human microbiome with the anticipation that these will be non-toxic in nature. Out of the total 1087 AMPs, 27 were screened on the basis of amino acid length and efficacy to cross the cell membrane barrier. From the list of 27 peptides, 4 candidates were selected through the docking score of these peptides with the DNA binding domain of H2A proteins. Further, the molecular dynamics simulation analysis demonstrated that 2 AMPs, i.e., peptides 7 and 25, are having considerable membrane permeation and DNA binding ability. Further, the in vitro analysis indicated that both peptides 7 and 25 could exhibit potent antibacterial and antibiofilm activities. In order to further enhance the antibiofilm potency, the above AMPs were used as supplements to silver nanoclusters (Ag NCs) to get synergistic activity. The synergistic activity of Ag NCs was found to be significantly increased with both the above AMPs.

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“…To conduct sitespecifc docking, a cocrystal ligand was selected to generate a receptor grid with internal coordinate values of X, Y, and Z as 6.04, −10.31, and −11.52, respectively. Phytochemicals from the L. siceraria extract were prepared by the LigPrep tool in Maestro and docked to the receptor using Glide [21]. Te docking poses were analyzed based on the glide score after diferent ionization states were generated at pH 7 by Epik, and stereoisomers were generated with the OPLS_2005 force feld.…”

Section: Molecular Docking and Simulation Studiesmentioning

confidence: 99%

Hypolipidemic Effect of Chloroform Extract of Lagenaria siceraria: Potential Inhibitory Activity of Phytochemicals Targeting the HMG-CoA Reductase Revealed by Molecular Docking and Simulation Studies

Kanwal,

Ahmed,

Ur-Rehman

et al. 2023

Journal of Chemistry

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Conventional systems of medicine play a crucial role in maintaining healthcare. Herbal medicines are intact and less harmful to human beings than synthetic medicines. This study aimed to investigate the phytochemicals and in vivo hypolipidemic effect of chloroform extract of Lagenaria siceraria in Triton X-100 (100 mg/kg body weight) induced hyperlipidemic Wistar rats. The phytochemical characterization and estimation were performed on the base of the GC-MS approach. The Lagenaria siceraria extract (250 and 500 mg/kg bw) was administered orally to hyperlipidemic-induced rats for 7 days to examine its hypolipidemic activity. The experimental animals did not display any acute toxicity. Atorvastatin (10 mg/kg bw) was used as a standard drug. Administration of Lagenaria siceraria extract lowers the total cholesterol (TC), triglyceride (TG), and low-density lipoproteins-cholesterol (LDL-C) levels whereas elevating the high-density lipoproteins-cholesterol (HDL-C) level. Histological studies of the liver and heart also showed the hypolipidemic effect of the extract. On the 8th day, no inflammation of the liver, myocardial necrosis, fibrosis, or atypia was seen. Furthermore, binding affinity and plausible binding mode of stigmastan-3-ol with HMG-CoA reductase were predicted by molecular docking studies which showed the same interaction patterns as atorvastatin. Moreover, the docking results were refined by 100 ns MD simulations which revealed that stigmastan-3-ol extract formed a stable complex with protein and did not induce any conformational changes in protein structure.

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Docking and molecular dynamics simulation for therapeutic repurposing in small cell lung cancer (SCLC) patients infected with COVID-19

Cited by 13 publications

References 34 publications

A review on in silico virtual screening methods in COVID-19 using anticancer drugs and other natural/chemical inhibitors

A review on in silico virtual screening methods in COVID-19 using anticancer drugs and other natural/chemical inhibitors

Finding Novel AMPs Secreted from the Human Microbiome as Potent Antibacterial and Antibiofilm Agents and Studying Their Synergistic Activity with Ag NCs

Hypolipidemic Effect of Chloroform Extract of Lagenaria siceraria: Potential Inhibitory Activity of Phytochemicals Targeting the HMG-CoA Reductase Revealed by Molecular Docking and Simulation Studies

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