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Characterization of Amino Acid Based Molecular Micelles with Molecular Modeling

Open Journal of Physical Chemistry 2019年第4期9卷 221-240页

作者： Alexander Billiot yayin fang Kevin F. Morris Department of Physical and Environmental Sciences Texas A & M University-Corpus Christi Corpus Christi TX USA Department of Biochemistry and Molecular Biology College of Medicine Howard University Washington DC USA Department of Chemistry Carthage College Kenosha WI USA

The enantiomers of chiral drugs often have different potencies, toxicities, and biochemical properties. Therefore, the FDA and other worldwide regulatory agencies require manufactures to test and prove the enantiomeric purity of chiral drugs. Amino acid based molecular micelles (AABMM) have been used in chiral CE separations since the 1990’s because of their low environmental impact and because their properties can easily be tuned by changing the amino acids in the chiral surfactant head groups. Using molecular dynamics simulations to investigate the structures and properties of AABMM is part of an ongoing study focusing on investigating and elucidating the factors responsible for chiral recognition with AABMM. The results will be useful for the proper design and selection of more efficient chiral selectors. The micelles investigated contained approximately twenty covalently linked surfactant monomers. Each monomer was in turn composed of an undecyl hydrocarbon chain bound to a dipeptide headgroup containing of all combinations of L-Alanine, L-Valine, and L-Leucine. These materials are of interest because they are effective chiral selectors in capillary electrophoresis separations. Molecular dynamics simulation analyses were used to investigate how the sizes and positions of the headgroup amino acid R-groups affected the solvent accessible surface areas of each AABMM chiral center. In addition, headgroup dihedral angle analyses were used to investigate how amino acid R-group size and position affected the overall headgroup conformations. Finally, distance measurements were used to study the structural and conformational flexibilities of each AABMM headgroup. All analyses were performed in the context of a broader study focused on developing structure-based predictive tools to identify the factors responsible for a) self-assembly, b) function, c) higher ordered structure and d) molecular recognition of these amino acid based molecular micelles.

关键词： Amino Acid Based Molecular Micelles Molecular Modeling Computational Chemistry

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Chiral Recognition of Dansyl Derivatives with an Amino Acid-Based Molecular Micelle: A Molecular Dynamics Investigation

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Open Journal of Physical Chemistry 2021年第2期11卷 64-86页

作者： Mauro Garcia Nathan Black Eugene Billiot Fereshteh Billiot Kevin F. Morris yayin fang Department of Physical and Environmental Sciences Texas A&M University-Corpus Christi Corpus Christi TX USA Department of Chemistry Carthage College Kenosha WI USA Department of Biochemistry and Molecular Biology Howard University Washington DC USA

In this study, the chiral separation mechanisms of Dansyl amino acids, including Dansyl-Leucine (Dans-Leu), Dansyl-Norleucine (Dans-Nor), Dansyl-Tryptophan (Dans-Trp) and Dansyl-Phenylalanine (Dans-Phe) binding to poly-sodium N-undecanoyl-(L)-Leucylvalinate, poly (SULV), were investigated using molecular dynamics simulations. Micellar electrokinetic chromatography (MEKC) has previously shown that when separating the enantiomers of these aforementioned Dansyl amino acids, the L-enantiomers bind stronger to poly (SULV) than the D-enantiomers. This study aims to investigate the molecular interactions that govern chiral recognition in these systems using computational methods. This study reveals that the computationally-calculated binding free energy values for Dansyl enantiomers binding to poly (SULV) are in agreement with the enantiomeric order produced in experimental MEKC studies. The L-enantiomers of Dans-Leu, Dans-Nor, Dans-Trp, and Dans-Phe binding to their preferred binding pockets in poly (SULV) yielded binding free energy values of -21.8938, -22.1763, -21.3329 and -13.3349 kJ·mol-1, respectively. The D-enantiomers of Dans-Leu, Dans-Nor

关键词： Amino Acid Based Molecular Micelles Molecular Modeling Computational Chemistry Chiral Recognition

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Molecular Docking Studies on Anticonvulsant Enaminones Inhibiting Voltage-Gated Sodium Channels

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Open Journal of Physical Chemistry 2019年第4期9卷 241-257页

