Molecular dynamics simulations and MM–PBSA calculations of the cyclodextrin inclusion complexes with 1-alkanols, para-substituted phenols and substituted imidazoles

El‐Barghouthi, Musa I.; Jaime, Carlos; Alsakhen, Nada; Issa, Ayman A.; Abdoh, A. A.; Omari, Mahmoud M. Al; Badwan, Adnan A.; Zughul, Mohammad B.

doi:10.1016/j.theochem.2007.12.005

Cited by 33 publications

(22 citation statements)

References 66 publications

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“…These system have been experimentally studied by x-ray crystallography [25][26][27] and affinity measurements, [25,28,29] as well as by theoretical methods [30][31][32]. Therefore, they are suitable for this benchmark study.…”

Section: Introductionmentioning

confidence: 99%

MM/GBSA and LIE estimates of host–guest affinities: dependence on charges and solvation model

Genheden

2011

J Comput Aided Mol Des

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The affinities of two sets of guest-host systems were estimated using the popular end-point methods MM/GBSA (molecular-mechanics with generalised Born and surface-area solvation) and LIE (linear interaction energy). A set of six primary alcohols that bind to α-cyclodextrin (α-CD) and a set of eight guest molecules to cucurbit[8]uril (CB8) were considered. Three different charge schemes were used to obtain charges for the host and guest molecules, viz., AM1-BCC, RESP, and the recently suggested xAvESP (which average ESP charges over a number of molecular dynamics snapshots). Furthermore, both the generalised Born and Poisson-Boltzmann solvation models were used in the MM/GBSA calculations. The two solvation models perform equally well in predicting relative affinities, and hence there is no point in using the more expensive Poisson-Boltzmann model for these systems. Both the LIE and MM/GBSA estimates are shown to be robust with respect to the charge model, and therefore it is recommended to use the cheapest AM1-BCC charges. Using AM1-BCC charges, the MM/GBSA method gave a MADtr (mean absolute deviation after removal of systematic error) of 17 kJ/mol and a correlation coefficient (r (2)) of 0.67 for the CB8 complexes, and a MADtr of 10 kJ/mol and an r (2) of 0.96 for the α-CD complexes. The LIE method gave a MADtr of 20 kJ/mol and an r (2) of 0.10 for the CB8 complexes, after optimisation of the non-polar scaling parameter. For the α-CD complexes, no optimisation was necessary and the method gave a MADtr of 2 kJ/mol and a r (2) of 0.96. These results indicate that both MM/GBSA and LIE are able to estimate host-guest affinities accurately.

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Section: Introductionmentioning

confidence: 99%

MM/GBSA and LIE estimates of host–guest affinities: dependence on charges and solvation model

Genheden

2011

J Comput Aided Mol Des

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“…[46] Today, hundreds of computational calculations describe drug-CD complexes reports. Table 1 classifies a number of present research studies in this field: molecular docking, [47][48][49] MD, [50][51][52][53] quantitative structure-activity/ property relationships (QSARs/QSPRs), [54][55][56] quantum mechanics (QM), [57][58][59] Monte Carlo (MC) simulations, [60][61][62] and machine learning.…”

Section: In Silico Methods For Discovery Of Cyclodextrinsmentioning

confidence: 99%

“…β-CD and four derivatives of β-CD Luteolin [47] Molecular docking HP-β-CD and methylated β-CD Voriconazole [58] β-CD 4,4′-Dihydroxybiphenyl [59] β-CD 57 Guest molecules [50] Molecular dynamics (MD) β-and γ-CD Amphotericin B [51] α-, β-, and γ-CD Cumene hydroperoxide [52] α-and β-CD 1-Alkanols, substituted phenols, and substituted imidazoles [53] α-CD Benzene derivatives [54] Quantitative structure-activity/ property relationships (QSARs/QSPRs) β-CD Multiple compounds [55] β-CD 233 Molecules [56] β-CD Dopamine and epinephrine [57] Quantum mechanics (QM) α-CD Carboplatin, oxaliplatin, nedaplatin [58] β-CD Aflatoxin B1 [59] β-CD Praziquantel [60] Monte Carlo (MC) simulations β-CD and methylated β-CD Niobocene dichloride [61] α-CD Water [62] Sulfobutylether β-CD Diverse organic molecules [63] Machine learning…”

Section: Methodsmentioning

confidence: 99%

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Computer‐aided drug design to explore cyclodextrin therapeutics and biomedical applications

Abdolmaleki

Ghasemi

2017

Chem Biol Drug Des

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Cyclodextrin (CD) is a subset of the macrocyclic structural class, which is an important class of small organic agents that are useful functional excipients. They have wide range application possibilities in different fields of sciences such as material preparation, medicine, analytical chemistry, and separation processes. They are used widely in pharmaceutical formulations and drug delivery for increasing the water solubility of low soluble drugs and drug candidates. Due to the ring structure, they behave differently than smaller molecules and may be capable of hitting new classes of targets. A macrocyclic molecule presents varied functionality and stereochemical complexity in a pre-organized conformation of the ring structure. This can result in high selectivity and affinity for protein targets while conserving enough bioavailability to arrive at intracellular locations. Regardless of these valuable features, and the verified success of several marketed macrocycle drugs isolated from natural compounds, this class has been little explored in drug development. This study describes some of the key features of the CDs therapeutic discovery. Also, the application of computational chemistry approaches such as QSAR/QSPR, molecular docking, and molecular/quantum mechanics for modeling of CD-drug system is reviewed briefly. K E Y W O R D Sbioavailability, computational, cyclodextrin, drug design, drug discovery, macrocyclic, therapeutic

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“…Molecular dynamic simulations (MD) have been employed as current methods for understanding molecular recognition processes occurring in organisms at an atomic level, and consequently free energy calculations, initially developed for biological systems, have become a powerful tool in estimating quantitatively molecular interactions in hostguest chemistry. Nevertheless, they have also been applied to supramolecular systems of organic structures 8,9 , even in predicting chiral discrimination 10,11 . The molecular mechanic-Poisson-Boltzmann (Generalized Born) surface area [MM/PB(GB)SA] is one of the most valuable methods, 12 which has successfully been applied to estimate the binding free energies of different biological systems.…”

Section: Introductionmentioning

confidence: 99%

Enantiomeric recognition of amino acid ester salts by β-cyclodextrin derivatives: an experimental and computational study

Řezanka¹,

Stibor²,

Azizoglu³

et al. 2016

Arkivoc

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β-cyclodextrin derivatives bearing benzoyl (β-CD-1) and naphthoyl (β-CD-2) moieties have been synthesized from salicylic acid and 3-hydroxy-2-naphthoic acid by a convenient method in 60% and 58% yields, respectively, and were tested for enantiomeric recognition of amino acid ester derivatives. Their ability to discriminate between various L-/D-amino acid methyl ester hydrochloride salts was examined using the

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Molecular dynamics simulations and MM–PBSA calculations of the cyclodextrin inclusion complexes with 1-alkanols, para-substituted phenols and substituted imidazoles

Cited by 33 publications

References 66 publications

MM/GBSA and LIE estimates of host–guest affinities: dependence on charges and solvation model

MM/GBSA and LIE estimates of host–guest affinities: dependence on charges and solvation model

Computer‐aided drug design to explore cyclodextrin therapeutics and biomedical applications

Enantiomeric recognition of amino acid ester salts by β-cyclodextrin derivatives: an experimental and computational study

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