自由能计算用于环糊精性质及药物分子包结机理研究
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摘要
环糊精(cyclodextrin,CD)“内疏水、外亲水”的性质使得它可以和许多客体分子形成包结物,在食品、制药等众多领域都有广泛的应用。虽然很多实验手段可以检测环糊精的包结过程,但是对于包结机理仍然存在很多不清楚的问题。而分子模拟方法则可以在原子水平上研究环糊精的结构性质、包结机理、结合自由能等。本论文采用分子模拟的方法对环糊精及其包结体系进行了研究,主要内容包括以下几个方面:
(1)在研究天然环糊精性质的过程中,β-环糊精溶解度的特异性引起了广泛的关注。为了解释这一实验现象,采用分子动力学模拟分别研究了α-、β-和γ-环糊精在水溶液中的行为。结果表明β-环糊精由于大口端糖单元间氢键的作用,使其大环结构刚性明显增强,引起水化层的结构化程度增高,熵的代价降低了β-环糊精在水中的溶解性。进一步利用自由能微扰的方法计算了α-、β-和γ-环糊精的水化自由能ΔG_(hyd),即环糊精分子从真空转移到水溶液过程中的自由能变化。但是从水化自由能的结果来看,ΔG_(hyd)随着α-、β-、γ-环糊精的顺序逐渐变化,β-环糊精并没有显示出它的特异性。因此,β-环糊精溶解度的反常现象不能仅从水化自由能方面进行解释,这有可能是由于没有考虑到环糊精在溶液中的自聚集行为引起的。
(2)环糊精分子在与客体分子进行包结时,除了以1:1的比例形成包结物外,还可以形成2:1或2:2的包结物,甚至是n:1式的轮烷分子项链,因此研究两个环糊精分子的聚集方式很重要。采用分子动力学方法模拟了天然α-、β-、γ-环糊精二聚体以及6-O-(4-hydroxybenzoyl)-β-CD(HB-β-CD)二聚体在真空和水溶液环境下的结构和相互作用。利用自由能微扰方法计算了三种取向二聚体的结合自由能,以判断其稳定性差异。结果表明,在真空中由于分子间氢键作用,三种天然环糊精均以大口端-大口端为优势稳定取向,在溶液中时,三种天然环糊精二聚体平衡后的结构因受到水的影响发生了很大的变化,且稳定性降低,而两个HB-β-CD形成的相互包结的二聚体结构变化不大。自由能计算的结果表明,无论在真空还是溶液中,由于包结作用HB-β-CD二聚体的小口端一小口端为明显的优势取向,且稳定性要远远大于天然β-环糊精二聚体。
(3)甾类化合物广泛存在于动植物体内,对动植物的生命活动起着极其重要的调节作用。但是它们的溶解度较低,生物适应性较差,因此大大限制了它们在医药方面的应用。为了克服这些缺点,可采用环糊精及其衍生物作为载体与其形成内包含复合物,从而增加它们的溶解度与适应新。但是,包结机理以及包结物的具体结构信息还不是非常明确。因此,本工作采用分子动力学、自适应偏置力和自由能微扰的方法研究了氢化可的松(Hyc)、黄体酮(Pro)、睾丸激素(Tes)经由两种可能的取向(Ⅰ和Ⅱ)穿过β-环糊精空腔时自由能的变化。采用自适应偏置力方法计算得到的自由能在包结过程中的变化曲线表明,对于Hyc和Tes,取向Ⅰ(甾核中A环进入环糊精空腔)是有利的,此时Hyc和Tes的A环进入环糊精空腔形成部分包结模式;但是对于Pro,取向Ⅱ(甾核中D环进入环糊精空腔)是有利的,并且出现了两种包结模式,即部分包结和深入包结;无论是哪种取向,β-环糊精对三种甾类化合物的结合能力为:Pro＞Tes＞Hyc,这与实验结果一致,而这一结果也得到了我们采用自由能微扰方法计算相对自由能变化结果的支持。将自由能分解为不同自由能组分项可知,优势取向的包结驱动力主要为范德华作用。另外,采用分子动力学模拟考察了各稳态点包结结构的稳定性。结果还表明,Pro-β-CD的热力学最稳定构型和第二极小点附近构型之间可以相互转化,这种现象在Hyc-β-CD和Tes-β-CD包结物中并不存在。
(4)丙咪嗪是三环类抗抑郁药物,但是在治疗过程中显示出一定的毒副作用,为了减少副作用的伤害,可采用β-环糊精作为赋形剂进行包结。为了研究丙咪嗪和环糊精分子的各种可能包结模式,我们采用分子动力学方法与自由能微扰方法结合研究了真空和溶液中环糊精和丙咪嗪以摩尔比分别为2:1、1:1和1:2所形成包结物的性质,其中1:1的情形,又根据包结丙咪嗪的不同部位分为三种模式。首先对所有五种初始结构在真空和溶剂分别进行平衡分子动力学模拟,结果表明除了1:2模式的包结物,其余四种均能稳定存在。基于所得到的平衡结构和所设计的热力学循环过程,利用自由能微扰方法计算相应的结合自由能,寻找优势包结模式和包结位点。结果表明无论真空还是溶液中,环糊精和丙咪嗪的摩尔比为2:1时形成的包结物最稳定,环糊精与苯环间的范德华作用以及两环糊精大口端间形成的分子间氢键是稳定性的主要因素。另外,三种1:1包结模式在真空中的稳定性相当,没有明显的倾向性,而在溶液中,当丙咪嗪的苯环部分进入环糊精的空腔时所形成的包结物相对稳定,且范德华力是稳定包结物的主要作用力。
Cyclodextrins(CDs) have a hydrophilic outer surface and a hydrophobic inner core,conducive for the formation of inclusion complexes through the binding of the small molecules into their cavity.This property has attracted increasing attention in food field,pharmaceutical science,etc.Although experimental methods have been employed to investigate the inclusion process,the association mechanism is until now somewhat fragmentary.Theoretical approaches offer the three-dimension structure, the stability of the complex structure and binding free energy information.In this dissertation,molecular simulations were used toinvestigate the properties of CDs and the complexes of CDs with different guests.