作者： yayin fang Jamiya Kirkland Isis J. Amaye Patrice Jackson-Ayotunde Matthew George Jr. Department of Biochemistry and Molecular Biology College of Medicine Howard University Washington DC USA Department of Pharmaceutical Sciences School of Pharmacy and Health Professions University of Maryland Eastern Shore Princess Anne MD USA

Epilepsy is described as the most common chronic brain disorder. A typical symptom of epilepsy results in uncontrolled convulsions caused by temporary excessive neuronal discharges. Although several new anticon-vulsants have been introduced, some types of seizures have still not been adequately controlled with these new and current therapies. There is an urgent need to develop new anticonvulsant drugs to control the many different types of seizures. Many studies have shown that the epilepsies involve more than one mechanism and therefore may be responsible for the various types of observed seizures. Recently reported studies have shown that a group of newly synthesized 6 Hz active anticonvulsant fluorinated N-benzamide enaminones exhibited selective inhibitions of voltage-gated sodium (Nav) channels. Nav channels are responsible for the initial inward currents during the depolarization phases of the action potential in excitable cells. The activation and opening of Nav channels result in the initial phases of action potentials. We hypothesize that there is an essential pharmacophore model for the interactions between these enaminones and the active sites of Nav channels. The research reported here is focused on molecular docking studies of the interactions that occur between the fluorinated N-benzamide enaminones and the Nav channels. These studies may open an avenue for designing anticonvulsant drugs by inhibiting Nav channels.

关键词： Anticonvulsant Enaminones Voltage-Gated Sodium Channels Structure-Based Drug Design Molecular Docking 3D QSAR

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Molecular Docking Studies on Streptomycin Antileishmanial Activity

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Open Journal of Physical Chemistry 2024年第2期14卷 36-48页

作者： Todd A. Young Matthew George Jr. Ayele Gugssa William M. Southerland yayin fang Clarence M. Lee Department of Biology Howard University Washington DC United States Department of Biochemistry and Molecular Biology Howard University Washington DC United States

Resistance to pentavalent antimonial drugs and the lack of vaccines make it urgent to find novel therapeutic options to treat Leishmaniasis, a tropical disease caused by the Leishmania protozoan parasite. The study reported here is to investigate if Streptomycin, an aminoglycoside, and Amphotericin B, the second-line treatment drug, exhibit antileishmanial activity through a similar mechanism. By using MOE (Molecular Operating Environment), we performed molecular docking studies on these drugs binding to a range of targets including ribosome targets in Leishmania and H. sapiens. Our study shows that the two drugs do not bind to the same pockets in Leishmania targets but to the same pockets in the human ribosome, with some differences in interactions. Moreover, our 2D maps indicated that Amphotericin B binds to the A-site in the human cytoplasmic ribosome, whereas streptomycin does not.

关键词： Leishmaniasis Streptomycin Amphotericin B Molecular Docking Aminoglycosides Antileishmanial

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Investigation of Chiral Molecular Micelles by NMR Spectroscopy and Molecular Dynamics Simulation

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Open Journal of Physical Chemistry 2012年第4期2卷 240-251页

作者： Kevin F. Morris Eugene J. Billiot Fereshteh H. Billiot Kenny B. Lipkowitz William M. Southerland yayin fang Department of Biochemistry and Molecular Biology Howard University College of Medicine Howard University Washington DC USA Department of Chemistry Carthage College Kenosha USA Department of Physical and Environmental Sciences Texas A & M University Corpus Christi USA Office of Naval Research Arlington USA

NMR spectroscopy and Molecular Dynamics (MD) simulation analyses of the chiral molecular micelles poly-(Sodium Undecyl-(L,L)-Leucine-Valine) (poly-SULV) and poly-(Sodium Undecyl-(L,L)-Valine-Leucine) (poly-(SUVL)) are reported. Both molecular micelles are used as chiral selectors in electrokinetic chromatography and each consists of covalently linked surfactant chains with chiral dipeptide headgroups. To provide experimental support for the structures from MD simulations, NOESY spectra were used to identify protons in close spatial proximity. Results from the NOESY analyses were then compared to radial distribution functions from MD simulations. In addition, the hydrodynamic radii of both molecular micelles were calculated from NMR-derived diffusion coefficients. Corresponding radii from the MD simulations were found to be in agreement with these experimental results. NMR diffusion experiments were also used to measure association constants for polar and non-polar binaphthyl analytes binding to both molecular micelles. Poly (SUVL) was found to bind the non-polar analyte enantiomers more strongly, while the more polar analyte enantiomers interacted more strongly with poly(SULV). MD simulations in turn showed that poly(SULV) had a more open structure that gave greater access for water molecules to the dipeptide headgroup region.

