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T PL, Mondal M, Ramadas K, Natarajan S. Molecular interaction of 2,4-diacetylphloroglucinol (DAPG) with human serum albumin (HSA): The spectroscopic, calorimetric and computational investigation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:90-102. [PMID: 28441541 DOI: 10.1016/j.saa.2017.04.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/29/2017] [Accepted: 04/14/2017] [Indexed: 06/07/2023]
Abstract
Drug molecule interaction with human serum albumin (HSA) affects the distribution and elimination of the drug. The compound, 2,4-diacetylphloroglucinol (DAPG) has been known for its antimicrobial, antiviral, antihelminthic and anticancer properties. However, its interaction with HSA is not yet reported. In this study, the interaction between HSA and DAPG was investigated through steady-state fluorescence, time-resolved fluorescence (TRF), circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetry (ITC), molecular docking and molecular dynamics simulation (MDS). Fluorescence spectroscopy results showed the strong quenching of intrinsic fluorescence of HSA due to interaction with DAPG, through dynamic quenching mechanism. The compound bound to HSA with reversible and moderate affinity which explained its easy diffusion from circulatory system to target tissue. The thermodynamic parameters from fluorescence spectroscopic data clearly revealed the contribution of hydrophobic forces but, the role of hydrogen bonds was not negligible according to the ITC studies. The interaction was exothermic and spontaneous in nature. Binding with DAPG reduced the helical content of protein suggesting the unfolding of HSA. Site marker fluorescence experiments revealed the change in binding constant of DAPG in the presence of site I (warfarin) but not site II marker (ibuprofen) which confirmed that the DAPG bound to site I. ITC experiments also supported this as site I marker could not bind to HSA-DAPG complex while site II marker was accommodated in the complex. In silico studies further showed the lowest binding affinity and more stability of DAPG in site I than in site II. Thus the data presented in this study confirms the binding of DAPG to the site I of HSA which may help in further understanding of pharmacokinetic properties of DAPG.
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Affiliation(s)
- Pragna Lakshmi T
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India
| | - Moumita Mondal
- Department of Biotechnology, Pondicherry University, Pondicherry, India
| | - Krishna Ramadas
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India.
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Mukhi P, Mohapatra SS, Bhattacharjee M, Ray KK, Muraleedharan TS, Arun A, Sathyavathi R, Juluri RR, Satyam PV, Panda AK, Biswas A, Nayak S, Bojja S, Pratihar S, Roy S. Mercury based drug in ancient India: The red sulfide of mercury in nanoscale. J Ayurveda Integr Med 2017; 8:93-98. [PMID: 28600164 PMCID: PMC5497007 DOI: 10.1016/j.jaim.2017.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 11/26/2022] Open
Abstract
Mercury is one of the elements which had attracted the attention of the chemists and physicians of ancient India and China. Among the various metal based drugs which utilize mercury, we became interested in the red sulfide of mercury which is known in ancient Indian literature as rasasindur (alias rasasindura, rasasindoor, rasasinduram, sindur, or sindoor) and is used extensively in various ailments and diseases. Following various physico-chemical characterizations it is concluded that rasasindur is chemically pure α-HgS with Hg:S ratio as 1:1. Analysis of rasasindur vide Transmission Electron Microscopy (TEM) showed that the particles are in nanoscale. Bio-chemical studies of rasasindur were also demonstrated. It interacts with Bovine Serum Albumin (BSA) with an association constant of (9.76 ± 0.56) × 103 M−1 and behaves as a protease inhibitor by inhibiting the proteolysis of BSA by trypsin. It also showed mild antioxidant properties.
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Affiliation(s)
- Priyabrata Mukhi
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751007, India
| | | | - M Bhattacharjee
- Chemistry Department, Indian Institute of Technology, Kharagpur 721302, India
| | - K K Ray
- Metallurgical & Materials Engineering Department, Indian Institute of Technology, Kharagpur 721302, India
| | | | - A Arun
- Arya Vaidya Sala, Kottakkal 676503, Kerala, India
| | - R Sathyavathi
- School of Physics, University of Hyderabad, Hyderabad 500046, India
| | - R R Juluri
- Institute of Physics, Bhubaneswar 751005, India
| | - P V Satyam
- Institute of Physics, Bhubaneswar 751005, India
| | - Alok K Panda
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751007, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751007, India
| | - S Nayak
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751007, India
| | | | - S Pratihar
- Department of Chemical Sciences, Tezpur University, 784028, India
| | - Sujit Roy
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751007, India.
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53
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Wang QL, Xie J, Li XD, Ding LS, Liang J, Luo P, Qing LS. Development of a nano-SiO 2 based enzyme-linked ligand binding assay for the determination of ibuprofen in human urine. Talanta 2017; 167:617-622. [DOI: 10.1016/j.talanta.2017.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 12/24/2022]
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Al-Ghobashy MA, ElMeshad AN, Abdelsalam RM, Nooh MM, Al-Shorbagy M, Laible G. Development and Pre-Clinical Evaluation of Recombinant Human Myelin Basic Protein Nano Therapeutic Vaccine in Experimental Autoimmune Encephalomyelitis Mice Animal Model. Sci Rep 2017; 7:46468. [PMID: 28425447 PMCID: PMC5397842 DOI: 10.1038/srep46468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/15/2017] [Indexed: 02/08/2023] Open
Abstract
Recombinant human myelin basic protein (rhMBP) was previously produced in the milk of transgenic cows. Differences in molecular recognition of either hMBP or rhMBP by surface-immobilized anti-hMBP antibodies were demonstrated. This indicated differences in immunological response between rhMBP and hMBP. Here, the activity of free and controlled release rhMBP poly(ε-caprolactone) nanoparticles (NPs), as a therapeutic vaccine against multiple sclerosis (MS) was demonstrated in experimental autoimmune encephalomyelitis (EAE) animal model. Following optimization of nanoformulation, discrete spherical, rough-surfaced rhMBP NPs with high entrapment efficiency and controlled release pattern were obtained. Results indicated that rhMBP was loaded into and electrostatically adsorbed onto the surface of NPs. Subcutaneous administration of free or rhMBP NPs before EAE-induction reduced the average behavioral score in EAE mice and showed only mild histological alterations and preservation of myelin sheath, with rhMBP NPs showing increased protection. Moreover, analysis of inflammatory cytokines (IFN-γ and IL-10) in mice brains revealed that pretreatment with free or rhMBP NPs significantly protected against induced inflammation. IN CONCLUSION i) rhMBP ameliorated EAE symptoms in EAE animal model, ii) nanoformulation significantly enhanced efficacy of rhMBP as a therapeutic vaccine and iii) clinical investigations are required to demonstrate the activity of rhMBP NPs as a therapeutic vaccine for MS.
