An insight into paracetamol and its metabolites using molecular docking and molecular dynamics simulation.

Abstract:

:Paracetamol is a relatively safe analgesia/antipyretic drug without the risks of addiction, dependence, tolerance, and withdrawal when used alone. However, when administrated in an opioid/paracetamol combination product, which often contains a large quantity of paracetamol, it can be potentially dangerous due to the risk of hepatotoxicity. Paracetamol is known to be metabolized into N-(4-hydroxyphenyl)-arachidonamide (AM404) via fatty acid amide hydrolase (FAAH) and into N-acetyl-p-benzoquinone imine (NAPQI) via cytochrome P450 (CYP) enzymes. However, the underlying mechanism of paracetamol is still unclear. In addition, paracetamol has the potential to interact with other drugs that are also involved with CYP family enzymes (inducer/inhibitor/substrate), an example being illicit drugs. In our present work, we looked into the relationship between paracetamol and its metabolites (AM404 and NAPQI) using molecular docking and molecular dynamics (MD) simulations. We first carried out a series of molecular docking studies between paracetamol/AM404/NAQPI and their reported targets, including CYP 2E1, FAAH, TRPA1, CB1, and TRPV1. Subsequently, we performed MD simulations and energy decomposition for CB1-AM404, TRPV1-AM404, and TRPV1-NAPQI for further investigation of the dynamics interactions. Finally, we summarized and discussed the reported drug-drug interactions between paracetamol and central nervous system drugs, especially illicit drugs. Overall, we are able to provide new insights into the structural and functional roles of paracetamol and its metabolites that can inform the potential prevention and treatment of paracetamol overdose. Graphical abstract Paracetamol and its metabolites.

journal_name

J Mol Model

authors

Wang Y,Lin W,Wu N,He X,Wang J,Feng Z,Xie XQ

doi

10.1007/s00894-018-3790-9

subject

Has Abstract

pub_date

2018-08-18 00:00:00

pages

243

issue

9

eissn

1610-2940

issn

0948-5023

pii

10.1007/s00894-018-3790-9

journal_volume

24

pub_type

杂志文章
  • Three-dimensional solution structure of Tropidechis carinatus venom extract trocarin: a structural homologue of Xa and prothrombin activator.

    abstract::Trocarin belongs to group D of prothrombin activators derived from snake venom of Tropidechis carinatus and is a rich non-hepatic source of Xa, the only known hepatic prothrombin activator. The structural and functional similarity with Xa makes trocarin an interesting target for exploring the structure-functional rela...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-002-0099-4

    authors: Venkateswarlu D,Krishnaswamy S,Darden TA,Pedersen LG

    更新日期:2002-10-01 00:00:00

  • Theoretical insights into thermal cyclophanediene to dihydropyrene electrocyclic reactions; a comparative study of Woodward Hoffmann allowed and forbidden reactions.

    abstract::The thermally allowed electrocyclic reaction syn-cyclophanediene (CPD) to dihydropyrene (DHP) was compared with the disallowed thermal electrocyclic reaction in anti CPD through density functional theory (DFT) calculations at the B3LYP/6-31 + G(d) level. Moreover, the results were also compared with the electrocycliza...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-2948-6

    authors: Saima B,Khan A,Nisa RU,Mahmood T,Ayub K

    更新日期:2016-04-01 00:00:00

  • Conformational and NMR study of some furan derivatives by DFT methods.

    abstract::4'-substituted neutral/protonated furfurylidenanilines and trans-styrylfurans are able to exist in two different conformations related to the rotation around the furan ring-bridge double bond. In this work, the equilibrium geometry and the corresponding rotational barrier of the benzene ring for each furan derivative ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1964-z

    authors: Santos-Carballal D,Suardíaz R,Crespo-Otero R,González L,Pérez CS

    更新日期:2013-10-01 00:00:00

  • TD-DFT investigation of D-π-A organic dyes with thiophene moieties as π-spacers for use as sensitizers in DSSCs.

    abstract::The geometrical, conformational, and electronic properties of a series of D-π-A metal-free dyes designed for use as sensitizers in DSSCs were studied using DFT and TD-DFT methods. A substituted triphenylamine moiety was used as the donor group and 2-cyanoacrylic acid as the acceptor group in these dyes. They also cont...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-2978-0

    authors: Hasanein AA,Elmarassi YR,Kassem EN

    更新日期:2016-05-01 00:00:00

  • Density functional studies of closed-shell attractions of S(AuPH3)2 and HS(AuPH3)2 + and their dimers.