(1) The molecular dynamics(MD) simulations describing the hydration process forα-,β-andγ-CDs have been performed.The results reported here demonstrate that the anomalous solubility forβ-CD can be essentially rationalized by its greater rigidity conferred by the participating intramolecular hydrogen bonds and the higher density of water molecules of lesser mobility.The hydration free energy ofα-,β-andγ-CD was computed using the free energy perturbation(FEP) method.This quantity is shown to increase with the number of glucose units,thereby suggesting that the anomalous solubility ofβ-CD cannot be explained by its free energy of hydration alone.
(2) The structures and interactions ofα-,β-,andγ-CD dimers and 6-O-(4-hydroxybenzoyl)-β-CD(HB-β-CD) dimers were simulated by MD methods in vacuum and in an aqueous solution,respectively.The binding free energies of three possible arrangements(head-to-head,head-to-tail,and tail-to-tail) of each dimer were calculated using the FEP method.The results show that the stable arrangements forα-,β-,andγ-CD dimers in vacuum are head-to-head motifs due to the contribution of the intermolecular hydrogen bonds.In the aqueous solution,the solvent exerts more influence on the structures of the natural CD dimers than on the HB-β-CD dimer, resulting in a decrease of the stability of the formers.From the calculated binding free energies,the HB-β-CD dimer in the aqueous solution is much more stable than theβ-CD dimer.
(3) Free-energy calculations characterizing the inclusion of three steroidal drugs, viz.hydrocortisone(Hyc),progesterone(Pro) and Testosterone(Tes),intoβ-CD, following two possible relative orientations,have been carried out,employing adaptive biasing force(ABF) and FEP methods.In the light of the analysis of the free-energy profiles determined using the ABF method along the chosen model reaction coordinate,orientationⅠis suggested to be favored for Hyc and Tes,albeit orientationⅡappears to be favored for Pro.Moreover,van der Waals interactions are shown to constitute the main driving forces responsible for the inclusion process in the preferred orientation.Additional MD simulations of the complexes at the global minimum of the free-energy surface were also performed.Analysis of the trajectories suggests that in contrast with Hyc-β-CD and Tes-β-CD,transition between the most thermodynamically stable structure of Pro-β-CD and the second stable structure can be witnessed.
(4) The inclusion complexes and interactions ofβ-CD and imipramine(IMI) with stoichiometries of 1:2,1:1,and 2:1 were simulated by MD methods in the gas phase and in an aqueous solution,respectively.The binding free energies of four possible complexes were calculated using the FEP method based on pre-designed thermodynamic cycles,suggesting that the 2:1 inclusion mode is the most energetically favorable,both in the gas and aqueous phases.The van der Waals interactions and intermolecular hydrogen-bond interactions between twoβ-CDs constitute the main contribution to the stability of the complex.In addition,at variance with in the gas phase,among three possible 1:1β-CD-IMI structures,two orientations of IMI with benzene ring located inside the cavity ofβ-CD are more favorable than that with the side chain inside the cavity in the aqueous solution.The van der Waals interactions are shown to play a major role in stabilizing the 1:1 complex structure in the two phases.