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Affiliation(s)
- Medhat A. Al-Ghobashy
- Analytical Chemistry Department of, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Bioanalysis Research Group, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Aliaa N. ElMeshad
- Pharmaceutics and Industrial Pharmacy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Rania M. Abdelsalam
- Pharmacology & Toxicology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mohammed M. Nooh
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Muhammad Al-Shorbagy
- Pharmacology & Toxicology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Götz Laible
- AgRresearch, Ruakura Research Centre, Hamilton, New Zealand
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Intrinsically Disordered Regions in Serum Albumin: What Are They For? Cell Biochem Biophys 2017; 76:39-57. [PMID: 28281231 DOI: 10.1007/s12013-017-0785-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/13/2017] [Indexed: 12/16/2022]
Abstract
Serum albumin is a major plasma protein in mammalian blood. The importance of this protein lies in its roles in both bioregulation and transport phenomena. Serum albumin binds various metal ions and participates in the transport and storage of fatty acids, bilirubin, steroids amino acids, and many other ligands, usually with regions of hydrophobic surface. Although the primary role of serum albumin is to transport various ligand, its versatile binding capacities and high concentration mean that it can assume a number of additional functions. The major goal of this article is to show how intrinsic disorder is encoded in the amino acid sequence of serum albumin, and how intrinsic disorder is related to functions of this important serum protein.
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Van Vleet TR, Liu H, Lee A, Blomme EAG. Acyl glucuronide metabolites: Implications for drug safety assessment. Toxicol Lett 2017; 272:1-7. [PMID: 28286018 DOI: 10.1016/j.toxlet.2017.03.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 02/17/2017] [Accepted: 03/05/2017] [Indexed: 12/23/2022]
Abstract
Acyl glucuronides are important metabolites of compounds with carboxylic acid moieties and have unique properties that distinguish them from other phase 2 metabolites. In particular, in addition to being often unstable, acyl glucuronide metabolites can be chemically reactive leading to covalent binding with macromolecules and toxicity. While there is circumstantial evidence that drugs forming acyl glucuronide metabolites can be associated with rare, but severe idiosyncratic toxic reactions, many widely prescribed drugs with good safety records are also metabolized through acyl glucuronidation. Therefore, there is a need to understand the various factors that can affect the safety of acyl glucuronide-producing drugs including the rate of acyl glucuronide formation, the relative reactivity of the acyl glucuronide metabolite formed, the rate of elimination, potential proteins being targeted, and the rate of aglucuronidation. In this review, these factors are discussed and various approaches to de-risk the safety liabilities of acyl glucuronide metabolites are evaluated.
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Affiliation(s)
- Terry R Van Vleet
- Abbvie, Development Sciences, Department of Preclinical Safety, United States.
| | - Hong Liu
- Abbvie, Development Sciences, Biomeasure and Metabolism, United States
| | - Anthony Lee
- Abbvie, Development Sciences, Biomeasure and Metabolism, United States
| | - Eric A G Blomme
- Abbvie, Development Sciences, Department of Preclinical Safety, United States
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Yang L, Yang W, Wu Z, Yi Z. Binding of hydroxylated polybrominated diphenyl ethers with human serum albumin: Spectroscopic characterization and molecular modeling. LUMINESCENCE 2017; 32:978-987. [DOI: 10.1002/bio.3280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 12/01/2016] [Accepted: 12/16/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Lulu Yang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area College of Chemistry and Bioengineering; Guilin University of Technology; Guilin China
| | - Wu Yang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area College of Chemistry and Bioengineering; Guilin University of Technology; Guilin China
| | - Zhiwei Wu
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area College of Chemistry and Bioengineering; Guilin University of Technology; Guilin China
| | - Zhongsheng Yi
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area College of Chemistry and Bioengineering; Guilin University of Technology; Guilin China
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58
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Tiwari G, Verma CS. Toward Understanding the Molecular Recognition of Albumin by p53-Activating Stapled Peptide ATSP-7041. J Phys Chem B 2017; 121:657-670. [PMID: 28048940 DOI: 10.1021/acs.jpcb.6b09900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactivation of tumor-suppressing activity of p53 protein by targeting its negative regulator MDM2/MDMX has been pursued as a potential anticancer strategy. A promising dual inhibitor of MDM2/MDMX that has been developed and is currently in clinical trials is the stapled peptide ATSP-7041. The activity of this molecule is reported to be modulated in the presence of serum. Albumin is the most abundant protein in serum and is known to bind reversibly to several molecules. To study this interaction, we develop a protocol combining molecular modeling, docking, and simulations. Exhaustive docking of the peptide with representative simulated structures of human serum albumin led to the identification of probable binding sites on the surface of the protein, including both known canonical and novel binding sites. Sequence differences at putative peptide-binding sites in human and mouse albumin result in differing interaction energies with the peptide and enable us to rationalize the observed differences in vivo. In general, the findings should help in guiding the design of features in such peptides that may affect their distribution and cell permeability, opening a new window in structure-guided design strategies.
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Affiliation(s)
- Garima Tiwari
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.,Department of Biological sciences, National University of Singapore , 14 Science Drive 4, Singapore 117543, Singapore.,School of Biological sciences, Nanyang Technological University , 50 Nanyang Drive, Singapore 637551, Singapore
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59
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Hamzeh-Mivehroud M, Sokouti B, Dastmalchi S. Molecular Docking at a Glance. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The current chapter introduces different aspects of molecular docking technique in order to give an overview to the readers about the topics which will be dealt with throughout this volume. Like many other fields of science, molecular docking studies has experienced a lagging period of slow and steady increase in terms of acquiring attention of scientific community as well as its frequency of application, followed by a pronounced era of exponential expansion in theory, methodology, areas of application and performance due to developments in related technologies such as computational resources and theoretical as well as experimental biophysical methods. In the following sections the evolution of molecular docking will be reviewed and its different components including methods, search algorithms, scoring functions, validation of the methods, and area of applications plus few case studies will be touched briefly.