    abstract::With the help of quantum chemical calculations, S(AuPH3)2, [HS(AuPH3)2]+ and their dimers have been examined by using scalar-relativistic theory. In agreement with experimental data, [HS(AuPH3)2 +]2 is a C(2h) structure. However, [S(AuPH3)2]2 is predicted to favor a D(2d) structure. Experimental structure parameters o...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-008-0427-4

    authors: Fang H,Zhang XG,Wang SG

    更新日期:2009-05-01 00:00:00

  • Chemical sensors based on N-substituted polyaniline derivatives: reactivity and adsorption studies via electronic structure calculations.

    abstract::Conjugated organic polymers represent an important class of materials for varied technological applications including in active layers of chemical sensors. In this context, polyaniline (PANI) derivatives are promising candidates, mainly due to their high chemical stability, good processability, versatility of synthesi...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-018-3660-5

    authors: Mandú LO,Batagin-Neto A

    更新日期:2018-06-09 00:00:00

  • Predicting functional residues of the Solanum lycopersicum aspartic protease inhibitor (SLAPI) by combining sequence and structural analysis with molecular docking.

    abstract::The Solanum lycopersicum aspartic protease inhibitor (SLAPI), which belongs to the STI-Kunitz family, is an effective inhibitor of the aspartic proteases human cathepsin D and Saccharomyces proteinase A. However, in contrast with the large number of studies on the inhibition mechanism of the serine proteases by the ST...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1290-2

    authors: Guerra Y,Valiente PA,Berry C,Pons T

    更新日期:2012-06-01 00:00:00

  • Core-dependent and ligand-dependent relativistic corrections to the nuclear magnetic shieldings in MH4-n Y n (n = 0-4; M = Si, Ge, Sn, and Y = H, F, Cl, Br, I) model compounds.

    abstract::The nuclear magnetic shieldings of Si, Ge, and Sn in MH(4-n) Y(n) (M = Si, Ge, Sn; Y = F, Cl, Br, I and n = 1-4) molecular systems are highly influenced by the substitution of one or more hydrogens by heavy-halogen atoms. We applied the linear response elimination of small components (LRESC) formalism to calculate tho...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2417-z

    authors: Maldonado AF,Aucar GA,Melo JI

    更新日期:2014-09-01 00:00:00

  • Stability and molecular properties of the boron-nitrogen alternating analogs of azulene and naphthalene: a computational study.

    abstract::In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investi...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3279-y

    authors: Catão AJ,López-Castillo A

    更新日期:2017-04-01 00:00:00

  • Anesthetic activity and the electrostatic potential (revisited).

    abstract::A survey of the fascinating history of anesthetics and the many critical findings that have improved our understanding of anesthetic activity is followed by an expanded analysis of the electrostatic potentials of 27 molecules and two noble gases with anesthetic activities ranging from high to totally inactive. We agai...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3547-x

    authors: Shields ZP,Seybold PG,Murray JS

    更新日期:2017-12-19 00:00:00

  • Computational simulations of structural role of the active-site W374C mutation of acetyl-coenzyme-A carboxylase: multi-drug resistance mechanism.

    abstract::Herbicides targeting grass plastidic acetyl-CoA carboxylase (ACCase, EC 6.4.1.2) are selectively effective against graminicides. The intensive worldwide use of this herbicide family has selected for resistance genes in a number of grass weed species. Recently, the active-site W374C mutation was found to confer multi-d...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-010-0742-4

    authors: Zhu XL,Yang WC,Yu NX,Yang SG,Yang GF

    更新日期:2011-03-01 00:00:00

  • DFT study on tautomerism and natural bond orbital analysis of 4-substituted 1,2,4-triazole and its derivatives: solvation and substituent effects.

    abstract::Density functional theory investigations at the DFT-B3LYP/6-311++G** theoretical level employed to determine the tautomerism, substituent effects of 4-substituted 4-amino-5-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, and its derivatives (4-R-H, 4-R-CH3, 4-R-F, 4-R-NO2) in the selected solvent (acetone, acetonitrile...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-4316-9

    authors: Shiroudi A,Safaei Z,Kazeminejad Z,Repo E,Pourshamsian K

    更新日期:2020-02-13 00:00:00

  • Theoretical study of the thermodynamic and burning properties of oxygen-rich hydrazine derivatives--green and powerful oxidants for energetic materials.