(1)在研究天然环糊精性质的过程中,β-环糊精溶解度的特异性引起了广泛的关注。为了解释这一实验现象,采用分子动力学模拟分别研究了α-、β-和γ-环糊精在水溶液中的行为。结果表明β-环糊精由于大口端糖单元间氢键的作用,使其大环结构刚性明显增强,引起水化层的结构化程度增高,熵的代价降低了β-环糊精在水中的溶解性。进一步利用自由能微扰的方法计算了α-、β-和γ-环糊精的水化自由能ΔG_(hyd),即环糊精分子从真空转移到水溶液过程中的自由能变化。但是从水化自由能的结果来看,ΔG_(hyd)随着α-、β-、γ-环糊精的顺序逐渐变化,β-环糊精并没有显示出它的特异性。因此,β-环糊精溶解度的反常现象不能仅从水化自由能方面进行解释,这有可能是由于没有考虑到环糊精在溶液中的自聚集行为引起的。
(2)环糊精分子在与客体分子进行包结时,除了以1:1的比例形成包结物外,还可以形成2:1或2:2的包结物,甚至是n:1式的轮烷分子项链,因此研究两个环糊精分子的聚集方式很重要。采用分子动力学方法模拟了天然α-、β-、γ-环糊精二聚体以及6-O-(4-hydroxybenzoyl)-β-CD(HB-β-CD)二聚体在真空和水溶液环境下的结构和相互作用。利用自由能微扰方法计算了三种取向二聚体的结合自由能,以判断其稳定性差异。结果表明,在真空中由于分子间氢键作用,三种天然环糊精均以大口端-大口端为优势稳定取向,在溶液中时,三种天然环糊精二聚体平衡后的结构因受到水的影响发生了很大的变化,且稳定性降低,而两个HB-β-CD形成的相互包结的二聚体结构变化不大。自由能计算的结果表明,无论在真空还是溶液中,由于包结作用HB-β-CD二聚体的小口端一小口端为明显的优势取向,且稳定性要远远大于天然β-环糊精二聚体。
(3)甾类化合物广泛存在于动植物体内,对动植物的生命活动起着极其重要的调节作用。但是它们的溶解度较低,生物适应性较差,因此大大限制了它们在医药方面的应用。为了克服这些缺点,可采用环糊精及其衍生物作为载体与其形成内包含复合物,从而增加它们的溶解度与适应新。但是,包结机理以及包结物的具体结构信息还不是非常明确。因此,本工作采用分子动力学、自适应偏置力和自由能微扰的方法研究了氢化可的松(Hyc)、黄体酮(Pro)、睾丸激素(Tes)经由两种可能的取向(Ⅰ和Ⅱ)穿过β-环糊精空腔时自由能的变化。采用自适应偏置力方法计算得到的自由能在包结过程中的变化曲线表明,对于Hyc和Tes,取向Ⅰ(甾核中A环进入环糊精空腔)是有利的,此时Hyc和Tes的A环进入环糊精空腔形成部分包结模式;但是对于Pro,取向Ⅱ(甾核中D环进入环糊精空腔)是有利的,并且出现了两种包结模式,即部分包结和深入包结;无论是哪种取向,β-环糊精对三种甾类化合物的结合能力为:Pro＞Tes＞Hyc,这与实验结果一致,而这一结果也得到了我们采用自由能微扰方法计算相对自由能变化结果的支持。将自由能分解为不同自由能组分项可知,优势取向的包结驱动力主要为范德华作用。另外,采用分子动力学模拟考察了各稳态点包结结构的稳定性。结果还表明,Pro-β-CD的热力学最稳定构型和第二极小点附近构型之间可以相互转化,这种现象在Hyc-β-CD和Tes-β-CD包结物中并不存在。
(4)丙咪嗪是三环类抗抑郁药物,但是在治疗过程中显示出一定的毒副作用,为了减少副作用的伤害,可采用β-环糊精作为赋形剂进行包结。为了研究丙咪嗪和环糊精分子的各种可能包结模式,我们采用分子动力学方法与自由能微扰方法结合研究了真空和溶液中环糊精和丙咪嗪以摩尔比分别为2:1、1:1和1:2所形成包结物的性质,其中1:1的情形,又根据包结丙咪嗪的不同部位分为三种模式。首先对所有五种初始结构在真空和溶剂分别进行平衡分子动力学模拟,结果表明除了1:2模式的包结物,其余四种均能稳定存在。基于所得到的平衡结构和所设计的热力学循环过程,利用自由能微扰方法计算相应的结合自由能,寻找优势包结模式和包结位点。结果表明无论真空还是溶液中,环糊精和丙咪嗪的摩尔比为2:1时形成的包结物最稳定,环糊精与苯环间的范德华作用以及两环糊精大口端间形成的分子间氢键是稳定性的主要因素。另外,三种1:1包结模式在真空中的稳定性相当,没有明显的倾向性,而在溶液中,当丙咪嗪的苯环部分进入环糊精的空腔时所形成的包结物相对稳定,且范德华力是稳定包结物的主要作用力。
Cyclodextrins(CDs) have a hydrophilic outer surface and a hydrophobic inner core,conducive for the formation of inclusion complexes through the binding of the small molecules into their cavity.This property has attracted increasing attention in food field,pharmaceutical science,etc.Although experimental methods have been employed to investigate the inclusion process,the association mechanism is until now somewhat fragmentary.Theoretical approaches offer the three-dimension structure, the stability of the complex structure and binding free energy information.In this dissertation,molecular simulations were used toinvestigate the properties of CDs and the complexes of CDs with different guests.
(1) The molecular dynamics(MD) simulations describing the hydration process forα-,β-andγ-CDs have been performed.The results reported here demonstrate that the anomalous solubility forβ-CD can be essentially rationalized by its greater rigidity conferred by the participating intramolecular hydrogen bonds and the higher density of water molecules of lesser mobility.The hydration free energy ofα-,β-andγ-CD was computed using the free energy perturbation(FEP) method.This quantity is shown to increase with the number of glucose units,thereby suggesting that the anomalous solubility ofβ-CD cannot be explained by its free energy of hydration alone.