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Affiliation(s)
| | | | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Iran & School of Pharmacy, Tabriz University of Medical Sciences, Iran
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60
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Takić MM, Jovanović VB, Pavićević ID, Uzelac TN, Aćimović JM, Ristić-Medić DK, Mandić LM. Binding of enterolactone and enterodiol to human serum albumin: increase of cysteine-34 thiol group reactivity. Food Funct 2016; 7:1217-26. [PMID: 26838610 DOI: 10.1039/c5fo01346a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interaction of polyphenolic molecules with human serum albumin (HSA) could lead to changes in the reactivity of the HSA Cys34 thiol group (HSA-SH). The influences of enterolactone (EL) and enterodiol (ED) binding on HSA-SH reactivity in fatty acid (FA)-free HSA, and in HSA with bound stearic acid (S) in S/HSA molar ratios of 1:1 and 4:1, were investigated by the determination of the pseudo first order rate constants (k') for the thiol reaction with 5,5'-dithiobis-(2-nitrobenzoic acid). The binding affinities and binding sites of EL and ED were also determined, using fluorescence measurements of the intrinsic fluorescence of Trp214 and diazepam (binding site marker). EL and ED binding to HSA increased the reactivity of HSA-SH in all assayed HSA-enterolignan complexes by 9.1-33.1%. The strongest effects were obtained for FA-free HSA-enterolignan complexes. S modulated/reduced the effect of EL on HSA-SH reactivity, while its influence on the effect of ED was negligible. The binding of enterolignans to HSA was investigated: the binding constants were the highest for FA-free HSA (EL: 11.64 × 10(4) M(-1) and ED: 5.59 × 10(4) M(-1) at 37 °C) and the lowest for S/HSA 4:1-enterolignan complexes (EL: 2.43 × 10(4) M(-1) and ED: 1.92 × 10(4) M(-1)). When the S/HSA ratio was increased, the binding affinities and number of binding sites for EL and ED were decreased. At the same time, a high correlation between binding constants and increased Cys34 reactivity was found (r = 0.974). Competitive experiments using diazepam indicated that the binding of ED and of EL was located in the hydrophobic pocket of site II in HSA. Overall, it is evident that stearic acid could modulate the enterolignan effects on HSA-SH reactivity as well as their binding to HSA. This finding could be important for pharmacokinetics and the expression of enterolignan antioxidant effects in vivo after an intake of lignan rich food.
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Affiliation(s)
- Marija M Takić
- Institute for Medical Research, Center of research excellence in nutrition and metabolism, University of Belgrade, Belgrade, Serbia
| | - Vesna B Jovanović
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11158, Serbia.
| | - Ivan D Pavićević
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11158, Serbia.
| | - Tamara N Uzelac
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11158, Serbia.
| | - Jelena M Aćimović
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11158, Serbia.
| | - Danijela K Ristić-Medić
- Institute for Medical Research, Center of research excellence in nutrition and metabolism, University of Belgrade, Belgrade, Serbia
| | - Ljuba M Mandić
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11158, Serbia.
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61
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Mohammadi T, Ghayeb Y, Sharifi T, Khayamian T. The effect of dichlorvos on the structural alteration of serum albumins: a combined spectroscopic and molecular dynamic simulation approach. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-016-1857-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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62
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Study of conformational changes in serum albumin by binding of chlorfenvinphos using multispectroscopic techniques and molecular dynamic simulation. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-016-1814-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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63
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Synthesis, spectroscopic characterization, X-ray structure, and in vivo neurotropic activity of new 1,5-benzodiazepin-2-ones. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1605-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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64
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Computational approaches to find the active binding sites of biological targets against busulfan. J Mol Model 2016; 22:142. [DOI: 10.1007/s00894-016-3015-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/19/2016] [Indexed: 10/21/2022]
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65
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Ding F, Xie Y, Peng W, Peng YK. Measuring the bioactivity and molecular conformation of typically globular proteins with phenothiazine-derived methylene blue in solid and in solution: A comparative study using photochemistry and computational chemistry. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:69-80. [PMID: 26950891 DOI: 10.1016/j.jphotobiol.2016.02.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Methylene blue is a phenothiazine agent, that possesses a diversity of biomedical and biological therapeutic purpose, and it has also become the lead compound for the exploitation of other pharmaceuticals such as chlorpromazine and the tricyclic antidepressants. However, the U.S. Food and Drug Administration has acquired cases of detrimental effects of methylene blue toxicities such as hemolytic anemia, methemoglobinemia and phototoxicity. In this work, the molecular recognition of methylene blue by two globular proteins, hemoglobin and lysozyme was characterized by employing fluorescence, circular dichroism (CD) along with molecular modeling at the molecular scale. The recognition of methylene blue with proteins appears fluorescence quenching via static type, this phenomenon does cohere with time-resolved fluorescence lifetime decay that nonfluorescent protein-drug conjugate formation has a strength of 10(4)M(-1), and the primary noncovalent bonds, that is hydrogen bonds, π-conjugated effects and hydrophobic interactions were operated and remained adduct stable. Meantime, the results of far-UV CD and synchronous fluorescence suggest that the α-helix of hemoglobin/lysozyme decreases from 78.2%/34.7% (free) to 58.7%/23.8% (complex), this elucidation agrees well with the elaborate description of three-dimensional fluorescence showing the polypeptide chain of proteins partially destabilized upon conjugation with methylene blue. Furthermore, both extrinsic fluorescent indicator and molecular modeling clearly exhibit methylene blue is situated within the cavity constituted by α1, β2 and α2 subunits of hemoglobin, while it was located at the deep fissure on the lysozyme surface and Trp-62 and Trp-63 residues are nearby. With the aid of computational analyses and combining the wet experiments, it can evidently be found that the recognition ability of proteins for methylene blue is patterned upon the following sequence: lysozyme<hemoglobin<albumin. Basically, the distinction originates from different spatial structures of proteins and noncovalent interactions between proteins and methylene blue. In addition, biological relevance of the biorecognition of methylene blue with proteins was briefly discussed. We hope that this study could provide further standpoint so that one explore the biological activity of methylene blue and also phenothiazines.