关键词： NOESY Chiral Recognition Polymeric Surfactant Molecular Modeling

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A Molecular Dynamics Simulation Study of Two Dipeptide Based Molecular Micelles: Effect of Amino Acid Order

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Open Journal of Physical Chemistry 2013年第1期3卷 20-29页

作者： Kevin F. Morris Eugene J. Billiot Fereshteh H. Billiot Kenny B. Lipkowitz William M. Southerland yayin fang Department of Biochemistry and Molecular Biology Howard University College of Medicine Howard University Washington USA Department of Chemistry Carthage College Kenosha USA Department of Physical and Environmental Sciences Texas A&M University-Corpus Christi Corpus Christi USA Office of Naval Research Arlington USA

Molecular dynamics (MD) simulations were used to compare the structures of the chiral molecular micelles (MM) poly-(sodium undecyl-(L,L)-leucine-valine) (poly(SULV)) and poly-(sodium undecyl-(L,L)-valine-leucine) (poly (SUVL)). Both MM contained polymerized surfactant monomers terminated by chiral dipeptide headgroups. The study was undertaken to investigate why poly(SULV) is generally a better chiral selector compared to poly(SUVL) in electrokinetic chromatography separations. When comparing poly(SULV) to poly(SUVL), poly(SULV) had the more conformational flexible dipeptide headgroup and hydrogen bond analyses revealed that the poly(SULV) headgroup conformation allowed a larger number of intramolecular hydrogen bonds to form between monomer chains. In addition, a larger number of water molecules surrounded the chiral centers of the poly(SULV) molecular micelle. Poly(SULV) was also found to have a larger solvent accessible surface area (SASA) than poly(SUVL) and fluctuations in the poly(SULV) SASA during the MD simulation allowed dynamic monomer chain motions expected to be important in chiral recognition to be identified. Finally, approximately 50% of the Na+ counterions were found in the first three solvation shells surrounding both MM, with the remainder located in the bulk. Overall the MD simulations point to both greater headgroup flexibility and solvent and analyte access to the chiral centers of the dipeptide headgroup as factors contributing to the enhanced chiral selectivity observed with poly(SULV).

关键词： Chiral Recognition Polymeric Surfactant Molecular Modeling

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固体超强酸ZrO2/SO4=和Fe2O3/SO4=催化苯乙烯烷基化甲苯反应的研究

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化学与粘合 1999年第2期21卷 69-69,71,99页

作者：陈勇方亚寅王彦中刘靖疆南开大学化学系

固体超强酸ＺｒＯ２／ＳＯ４＝和Ｆｅ２Ｏ３／ＳＯ４＝在室温下即可高活性地催化苯乙烯烷基化甲苯的反应。于２０分钟时苯乙烯转化率可达４０％～５０％。在连续使用三次时。

关键词：固体超强酸苯乙烯甲苯催化剂苯基乙基甲苯

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成都市HIV单阳家庭阳性患者抗病毒治疗及时性及其影响因素分析

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预防医学情报杂志 2020年第9期36卷 1103-1107页

作者：刘芳施雅莹吴学庆代珍何勤英成都市疾病预防控制中心成都610047

目的分析成都市HIV单阳家庭阳性患者艾滋病抗病毒治疗(ART)及时性及影响因素。方法利用艾滋病防治基本信息系统,整理截至2018-12-31成都市HIV单阳家庭阳性患者的基本信息、随访与治疗数据,采用多因素Logistic回归分析HIV单阳家庭阳性患... 详细信息