(2) The structures and interactions ofα-,β-,andγ-CD dimers and 6-O-(4-hydroxybenzoyl)-β-CD(HB-β-CD) dimers were simulated by MD methods in vacuum and in an aqueous solution,respectively.The binding free energies of three possible arrangements(head-to-head,head-to-tail,and tail-to-tail) of each dimer were calculated using the FEP method.The results show that the stable arrangements forα-,β-,andγ-CD dimers in vacuum are head-to-head motifs due to the contribution of the intermolecular hydrogen bonds.In the aqueous solution,the solvent exerts more influence on the structures of the natural CD dimers than on the HB-β-CD dimer, resulting in a decrease of the stability of the formers.From the calculated binding free energies,the HB-β-CD dimer in the aqueous solution is much more stable than theβ-CD dimer.
(3) Free-energy calculations characterizing the inclusion of three steroidal drugs, viz.hydrocortisone(Hyc),progesterone(Pro) and Testosterone(Tes),intoβ-CD, following two possible relative orientations,have been carried out,employing adaptive biasing force(ABF) and FEP methods.In the light of the analysis of the free-energy profiles determined using the ABF method along the chosen model reaction coordinate,orientationⅠis suggested to be favored for Hyc and Tes,albeit orientationⅡappears to be favored for Pro.Moreover,van der Waals interactions are shown to constitute the main driving forces responsible for the inclusion process in the preferred orientation.Additional MD simulations of the complexes at the global minimum of the free-energy surface were also performed.Analysis of the trajectories suggests that in contrast with Hyc-β-CD and Tes-β-CD,transition between the most thermodynamically stable structure of Pro-β-CD and the second stable structure can be witnessed.
(4) The inclusion complexes and interactions ofβ-CD and imipramine(IMI) with stoichiometries of 1:2,1:1,and 2:1 were simulated by MD methods in the gas phase and in an aqueous solution,respectively.The binding free energies of four possible complexes were calculated using the FEP method based on pre-designed thermodynamic cycles,suggesting that the 2:1 inclusion mode is the most energetically favorable,both in the gas and aqueous phases.The van der Waals interactions and intermolecular hydrogen-bond interactions between twoβ-CDs constitute the main contribution to the stability of the complex.In addition,at variance with in the gas phase,among three possible 1:1β-CD-IMI structures,two orientations of IMI with benzene ring located inside the cavity ofβ-CD are more favorable than that with the side chain inside the cavity in the aqueous solution.The van der Waals interactions are shown to play a major role in stabilizing the 1:1 complex structure in the two phases.
引文
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