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Affiliation(s)
- Fei Ding
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China; Department of Chemistry, China Agricultural University, Beijing 100193, China; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Yong Xie
- State Key Laboratory of the Discovery and Development of Novel Pesticide, Shenyang Research Institute of Chemical Industry Co. Ltd., Shenyang 110021, China
| | - Wei Peng
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China; College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - Yu-Kui Peng
- Center for Food Quality Supervision & Testing, Ministry of Agriculture, College of Food Science & Engineering, Northwest A&F University, Yangling 712100, China
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66
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Binding interaction, conformational change, and molecular docking study of N-(pyridin-2-ylmethylene)aniline derivatives and carbazole Ru(II) complexes with human serum albumins. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.01.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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67
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Hjort M, Bauer M, Gunnarsson S, Mårsell E, Zakharov AA, Karlsson G, Sanfins E, Prinz CN, Wallenberg R, Cedervall T, Mikkelsen A. Electron microscopy imaging of proteins on gallium phosphide semiconductor nanowires. NANOSCALE 2016; 8:3936-43. [PMID: 26838122 DOI: 10.1039/c5nr08888g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We have imaged GaP nanowires (NWs) incubated with human laminin, serum albumin (HSA), and blood plasma using both cryo-transmission electron microscopy and synchrotron based X-ray photoemission electron microscopy. This extensive imaging methodology simultaneously reveals structural, chemical and morphological details of individual nanowires and the adsorbed proteins. We found that the proteins bind to NWs, forming coronas with thicknesses close to the proteins' hydrodynamic diameters. We could directly image how laminin is extending from the NWs, maximizing the number of proteins bound to the NWs. NWs incubated with both laminin and HSA show protein coronas with a similar appearance to NWs incubated with laminin alone, indicating that the presence of HSA does not affect the laminin conformation on the NWs. In blood plasma, an intermediate sized corona around the NWs indicates a corona with a mixture of plasma proteins. The ability to directly visualize proteins on nanostructures in situ holds great promise for assessing the conformation and thickness of the protein corona, which is key to understanding and predicting the properties of engineered nanomaterials in a biological environment.
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Affiliation(s)
- Martin Hjort
- Division of Synchrotron Radiation Research, Department of Physics, Lund University, P.O. Box 118, 221 00 Lund, Sweden.
| | - Mikael Bauer
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| | - Stefan Gunnarsson
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| | - Erik Mårsell
- Division of Synchrotron Radiation Research, Department of Physics, Lund University, P.O. Box 118, 221 00 Lund, Sweden.
| | - Alexei A Zakharov
- The MAX-IV Laboratory, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| | - Gunnel Karlsson
- nCHREM/Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Elodie Sanfins
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| | - Christelle N Prinz
- Division of Solid State Physics, Department of Physics, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| | - Reine Wallenberg
- nCHREM/Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Tommy Cedervall
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| | - Anders Mikkelsen
- Division of Synchrotron Radiation Research, Department of Physics, Lund University, P.O. Box 118, 221 00 Lund, Sweden.
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68
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Systems Pharmacology in Small Molecular Drug Discovery. Int J Mol Sci 2016; 17:246. [PMID: 26901192 PMCID: PMC4783977 DOI: 10.3390/ijms17020246] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 12/15/2022] Open
Abstract
Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity), target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level.
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Abstract
In recent decades, in silico absorption, distribution, metabolism, excretion (ADME), and toxicity (T) modelling as a tool for rational drug design has received considerable attention from pharmaceutical scientists, and various ADME/T-related prediction models have been reported. The high-throughput and low-cost nature of these models permits a more streamlined drug development process in which the identification of hits or their structural optimization can be guided based on a parallel investigation of bioavailability and safety, along with activity. However, the effectiveness of these tools is highly dependent on their capacity to cope with needs at different stages, e.g. their use in candidate selection has been limited due to their lack of the required predictability. For some events or endpoints involving more complex mechanisms, the current in silico approaches still need further improvement. In this review, we will briefly introduce the development of in silico models for some physicochemical parameters, ADME properties and toxicity evaluation, with an emphasis on the modelling approaches thereof, their application in drug discovery, and the potential merits or deficiencies of these models. Finally, the outlook for future ADME/T modelling based on big data analysis and systems sciences will be discussed.
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70
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All-Purpose Containers? Lipid-Binding Protein - Drug Interactions. PLoS One 2015; 10:e0132096. [PMID: 26167932 PMCID: PMC4500398 DOI: 10.1371/journal.pone.0132096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 06/10/2015] [Indexed: 01/30/2023] Open
Abstract
The combined use of in vitro (19F-NMR) and in silico (molecular docking) procedures demonstrates the affinity of a number of human calycins (lipid-binding proteins from ileum, liver, heart, adipose tissue and epidermis, and retinol-binding protein from intestine) for different drugs (mainly steroids and vastatins). Comparative evaluations on the complexes outline some of the features relevant for interaction (non-polar character of the drugs; amino acids and water molecules in the protein calyx most often involved in binding). Dissociation constants (Ki) for drugs typically lie in the same range as Ki for natural ligands; in most instances (different proteins and docking conditions), vastatins are the strongest interactors, with atorvastatin ranking top in half of the cases. The affinity of some calycins for some of the vastatins is in the order of magnitude of the drug Cmax after systemic administration in humans. The possible biological implications of this feature are discussed in connection with drug delivery parameters (route of administration, binding to carrier proteins, distribution to, and accumulation in, human tissues).
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71
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Recent progresses in the exploration of machine learning methods as in-silico ADME prediction tools. Adv Drug Deliv Rev 2015; 86:83-100. [PMID: 26037068 DOI: 10.1016/j.addr.2015.03.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/18/2015] [Accepted: 03/22/2015] [Indexed: 02/05/2023]
Abstract
In-silico methods have been explored as potential tools for assessing ADME and ADME regulatory properties particularly in early drug discovery stages. Machine learning methods, with their ability in classifying diverse structures and complex mechanisms, are well suited for predicting ADME and ADME regulatory properties. Recent efforts have been directed at the broadening of application scopes and the improvement of predictive performance with particular focuses on the coverage of ADME properties, and exploration of more diversified training data, appropriate molecular features, and consensus modeling. Moreover, several online machine learning ADME prediction servers have emerged. Here we review these progresses and discuss the performances, application prospects and challenges of exploring machine learning methods as useful tools in predicting ADME and ADME regulatory properties.
