<i>In silico</i> and POM analysis for potential antimicrobial agents of thymidine analogs by using molecular docking, molecular dynamics and ADMET profiling
Creators: name: Hosen, Mohammed A.
name: Qais, Faizan A.
name: Chtita, Samir
name: Rahman, Ibrahim A.
name: Almehdi, Ahmed M.
name: Ali, Ferdausi
name: Almalki, Faisal A.
name: Hadda, Taibi B.
name: Laaroussi, Hamid
name: Kawsar, Sarkar M. A.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified

description: Nucleoside analogs are an important, well-established class of clinically useful medicinal agents that exhibit potent antimicrobial activity. Thus, we designed to explore the synthesis and spectral characterization of 5′-<i>O-</i>(myristoyl)thymidine esters (2–6) for <i>in vitro</i> antimicrobial, molecular docking, molecular dynamics, SAR, and POM analyses. An unimolar myristoylation of thymidine under controlled conditions furnished the 5′-<i>O-</i>(myristoyl)thymidine and it was further converted into four 3′-<i>O</i>-(acyl)-5′-<i>O</i>-(myristoyl)thymidine analogs. The chemical structures of the synthesized analogs were ascertained by analyzing their physicochemical, elemental, and spectroscopic data. <i>In vitro</i> antimicrobial tests along with PASS, prediction indicated expectant antibacterial functionality of these thymidine esters compared to the antifungal activities. In support of this observation, their molecular docking studies have been performed against lanosterol 14α-demethylase (CYP51A1) and <i>Aspergillus flavus</i> (1R51) and significant binding affinities and non-bonding interactions were observed. The stability of the protein-ligand complexes was monitored by a 100 ns MD simulation and found the stable conformation and binding mode in a stimulating environment of thymidine esters. Pharmacokinetic predictions were studied to assess their ADMET properties and showed promising results <i>in silico</i>. SAR investigation indicated that acyl chains, lauroyl (C-12) and myristoyl (C-14), combined with deoxyribose, were most effective against the tested bacterial and fungal pathogens. The POM analyses provide the structural features responsible for their combined antibacterial/antifungal activity and provide guidelines for further modifications, with the aim of improving each activity and selectivity of designed drugs targeting potentially drug-resistant microorganisms. It also opens avenues for the development of newer antimicrobial agents targeting bacterial and fungal pathogens. A novel series of 5´-<i>O-</i>(myristoyl)thymidine derivatives were synthesized and characterized by FTIR, <sup>1</sup>H-NMR, 2D-NMR, <sup>13</sup>C-NMR, mass and physicochemical studies. In vitro antimicrobial susceptibility revealed that alkyl chain and aromatic substituents can improve the antimicrobial efficacy of the thymidine structure which was also supported by PASS enumeration. Molecular docking study against lanosterol 14α-demethylase (CYP51A1) and <i>Aspergillus flavus</i> (1R51) exhibited a promising binding score and interaction in the catalytic active site. A 100ns MD simulation revealed the stable conformation and binding pattern in a stimulating environment of thymidine derivatives. ADMET analysis revealed that most of the compounds are non-toxic and most of them have an inhibitory property to the CYP1A2 and CYP3A4 In silico and POM analyses provide substantial ideas about the structural features responsible for their combined antibacterial/antifungal agents and provide guidelines for further modifications.