Computer-based identification of potential compounds from<i>Salviae miltiorrhizae</i>against Neirisaral adhesion A regulatory protein

Rafi, Md. Oliullah; Al-Khafaji, Khattab; Tok, Tuğba Taşkın; Rahman, Shahedur

doi:10.1080/07391102.2020.1856189

Cited by 14 publications

(6 citation statements)

References 41 publications

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“…All the values obtained from the ADMET analysis for our studied compounds are presented in Table 3. Lipinski's rule of five is a widely used method for drug development [49]. All compounds in our study complied with Lipinski's rules of five.…”

Section: Admet Properties and Drug-likeness Model Scorementioning

confidence: 86%

In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2

El-Mageed

Abdelrheem

Rafi³

et al. 2021

Biologics

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The ongoing pandemic situation of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a global threat to both the world economy and public health. Therefore, there is an urgent need to discover effective vaccines or drugs to fight against this virus. The flavonoids and their medicinal plant sources have already exhibited various biological effects, including antiviral, anti-inflammatory, antioxidant, etc. This study was designed to evaluate different flavonoids from medicinal plants as potential inhibitors against the spike protein (Sp) and main protease (Mpro) of SARS-CoV-2 using various computational approaches such as molecular docking, molecular dynamics. The binding affinity and inhibitory effects of all studied flavonoids were discussed and compared with some antiviral drugs that are currently being used in COVID-19 treatment namely favipiravir, lopinavir, and hydroxychloroquine, respectively. Among all studies flavonoids and proposed antiviral drugs, luteolin and mundulinol exhibited the highest binding affinity toward Mpro and Sp. Drug-likeness and ADMET studies revealed that the chosen flavonoids are safe and non-toxic. One hundred ns-MD simulations were implemented for luteolin-Mpro, mundulinol-Mpro, luteolin-Sp, and mundulinol-Sp complexes and the results revealed strong stability of these flavonoid-protein complexes. Furthermore, MM/PBSA confirms the stability of luteolin and mundulinol interactions within the active sites of this protein. In conclusion, our findings reveal that the promising activity of luteolin and mundulinol as inhibitors against COVID-19 via inhibiting the spike protein and major protease of SARS CoV-2, and we urge further research to achieve the clinical significance of our proposed molecular-based efficacy.

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Section: Admet Properties and Drug-likeness Model Scorementioning

confidence: 86%

In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2

El-Mageed

Abdelrheem

Rafi³

et al. 2021

Biologics

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“…The normal simulation time step (1.25 fs) was maintained, and simulated trajectories were set at 100-ps intervals for analysis (Krieger and Vriend 2015 ). Finally, MD simulations of the vaccine/TLR4 and vaccine/TLR2 complexes were run for 500 ns, and root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) were estimated to understand the conformational variations and stability of the complex (Rafi et al 2022b ). RMSD is calculated using the following formula: where R i represents the vector that links the positions of atom i (out of N atoms) in the reference snapshot to the current snapshot after optimal superposition.…”

Section: Methodsmentioning

confidence: 99%

A subunit vaccine against pneumonia: targeting Streptococcus pneumoniae and Klebsiella pneumoniae

Rafi¹,

Al-Khafaji²,

Mandal

et al. 2023

Netw Model Anal Health Inform Bioinforma

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Community-acquired pneumonia is primarily caused by Streptococcus pneumoniae and Klebsiella pneumoniae , two pathogens that have high morbidity and mortality rates. This is largely due to bacterial resistance development against current antibiotics and the lack of effective vaccines. The objective of this work was to develop an immunogenic multi-epitope subunit vaccine capable of eliciting a robust immune response against S. pneumoniae and K. pneumoniae . The targeted proteins were the pneumococcal surface proteins (PspA and PspC) and choline-binding protein (CbpA) of S. pneumoniae and the outer membrane proteins (OmpA and OmpW) of K. pneumoniae . Different computational approaches and various immune filters were employed for designing a vaccine. The immunogenicity and safety of the vaccine were evaluated by utilizing many physicochemical and antigenic profiles. To improve structural stability, disulfide engineering was applied to a portion of the vaccine structure with high mobility. Molecular docking was performed to examine the binding affinities and biological interactions at the atomic level between the vaccine and Toll-like receptors (TLR2 and 4). Further, the dynamic stabilities of the vaccine and TLRs complexes were investigated by molecular dynamics simulations. While the immune response induction capability of the vaccine was assessed by the immune simulation study. Vaccine translation and expression efficiency was determined through an in silico cloning experiment utilizing the pET28a(+) plasmid vector. The obtained results revealed that the designed vaccine is structurally stable and able to generate an effective immune response to combat pneumococcal infection. Supplementary Information The online version contains supplementary material available at 10.1007/s13721-023-00416-3.

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“…Dynamic simulations are vital for researchers in the field of computer-assisted drug discovery. 24,29 Therefore, we use molecular dynamics simulations to provide information on structural stability. 32 Molecular dynamics simulation consists of a set of standard protocols of GROMACS 2018 33 and an application.…”

Section: Molecular Dynamics Simulation Methodsmentioning

confidence: 99%

“…Herein, ZnPc-1 (Zinc( ii ) (9(10),16(17),23(24)-tri-( tert -butyl)-2(3) (2-methyl-1Himidazol-1-yl)-phthalocyaninato-(2-)-N, 26 N, 27 N, 28 N 29 ) and ZnPc-2 (C 45 H 40 N 8 O 2 Zn) were immobilized onto TiO 2 nanoparticles from imidazole and carboxylic acid anchoring groups and the antibiofilm/antibacterial properties of ZnPc-1/TiO 2 and ZnPc-2/TiO 2 on E. coli and S. aureus were investigated under the irradiation of white LED light. The ZnPcs used in this article were used for the first time in an antibacterial study.…”

Section: Introductionmentioning

confidence: 99%

Superior photo-induced antibacterial/antibiofilm activities of ZnPcs/TiO₂ and computational simulation studies

Özcan,

Çekceoğlu,

Al-Khafaji

et al. 2023

J. Mater. Chem. B

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Computer-based identification of potential compounds fromSalviae miltiorrhizaeagainst Neirisaral adhesion A regulatory protein

Cited by 14 publications

References 41 publications

In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2

In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2

A subunit vaccine against pneumonia: targeting Streptococcus pneumoniae and Klebsiella pneumoniae

Superior photo-induced antibacterial/antibiofilm activities of ZnPcs/TiO₂ and computational simulation studies

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Computer-based identification of potential compounds fromSalviae miltiorrhizaeagainst Neirisaral adhesion A regulatory protein

Cited by 14 publications

References 41 publications

In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2

In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2

A subunit vaccine against pneumonia: targeting Streptococcus pneumoniae and Klebsiella pneumoniae

Superior photo-induced antibacterial/antibiofilm activities of ZnPcs/TiO2 and computational simulation studies

Contact Info

Product

Resources

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Superior photo-induced antibacterial/antibiofilm activities of ZnPcs/TiO₂ and computational simulation studies