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72
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Lambrinidis G, Vallianatou T, Tsantili-Kakoulidou A. In vitro, in silico and integrated strategies for the estimation of plasma protein binding. A review. Adv Drug Deliv Rev 2015; 86:27-45. [PMID: 25819487 DOI: 10.1016/j.addr.2015.03.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 02/11/2015] [Accepted: 03/20/2015] [Indexed: 12/28/2022]
Abstract
Plasma protein binding (PPB) strongly affects drug distribution and pharmacokinetic behavior with consequences in overall pharmacological action. Extended plasma protein binding may be associated with drug safety issues and several adverse effects, like low clearance, low brain penetration, drug-drug interactions, loss of efficacy, while influencing the fate of enantiomers and diastereoisomers by stereoselective binding within the body. Therefore in holistic drug design approaches, where ADME(T) properties are considered in parallel with target affinity, considerable efforts are focused in early estimation of PPB mainly in regard to human serum albumin (HSA), which is the most abundant and most important plasma protein. The second critical serum protein α1-acid glycoprotein (AGP), although often underscored, plays also an important and complicated role in clinical therapy and thus the last years it has been studied thoroughly too. In the present review, after an overview of the principles of HSA and AGP binding as well as the structure topology of the proteins, the current trends and perspectives in the field of PPB predictions are presented and discussed considering both HSA and AGP binding. Since however for the latter protein systematic studies have started only the last years, the review focuses mainly to HSA. One part of the review highlights the challenge to develop rapid techniques for HSA and AGP binding simulation and their performance in assessment of PPB. The second part focuses on in silico approaches to predict HSA and AGP binding, analyzing and evaluating structure-based and ligand-based methods, as well as combination of both methods in the aim to exploit the different information and overcome the limitations of each individual approach. Ligand-based methods use the Quantitative Structure-Activity Relationships (QSAR) methodology to establish quantitate models for the prediction of binding constants from molecular descriptors, while they provide only indirect information on binding mechanism. Efforts for the establishment of global models, automated workflows and web-based platforms for PPB predictions are presented and discussed. Structure-based methods relying on the crystal structures of drug-protein complexes provide detailed information on the underlying mechanism but are usually restricted to specific compounds. They are useful to identify the specific binding site while they may be important in investigating drug-drug interactions, related to PPB. Moreover, chemometrics or structure-based modeling may be supported by experimental data a promising integrated alternative strategy for ADME(T) properties optimization. In the case of PPB the use of molecular modeling combined with bioanalytical techniques is frequently used for the investigation of AGP binding.
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73
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Sun J, Huang Y, Zheng C, Zhou Y, Liu Y, Liu J. Ruthenium (II) complexes interact with human serum albumin and induce apoptosis of tumor cells. Biol Trace Elem Res 2015; 163:266-74. [PMID: 25398541 DOI: 10.1007/s12011-014-0165-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/24/2014] [Indexed: 10/24/2022]
Abstract
The interaction of ruthenium (II) complex [Ru(bpy)2(mal)](2+) (RBM) and [Ru(phen)2(mal)](2+) (RPM) (bpy = 2, 2-bipyridine, phen = 1,10-phenanthroline, mal = malonyl carboxylate) with human serum albumin (HSA) has been investigated by using fluorescence, UV absorption and circular dichroism (CD) spectroscopy approaches. A strong fluorescence quenching reaction of complexes to HSA was observed and the quenching mechanism was suggested as static quenching according to the Stern-Volmer (S-V) equation. The number of binding sites n and observed binding constant Kb was measured by fluorescence quenching method. The thermodynamic parameters ΔH, ΔS, and ΔG at different temperatures were calculated and the results indicate the binding reaction is mainly entropy-driven and Vander Waals force played a major role in the reaction. The result of CD showed that the secondary structure of HSA molecules was changed in the presence of the ruthenium (II) complexes. Furthermore, the cell viability of ruthenium (II) complexes was evaluated by MTT and complex RPM has shown significant higher anticancer potency than RBM against all the cell lines screened. RPM showed a significant antitumor activity through induction of apoptosis in A549 cells.
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Affiliation(s)
- Jing Sun
- Department of Chemistry, Jinan University, Guangzhou, 510632, People's Republic of China
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74
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Yang H, Zhang W, Huang C, Zhou W, Yao Y, Wang Z, Li Y, Xiao W, Wang Y. A novel systems pharmacology model for herbal medicine injection: a case using Reduning injection. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 14:430. [PMID: 25366653 PMCID: PMC4506441 DOI: 10.1186/1472-6882-14-430] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 10/09/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Compared with the traditional oral administration form, injection administration is basically superior in terms of both biological availability and therapeutic effects. However, few researches have focused on the traditional Chinese medicinal injection due to the complicated constituents and the intricate mechanism of action. METHODS In the present work, a novel systems pharmacology model, integrating ADME (absorption, distribution, metabolism, and excretion) filtering such as half-life evaluation, network targeting, pathway and systems analyses, is specifically developed for the identification of active compounds and the study of the mechanism of action of TCM injection, which is exemplified by Reduning injection confronting the influenza. RESULTS The ADME filter successfully identifies 35 bioactive compounds (31 molecules and 4 metabolites) from the Reduning injection. The systems analysis and experimental validation further reveal a new way of confronting influenza disease of this injection: 1) stimulating the immunomodulatory agents for immune response activation, and 2) regulating the inflammatory agents for anti-inflammation. CONCLUSIONS The novel systems pharmacology method used in this study has the potential to advance the understanding of the molecular mechanisms of action of multicomponent herbal injections, and provide clues to discovering more effective drugs against complex diseases.