    abstract::A series of no-chlorine and oxygen-rich hydrazine derivatives (hydrazine modified with -NO₂ and NO₃(-) groups) was designed and optimized to obtain molecular geometries and electronic structures at density functional theory-B3PW91/6-311++G(3df,3pd) level. Some important properties such as bond dissociation enthalpy, d...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1792-1

    authors: Wang PC,Zhu ZS,Xu J,Zhao XJ,Lu M

    更新日期:2013-06-01 00:00:00

  • Tunable electronic properties of ultra-thin boron-carbon-nitrogen heteronanotubes for various compositions.

    abstract::A first-principles calculation was carried out to investigate the stability and electronic properties of ultra-thin Cx(BN)y heteronanotubes which were composed by joining pure CNT and BNNT segments with different composition and configurations. We found that the stability of Cx(BN)y heteronanotubes is increased with t...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2371-9

    authors: Wang Y,Huang G,Zhang J,Shao Q

    更新日期:2014-08-01 00:00:00

  • Buckling analysis of defective cross-linked functionalized single- and double-walled carbon nanotubes with polyethylene chains using molecular dynamics simulations.

    abstract::Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two d...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-3157-z

    authors: Ajori S,Ansari R,Parsapour H

    更新日期:2016-12-01 00:00:00

  • Theoretical prediction of the trigger linkages, surface electrostatic potentials, and explosive sensitivities of 1,4-dinitroimidazole-N-oxide in the external electric fields.

    abstract::In order to introduce effectively the external electric fields into the explosive systems, the change trends of the strengths of trigger linkages, nitro group charges, and explosive sensitivities of 1,4-dinitroimidazole-N-oxide (1,4-DNIO) were investigated in the external electric fields at the B3LYP/6-311++G(2d,p) an...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4258-2

    authors: Wang BG,Ren FD,Wang Y

    更新日期:2019-11-28 00:00:00

  • 3D-QSAR studies of orvinol analogs as kappa-opioid agonists.

    abstract::Orvinols are potent analgesics that target opioid receptors. However, their analgesic mechanism remains unclear and no significant preference for subtype opioid receptor has been achieved. In order to find new orvinols that target the kappa-receptor, comparative 3D-QSAR studies were performed on 26 orvinol analogs usi...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-005-0084-9

    authors: Li W,Tang Y,Xie Q,Sheng W,Qiu ZB

    更新日期:2006-09-01 00:00:00

  • Computation of multicenter overlap integrals with Slater-type orbitals using psi(alpha)-ETOs.

    abstract::Multicenter overlap integrals appearing in the evaluation of multicenter-multielectron integrals of central and noncentral interaction potentials are calculated using complete orthonormal sets of psi(alpha)-ETOs (alpha=1, 0, -1, -2,...). The final results are expressed in terms of two-center overlap integrals between ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-003-0151-z

    authors: Guseinov I,Aydin R,Mamedov B

    更新日期:2003-10-01 00:00:00

  • Hydrogen-mediated Stone-Wales isomerization of dicyclopenta[de,mn]anthracene.

    abstract::The mechanism of transformation of two radicals (R1p and R1i) obtained by addition of a hydrogen atom to an external and internal carbon atom of dicyclopenta[de,mn]anthracene (P1) was investigated. Two pathways were revealed. The first mechanism is a one-step process, whereas the second mechanism includes two transiti...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-010-0669-9

    authors: Stanković S,Marković S,Gutman I,Sretenović S

    更新日期:2010-09-01 00:00:00

  • Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study.

    abstract::Hydrogenoxalate (charge -1) and oxalate (charge -2) anions and their solvated forms were studied by various computational techniques. Ab initio quantum chemical calculations in gas phase, in implicit solvent and microsolvated (up to 32 water molecules) environment were performed in order to explore a potential energy ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-3075-0

    authors: Kroutil O,Minofar B,Kabeláč M

    更新日期:2016-09-01 00:00:00

  • Bonding analysis of the donor-acceptor sandwiches CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η⁵-C₅H₅).

    abstract::The nature of E-M bonds in CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η (5)-C5H5) donor-acceptor sandwiches was studied using the atoms in molecules (AIM) theory, electron localization function (ELF), energy decomposition analysis (EDA), and natural bond orbital analysis (NBO) methods. Both topological and orbital an...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2455-6

    authors: Huo S,Meng D,Zhang X,Meng L,Li X

    更新日期:2014-10-01 00:00:00

  • Monoterpenes as nitrofurantoin resistance modulating agents: minimal structural requirements, molecular dynamics simulations, and the effect of piperitone on the emergence of nitrofurantoin resistance in Enterobacteriaceae.