目的分析成都市HIV单阳家庭阳性患者艾滋病抗病毒治疗(ART)及时性及影响因素。方法利用艾滋病防治基本信息系统,整理截至2018-12-31成都市HIV单阳家庭阳性患者的基本信息、随访与治疗数据,采用多因素Logistic回归分析HIV单阳家庭阳性患者及时进行抗病毒治疗的影响因素。结果 3 163例HIV单阳家庭阳性患者中,及时开展抗病毒治疗比例为74.01%(2 341/3 163)。HIV单阳家庭阳性患者治疗及时性多因素Logistic回归分析结果显示:30~49岁、50岁及以上与30岁以下相比,远郊区与中心城区相比,2012年及以后发现与2011年及以前相比及时治疗的OR(95%CI)分别为1.66(1.24~2.22)、1.80(1.30~2.48),1.60(1.22~2.10),7.08(4.68~10.71)。汉族、已婚有配偶、CD4^+T淋巴细胞计数<200、有非婚商业接触史、医疗机构检测发现是及时治疗的促进因素。结论艾滋病单阳家庭阳性患者抗病毒治疗及时率有待提高,其在年龄、民族、地域、首次CD4+T淋巴细胞计数水平、高危行为接触史、检测来源、发现年份上有差异。在促进单阳家庭阳性方及时接受抗病毒治疗时,需根据其社会文化、所在地域及疾病状况等特点采取针对性综合干预措施。

关键词：艾滋病单阳家庭抗病毒治疗影响因素

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miRNA对细菌性脑膜炎中血脑屏障影响的研究进展

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现代畜牧兽医 2021年第12期 83-86页

作者：陈明杰曹梦园曹芳王晨豫闫雪琪齐亚银石河子大学动物科技学院新疆石河子832000

微小RNA(MicroRNA,miRNA)是动物机体内源性非编码小分子RNA,长度约为18~25个核苷酸,在细胞增殖、分化、凋亡、代谢及机体免疫等生命活动的调节和控制中发挥重要作用。炎症条件下,miRNA对维持血脑屏障(blood-brain barrier,BBB)的完整性... 详细信息

微小RNA(MicroRNA,miRNA)是动物机体内源性非编码小分子RNA,长度约为18~25个核苷酸,在细胞增殖、分化、凋亡、代谢及机体免疫等生命活动的调节和控制中发挥重要作用。炎症条件下,miRNA对维持血脑屏障(blood-brain barrier,BBB)的完整性起重要作用。文章综述了miRNA研究近况及对血脑屏障影响机制及研究进展,以期为miRNA在细菌性脑膜炎方面的后续研究提供参考。

关键词： miRNA 血脑屏障细菌性脑膜炎

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某规模化牧场致犊牛腹泻的大肠杆菌分离鉴定及耐药性检测

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中国乳业 2024年第2期 71-75页

作者：曹芳魏勇吴忧赵鹏飞陈钊铭任静静齐亚银石河子大学动物科技学院新疆石河子832003 新疆天润科技股份有限公司新疆乌鲁木齐830063

[目的]为确定引起石河子某规模化牧场犊牛腹泻的主要病原菌及其耐药情况,并针对犊牛腹泻提出合理应对措施,为该牧场防治犊牛腹泻提供参考。[方法]本研究采取现场流行病学检查,无菌采集15份犊牛腹泻病料,对其进行病原菌分离纯化;通过生... 详细信息

[目的]为确定引起石河子某规模化牧场犊牛腹泻的主要病原菌及其耐药情况,并针对犊牛腹泻提出合理应对措施,为该牧场防治犊牛腹泻提供参考。[方法]本研究采取现场流行病学检查,无菌采集15份犊牛腹泻病料,对其进行病原菌分离纯化;通过生化试验以及分子生物学鉴定,确定致犊牛腹泻的病原菌;对病原菌进行药敏试验,确定耐药情况。[结果]经生化试验以及分子生物学鉴定发现,15份犊牛腹泻病料中,有12份分离到了大肠杆菌。药敏试验结果显示,13株大肠杆菌对链霉素耐药率最高为46.15%(6/13),对青霉素、氨苄西林耐药率为38.46%(5/13),且敏感菌株多为中低敏;对四环素敏感性为76.92%(10/13),13株菌株对头孢噻肟和万古霉素敏感性最高,为84.62%(11/13),多数菌株为多重耐药菌株。[结论]本研究针对腹泻犊牛进行病原菌分离鉴定、药敏试验,为该牧场犊牛腹泻诊治提供参考。

关键词：犊牛腹泻大肠杆菌分离鉴定耐药性

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