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75
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Del Giudice A, Leggio C, Balasco N, Galantini L, Pavel NV. Ibuprofen and Propofol Cobinding Effect on Human Serum Albumin Unfolding in Urea. J Phys Chem B 2014; 118:10043-51. [DOI: 10.1021/jp504280n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Alessandra Del Giudice
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
| | - Claudia Leggio
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
| | - Nicole Balasco
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
| | - Luciano Galantini
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
| | - Nicolae V. Pavel
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
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76
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Indurthi VS, Leclerc E, Vetter SW. Calorimetric investigation of diclofenac drug binding to a panel of moderately glycated serum albumins. Eur J Pharm Sci 2014; 59:58-68. [DOI: 10.1016/j.ejps.2014.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 01/27/2023]
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77
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Prashanth AK, Anand U. Clinical significance of ischemia modified albumin in critically ill patients with sepsis. Indian J Clin Biochem 2014; 30:194-7. [PMID: 25883428 DOI: 10.1007/s12291-014-0434-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/15/2014] [Indexed: 11/24/2022]
Abstract
The study was conducted on 38 patients admitted into the intensive care unit with a provisional diagnosis of sepsis and 25 apparently healthy volunteers as controls. Serum procalcitonin (PCT) was assayed by an electrochemiluminescence method. Serum ischemia modified albumin (IMA), expressed as absorbance units was assayed by the albumin cobalt binding test. Patients with sepsis had significantly higher IMA levels (1.087 ± 0.786) as compared with those without sepsis (0.085 ± 0.234) with a p value <0.0001. The receiver operator characteristic (ROC) plot showed a sensitivity of 100 % and a specificity of 86.2 %. The area under the curve of the ROC plot was 0.917 with a p value of <0.0001. The higher levels of IMA serve to highlight the occurrence of ischemic damage which could be a prelude to poorer prognosis. The performance characteristics of IMA warrants its inclusion along with PCT as a parameter in the diagnosis of sepsis.
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Affiliation(s)
- A K Prashanth
- PSG Institute of Medical Sciences and Research, Peelamedu, Coimbatore, 641004 Tamil Nadu India
| | - Usha Anand
- Department of Biochemistry, PSG Institute of Medical Sciences and Research, Peelamedu, Coimbatore, 641004 Tamil Nadu India ; Clinical Biochemistry, Anand Diagnostic Laboratory, Blue Cross Chambers, Shivaji Nagar, Bangalore, 560001 India
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78
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Lexa KW, Dolghih E, Jacobson MP. A structure-based model for predicting serum albumin binding. PLoS One 2014; 9:e93323. [PMID: 24691448 PMCID: PMC3972100 DOI: 10.1371/journal.pone.0093323] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/04/2014] [Indexed: 11/21/2022] Open
Abstract
One of the many factors involved in determining the distribution and metabolism of a compound is the strength of its binding to human serum albumin. While experimental and QSAR approaches for determining binding to albumin exist, various factors limit their ability to provide accurate binding affinity for novel compounds. Thus, to complement the existing tools, we have developed a structure-based model of serum albumin binding. Our approach for predicting binding incorporated the inherent flexibility and promiscuity known to exist for albumin. We found that a weighted combination of the predicted logP and docking score most accurately distinguished between binders and nonbinders. This model was successfully used to predict serum albumin binding in a large test set of therapeutics that had experimental binding data.
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Affiliation(s)
- Katrina W. Lexa
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| | - Elena Dolghih
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
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79
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Regenhardt RW, Bennion DM, Sumners C. Cerebroprotective action of angiotensin peptides in stroke. Clin Sci (Lond) 2014; 126:195-205. [PMID: 24102099 PMCID: PMC7453725 DOI: 10.1042/cs20130324] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The goal of the present review is to examine the evidence for beneficial actions of manipulation of the RAS (renin-angiotensin system) in stroke, with particular focus on Ang-(1-7) [angiotensin-(1-7)] and its receptor Mas. The RAS appears to be highly involved in the multifactorial pathophysiology of stroke. Blocking the effects of AngII (angiotensin II) at AT1R (AngII type 1 receptor), through the use of commonly prescribed ACE (angiotensin-converting enzyme) inhibitors or AT1R blockers, has been shown to have therapeutic effects in both ischaemic and haemorrhagic stroke. In contrast with the deleterious actions of over activation of AT1R by AngII, stimulation of AT2Rs (AngII type 2 receptors) in the brain has been demonstrated to elicit beneficial effects in stroke. Likewise, the ACE2/Ang-(1-7)/Mas axis of the RAS has been shown to have therapeutic effects in stroke when activated, countering the effects of the ACE/AngII/AT1R axis. Studies have demonstrated that activating this axis in the brain elicits beneficial cerebral effects in rat models of ischaemic stroke, and we have also demonstrated the cerebroprotective potential of this axis in haemorrhagic stroke using stroke-prone spontaneously hypertensive rats and collagenase-induced striatal haemorrhage. The mechanism of cerebroprotection elicited by ACE2/Ang-(1-7)/Mas activation includes anti-inflammatory effects within the brain parenchyma. The major hurdle to overcome in translating these results to humans is devising strategies to activate the ACE2/Ang-(1-7)/Mas cerebroprotective axis using post-stroke treatments that can be administered non-invasively.
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Affiliation(s)
- Robert W. Regenhardt
- Department of Physiology and Functional Genomics & McKnight Brain Institute, University of Florida, 1600 SW Archer Road, PO Box 100274, Gainesville, FL 32610-0274, USA
| | - Douglas M. Bennion
- Department of Physiology and Functional Genomics & McKnight Brain Institute, University of Florida, 1600 SW Archer Road, PO Box 100274, Gainesville, FL 32610-0274, USA
| | - Colin Sumners
- Department of Physiology and Functional Genomics & McKnight Brain Institute, University of Florida, 1600 SW Archer Road, PO Box 100274, Gainesville, FL 32610-0274, USA
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80
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Díaz Velázquez H, Ruiz García Y, Vandichel M, Madder A, Verpoort F. Water-soluble NHC-Cu catalysts: applications in click chemistry, bioconjugation and mechanistic analysis. Org Biomol Chem 2014; 12:9350-6. [DOI: 10.1039/c4ob01350f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A series of novel bis(NHC) Cu(i) catalysts enables the production of triazoles with different substitution patterns and bioconjugation via “click” chemistry under homogeneous and/or heterogeneous catalytic conditions in aqueous media.