    abstract::The effects of different monoterpenes and 2-cyclohexen-1-one on the antibacterial activity of nitrofurantoin against resistant Enterobacter cloacae, were compared and the minimal structural component of monoterpene required for the highest level of resistance-modulating activity was determined. Subinhibitory concentra...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-015-2741-y

    authors: Shahverdi AR,Mirzaie S,Rafii F,Kakavand M,Foroumadi A

    更新日期:2015-08-01 00:00:00

  • Bloch Oscillations in Fibonacci lattices: polaron formation.

    abstract::We investigated the dynamics of an electron subjected to a uniform electric field in the scope of a tight-binding electron-phonon interacting approach. We aimed at describing the transport in a one-dimensional lattice in which the on-site energies are distributed according to a Fibonacci sequence. Within this physical...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-3972-0

    authors: de Brito PE,Enders BG,Ribeiro LA Jr,Nazareno HN

    更新日期:2019-03-28 00:00:00

  • Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I).

    abstract::Quantum chemical calculations are performed to study the interplay between halogen⋯nitrogen and halogen⋯carbene interactions in NCX⋯NCX⋯CH2 complexes, where X = F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that t...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1983-9

    authors: Esrafili MD,Mohammdain-Sabet F,Esmailpour P

    更新日期:2013-11-01 00:00:00

  • Structure-based discovery of small molecule APC-Asef interaction inhibitors: In silico approaches and molecular dynamics simulations.

    abstract::Colorectal cancer, which is considered one of the leading causes of mortality worldwide, develops through the formation of benign polyps on the inner colon or rectum wall. Truncations in adenomatous polyposis coli (APC) gene lead to the spread of the disease in the entire colon region when combined with the guanine nu...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04467-5

    authors: Jadav SS,Macalino SJY,Alluri R

    更新日期:2020-07-16 00:00:00

  • Free-energy force-field three-dimensional quantitative structure-activity relationship analysis of a set of p38-mitogen activated protein kinase inhibitors.

    abstract::The p38-mitogen-activated protein kinases (p38-MAPKs) belong to a family of serine-threonine kinases activated by pro-inflammatory or stressful stimuli that are known to be involved in several diseases. Their biological importance, related to the release of inflammatory pro-cytokines such as tumor necrosis factor-alph...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-006-0106-2

    authors: Romeiro NC,Albuquerque MG,de Alencastro RB,Ravi M,Hopfinger AJ

    更新日期:2006-09-01 00:00:00

  • A molecular-dynamics simulation study of diffusion of a single model carbonic chain on a graphite (001) surface.

    abstract::Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the sol...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-005-0064-0

    authors: Yang H,Lu ZY,Li ZS,Sun CC

    更新日期:2006-03-01 00:00:00

  • Properties and applications of the average interparticle distance.

    abstract::The first and second moment operators are used to define the origin invariant shape and size of a molecule or functional group, as well as expressions for the distance between two electrons and the distance between an electron and a nucleus. The measure of molecular size correlates quite well with an existing theoreti...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-008-0391-z

    authors: Hollett JW,Poirier RA

    更新日期:2009-06-01 00:00:00

  • A comparative study on the B12N12, Al12N12, B12P12 and Al12P12 fullerene-like cages.

    abstract::The stability, geometry and electronic structure of the title nanoclusters were compared by using density functional theory (DFT) calculations. Their electrical property analysis showed that the relative magnitude of the HOMO-LUMO gaps (eV) that are average values from the calculated results with five different DFT fu...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1286-y

    authors: Beheshtian J,Bagheri Z,Kamfiroozi M,Ahmadi A

    更新日期:2012-06-01 00:00:00

  • In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus.

    abstract::White spot disease caused by the white spot syndrome virus (WSSV) incurs a huge loss to the shrimp farming industry. Since no effective therapeutic measures are available, early detection and prevention of the disease are indispensable. Towards this goal, we previously identified a 12-mer phage displayed peptide (desi...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04524-z

    authors: Jamalpure S,Panditrao G,Kulabhusan PK,Hameed ASS,Paknikar KM,Joshi M,Rajwade JM

    更新日期:2020-09-10 00:00:00