Synthesis, antimicrobial, molecular docking and molecular dynamics studies of lauroyl thymidine analogs against SARS-CoV-2: POM study and identification of the pharmacophore sites

Hosen, Anowar; Munia, Nasrin S; Al‐Ghorbani, Mohammed; Baashen, Mohammed; Almalki, Faisal A.; Hadda, Taîbi Ben; Ali, Ferdausi; Mahmud, Shafi; Saleh, Md. Abu; Laaroussi, Hamid; Kawsar, Sarkar M. A.

doi:10.1016/j.bioorg.2022.105850

Cited by 19 publications

(13 citation statements)

References 63 publications

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“…The assessment of a compound's potential as a drug candidate involves the computation of a drug score (DS), which integrates drug-likeness, cLogP, TPSA, and molecular weight derived from an antifungal (O δ− , O δ− ) pharmacophore. The hypothesis site is supported by atomic charge analysis, as reported in Hosen et al (2022).…”

Section: Molinspiration Analysissupporting

confidence: 63%

Black seeds (Nigella sativa) for the management of Dengue viral disease: POM analyses for the identification of new antiviral pharmacophore sites

Maideen

Hadda

Almalki

et al. 2023

Preprint

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The number of Dengue virus (DENV) infection cases has increased dramatically over the past two decades with an estimate of 3.9 billion cases across the globe are potentially at risk. Patients with a DENV infection are managed symptomatically and by supportive care since there is no approved antiviral drug yet for its management. On the other hand, Nigella sativa has been highlighted as a potential antiviral particularly against DENV. Hence, the anti-DENV potential of N. sativa is analyzed in this review using major databases including Medline/PMC/PubMed, Scopus, EBSCO, EMBASE, Google Scholar, and Science Direct. Moreover, the Petra/Osiris/Molinspiration (POM) bioinformatics platform-2019 was used to analyze a series of compounds (1-15) identified in N. sativa(the Black seeds) to identify those with promising antiviral pharmacophore sites. Preliminary research showed the potential of N. sativa in the control of Aedes aegypti mosquitoes and the enhancement of platelet counts. Besides, several clinical, animal, in vitro and in vivo studies have demonstrated the antiviral, immunomodulatory and antiinflammatory properties of N. sativa. Furthermore, calculation of the physico-chemical properties of N. sativa compounds using POM analyses indicated that dithymoquinone possesses a potential antiviral activity with two (O, O’) pharmacophore sites. As a result, N. sativa can be employed as an adjuvant/ supportive therapy in the management of DENV infection in the early stages of the illness. Furthermore, N. sativa can be a source of new lead anti-DENV drug.

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Section: Molinspiration Analysissupporting

confidence: 63%

Black seeds (Nigella sativa) for the management of Dengue viral disease: POM analyses for the identification of new antiviral pharmacophore sites

Maideen

Hadda

Almalki

et al. 2023

Preprint

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“…This validation step bolsters confidence in the reliability of the molecular docking technique and its utility in drug discovery and protein-ligand interaction studies. [189] Hosen et al [147] Scheme 11, in their study aimed to understand the binding behavior of thymidine analogs with the main SARS-CoV-2 protease (6LU7, 6Y84, 7BQY) using molecular docking techniques. [190,191] The results showed that aromatic analogs had superior binding scores compared to those of their aliphatic counterparts.…”

Section: Computational Studies Revealing Potential Sars-cov-2 Main Pr...mentioning

confidence: 99%

“…Hosen et al [147] . Scheme 11, in their study aimed to understand the binding behavior of thymidine analogs with the main SARS‐CoV‐2 protease (6LU7, 6Y84, 7BQY) using molecular docking techniques [190,191] .…”

Section: Computational Studies Revealing Potential Sars‐cov‐2 Main Pr...mentioning

confidence: 99%

“…This information provides valuable insights into the structural dynamics and stability of these complexes, which is essential for understanding their potential as antiviral agents. [195,196] According to Maowa et al, [197] thirteen uridine derivatives with varying amounts of aromatic and aliphatic chains (141)(142)(143)(144)(145)(146)(147)(148)(149)(150)(151)(152)(153) were synthesized and investigated (Figure 15). Mulliken population analysis and natural bond orbital methods were used to calculate the partial charges of atoms involved in the drug-protein interactions.…”

Section: Computational Studies Revealing Potential Sars-cov-2 Main Pr...mentioning

confidence: 99%

“… The molecular dynamics simulation trajectories from 100‐ns simulation time for compounds 122, 123 and 126 : ( a ) root mean square deviation of the C‐alpha atoms; ( b ) solvent accessible surface area of the docked complex to understand the change in protein area; ( c ) radius of gyration of the complexes; ( d ) hydrogen bond of the complexes; ( e ) root mean square fluctuation; and ( f ) free energy of the complexes [147] …”

Section: Computational Studies Revealing Potential Sars‐cov‐2 Main Pr...mentioning

confidence: 99%

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This review article aims to significantly advance the scientific community's efforts to develop effective nucleoside‐based drugs for treating severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and other emerging infectious diseases. This study concentrates on the main viral protease (Mpro) and explores nucleoside‐based compounds as potential therapeutic agents. This investigation investigated the impact of acylation‐induced modifications on the nucleoside hydroxyl group and subsequent properties. Nucleoside analogs, which are recognized for their diverse biochemical properties, were synthesized and rigorously screened to evaluate their antimicrobial efficacy. In the domain of pharmaceutical research, computational pharmacokinetics has emerged as a critical tool, especially in the pursuit of nucleoside analogs as potential therapeutics. In silico methods aid in predicting pharmacokinetic traits, interactions with crucial enzymes, and the stability of these analogs in biological environments, thereby streamlining drug design and reducing experimental costs. Concurrently, computational studies revealed the intricate interactions between the analogs and the active site of the main protease. The amalgamation of experimental screening and computational insights underscores the emergence of potent nucleoside candidates with inhibitory activity against SARS‐CoV‐2 Mpro. Additionally, this review integrates computational studies that provide valuable insights into the interactions between nucleoside analogs and the main protease of SARS‐CoV‐2.

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Synthesis, antimicrobial, molecular docking and molecular dynamics studies of lauroyl thymidine analogs against SARS-CoV-2: POM study and identification of the pharmacophore sites

Cited by 19 publications

References 63 publications

Black seeds (Nigella sativa) for the management of Dengue viral disease: POM analyses for the identification of new antiviral pharmacophore sites

Black seeds (Nigella sativa) for the management of Dengue viral disease: POM analyses for the identification of new antiviral pharmacophore sites

Nucleoside‐Based Drug Target with General Antimicrobial Screening and Specific Computational Studies against SARS‐CoV‐2 Main Protease

Natural Isatin Derivatives Against Black Fungus: In Silico Studies

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