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Affiliation(s)
- Heriberto Díaz Velázquez
- Laboratory of Organometallics
- Catalysis and Ordered Materials
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing; Center for Chemical and Material Engineering
- Wuhan University of Technology; Department of Applied Chemistry
- Faculty of Sciences
| | - Yara Ruiz García
- Department of Organic Chemistry
- Ghent University
- 9000 Ghent, Belgium
| | - Matthias Vandichel
- Department of Molecular Modelling
- Ghent University
- 9052 Zwijnaarde, Belgium
| | - Annemieke Madder
- Department of Organic Chemistry
- Ghent University
- 9000 Ghent, Belgium
| | - Francis Verpoort
- Laboratory of Organometallics
- Catalysis and Ordered Materials
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing; Center for Chemical and Material Engineering
- Wuhan University of Technology; Department of Applied Chemistry
- Faculty of Sciences
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81
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Castellanos MM, Colina CM. Molecular Dynamics Simulations of Human Serum Albumin and Role of Disulfide Bonds. J Phys Chem B 2013; 117:11895-905. [DOI: 10.1021/jp402994r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Maria Monica Castellanos
- Department of Materials Science
and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Coray M. Colina
- Department of Materials Science
and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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82
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Zhu XW, Sedykh A, Zhu H, Liu SS, Tropsha A. The use of pseudo-equilibrium constant affords improved QSAR models of human plasma protein binding. Pharm Res 2013; 30:1790-8. [PMID: 23568522 DOI: 10.1007/s11095-013-1023-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 03/04/2013] [Indexed: 12/21/2022]
Abstract
PURPOSE To develop accurate in silico predictors of Plasma Protein Binding (PPB). METHODS Experimental PPB data were compiled for over 1,200 compounds. Two endpoints have been considered: (1) fraction bound (%PPB); and (2) the logarithm of a pseudo binding constant (lnKa) derived from %PPB. The latter metric was employed because it reflects the PPB thermodynamics and the distribution of the transformed data is closer to normal. Quantitative Structure-Activity Relationship (QSAR) models were built with Dragon descriptors and three statistical methods. RESULTS Five-fold external validation procedure resulted in models with the prediction accuracy (R²) of 0.67 ± 0.04 and 0.66 ± 0.04, respectively, and the mean absolute error (MAE) of 15.3 ± 0.2% and 13.6 ± 0.2%, respectively. Models were validated with two external datasets: 173 compounds from DrugBank, and 236 chemicals from the US EPA ToxCast project. Models built with lnKa were significantly more accurate (MAE of 6.2-10.7 %) than those built with %PPB (MAE of 11.9-17.6 %) for highly bound compounds both for the training and the external sets. CONCLUSIONS The pseudo binding constant (lnKa) is more appropriate for characterizing PPB binding than conventional %PPB. Validated QSAR models developed herein can be applied as reliable tools in early drug development and in chemical risk assessment.
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Affiliation(s)
- Xiang-Wei Zhu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science & Engineering, Tongji University, 417 Mingjing Building, Shanghai 200092, China
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83
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Hall ML, Jorgensen WL, Whitehead L. Automated Ligand- and Structure-Based Protocol for in Silico Prediction of Human Serum Albumin Binding. J Chem Inf Model 2013; 53:907-22. [DOI: 10.1021/ci3006098] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michelle Lynn Hall
- Novartis Institutes for Biomedical Research, 100 Technology Square, Cambridge,
Massachusetts 02143, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Lewis Whitehead
- Novartis Institutes for Biomedical Research, 100 Technology Square, Cambridge,
Massachusetts 02143, United States
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84
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Bruno JG. A review of therapeutic aptamer conjugates with emphasis on new approaches. Pharmaceuticals (Basel) 2013; 6:340-57. [PMID: 24276022 PMCID: PMC3816688 DOI: 10.3390/ph6030340] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/09/2013] [Accepted: 03/11/2013] [Indexed: 12/14/2022] Open
Abstract
The potential to emulate or enhance antibodies with nucleic acid aptamers while lowering costs has prompted development of new aptamer-protein, siRNA, drug, and nanoparticle conjugates. Specific focal points of this review discuss DNA aptamers covalently bound at their 3' ends to various proteins for enhanced stability and greater pharmacokinetic lifetimes in vivo. The proteins can include Fc tails of IgG for opsonization, and the first component of complement (C1q) to trigger complement-mediated lysis of antibiotic-resistant Gram negative bacteria, cancer cells and possibly some parasites during vulnerable stages. In addition, the 3' protein adduct may be a biotoxin, enzyme, or may simply be human serum albumin (HSA) or a drug known to bind HSA, thereby retarding kidney and other organ clearance and inhibiting serum exonucleases. In this review, the author summarizes existing therapeutic aptamer conjugate categories and describes his patented concept for PCR-based amplification of double-stranded aptamers followed by covalent attachment of proteins or other agents to the chemically vulnerable overhanging 3' adenine added by Taq polymerase. PCR amplification of aptamers could dramatically lower the current $2,000/gram cost of parallel chemical oligonucleotide synthesis, thereby enabling mass production of aptamer-3'-protein or drug conjugates to better compete against expensive humanized monoclonal antibodies.
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Affiliation(s)
- John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 230, San Antonio, TX 78229, USA.
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85
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Vallianatou T, Lambrinidis G, Tsantili-Kakoulidou A. In silicoprediction of human serum albumin binding for drug leads. Expert Opin Drug Discov 2013; 8:583-95. [DOI: 10.1517/17460441.2013.777424] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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86
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In Silico Prediction of Interactions between Site II on Human Serum Albumin and Profen Drugs. ISRN PHARMACEUTICS 2013; 2013:818364. [PMID: 23533820 PMCID: PMC3606801 DOI: 10.1155/2013/818364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 02/06/2013] [Indexed: 12/04/2022]
Abstract
Since binding of a drug molecule to human serum albumin (HSA) significantly affects the pharmacokinetics of the drug, it is highly desirable to predict the binding affinity of the drug. Profen drugs are a widely used class of nonsteroidal anti-inflammatory drugs and it has been reported that several members of the profen class specifically bind to one of the main binding sites named site II. The actual binding mode of only ibuprofen has been directly confirmed by X-ray crystallography. Therefore, it is of interest whether other profen drugs are site II binders. Docking simulations using multiple template structures of HSA from three crystal structures of complexes between drugs and HSA have demonstrated that most of the currently available profen drugs should be site II binders.
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87
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De D, Kaur H, Datta A. Unusual Binding of a Potential Biomarker with Human Serum Albumin. Chem Asian J 2013; 8:728-35. [DOI: 10.1002/asia.201201060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Indexed: 11/10/2022]
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88
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Abou-Zied OK, Al-Lawatia N, Elstner M, Steinbrecher TB. Binding of Hydroxyquinoline Probes to Human Serum Albumin: Combining Molecular Modeling and Förster’s Resonance Energy Transfer Spectroscopy to Understand Flexible Ligand Binding. J Phys Chem B 2013; 117:1062-74. [DOI: 10.1021/jp311238n] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Osama K. Abou-Zied
- Department of Chemistry, Faculty
of Science, Sultan Qaboos University, P.O.
Box 36, Postal Code 123, Muscat, Sultanate of Oman
| | - Najla Al-Lawatia
- Department of Chemistry, Faculty
of Science, Sultan Qaboos University, P.O.
Box 36, Postal Code 123, Muscat, Sultanate of Oman
| | - Marcus Elstner
- Department for Theoretical Chemical
Biology, Institute for Physical Chemistry, Kaiserstr. 12, Karlsruhe Institute of Technology, 76131 Karlsruhe,
Germany
| | - Thomas B. Steinbrecher
- Department for Theoretical Chemical
Biology, Institute for Physical Chemistry, Kaiserstr. 12, Karlsruhe Institute of Technology, 76131 Karlsruhe,
Germany
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89
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Dixit N, Zeng DL, Kalonia DS. Application of maximum bubble pressure surface tensiometer to study protein–surfactant interactions. Int J Pharm 2012; 439:317-23. [DOI: 10.1016/j.ijpharm.2012.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 09/07/2012] [Accepted: 09/08/2012] [Indexed: 12/20/2022]
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90
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Zhivkova Z, Doytchinova I. Quantitative structure—plasma protein binding relationships of acidic drugs. J Pharm Sci 2012; 101:4627-41. [DOI: 10.1002/jps.23303] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 07/24/2012] [Accepted: 08/02/2012] [Indexed: 11/08/2022]
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91
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Chatterjee T, Pal A, Dey S, Chatterjee BK, Chakrabarti P. Interaction of virstatin with human serum albumin: spectroscopic analysis and molecular modeling. PLoS One 2012; 7:e37468. [PMID: 22649528 PMCID: PMC3359307 DOI: 10.1371/journal.pone.0037468] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 04/24/2012] [Indexed: 12/20/2022] Open
Abstract
Virstatin is a small molecule that inhibits Vibrio cholerae virulence regulation, the causative agent for cholera. Here we report the interaction of virstatin with human serum albumin (HSA) using various biophysical methods. The drug binding was monitored using different isomeric forms of HSA (N form ∼pH 7.2, B form ∼pH 9.0 and F form ∼pH 3.5) by absorption and fluorescence spectroscopy. There is a considerable quenching of the intrinsic fluorescence of HSA on binding the drug. The distance (r) between donor (Trp214 in HSA) and acceptor (virstatin), obtained from Forster-type fluorescence resonance energy transfer (FRET), was found to be 3.05 nm. The ITC data revealed that the binding was an enthalpy-driven process and the binding constants K(a) for N and B isomers were found to be 6.09×10(5 )M(-1) and 4.47×10(5) M(-1), respectively. The conformational changes of HSA due to the interaction with the drug were investigated from circular dichroism (CD) and Fourier Transform Infrared (FTIR) spectroscopy. For 1:1 molar ratio of the protein and the drug the far-UV CD spectra showed an increase in α- helicity for all the conformers of HSA, and the protein is stabilized against urea and thermal unfolding. Molecular docking studies revealed possible residues involved in the protein-drug interaction and indicated that virstatin binds to Site I (subdomain IIA), also known as the warfarin binding site.
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Affiliation(s)
| | - Aritrika Pal
- Department of Biochemistry, Bose Institute, Kolkata, India
| | - Sucharita Dey
- Bioinformatics Centre, Bose Institute, Kolkata, India
| | | | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, Kolkata, India
- Bioinformatics Centre, Bose Institute, Kolkata, India
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92
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Ding F, Li XN, Diao JX, Sun Y, Zhang L, Sun Y. Chiral recognition of metalaxyl enantiomers by human serum albumin: evidence from molecular modeling and photophysical approach. Chirality 2012; 24:471-80. [DOI: 10.1002/chir.22024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/23/2012] [Indexed: 01/27/2023]
Affiliation(s)
- Fei Ding
- Department of Chemistry; China Agricultural University; Beijing; China
| | - Xiu-Nan Li
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing; China
| | - Jian-Xiong Diao
- College of Resources and Environmental Sciences; China Agricultural University; Beijing; China
| | - Ye Sun
- Department of Chemistry; China Agricultural University; Beijing; China
| | - Li Zhang
- Key Laboratory of Pesticide Chemistry and Application Technology, Ministry of Agriculture, Department of Applied Chemistry; China Agricultural University; Beijing; China
| | - Ying Sun
- College of Resources and Environmental Sciences; China Agricultural University; Beijing; China
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93
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Moroy G, Martiny VY, Vayer P, Villoutreix BO, Miteva MA. Toward in silico structure-based ADMET prediction in drug discovery. Drug Discov Today 2011; 17:44-55. [PMID: 22056716 DOI: 10.1016/j.drudis.2011.10.023] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/07/2011] [Accepted: 10/21/2011] [Indexed: 12/12/2022]
Abstract
Quantitative structure-activity relationship (QSAR) methods and related approaches have been used to investigate the molecular features that influence the absorption, distribution, metabolism, excretion and toxicity (ADMET) of drugs. As the three-dimensional structures of several major ADMET proteins become available, structure-based (docking-scoring) computations can be carried out to complement or to go beyond QSAR studies. Applying docking-scoring methods to ADMET proteins is a challenging process because they usually have a large and flexible binding cavity; however, promising results relating to metabolizing enzymes have been reported. After reviewing current trends in the field we applied structure-based methods in the context of receptor flexibility in a case study involving the phase II metabolizing sulfotransferases. Overall, the explored concepts and results suggested that structure-based ADMET profiling will probably join the mainstream during the coming years.
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Affiliation(s)
- Gautier Moroy
- Inserm UMR-S 973, Molécules Thérapeutiques In Silico, Université Paris Diderot, Sorbonne Paris Cité, 35 Rue Helene Brion, 75013 Paris, France
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94
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Krasowski MD, Hopfinger AJ. The discovery of new anesthetics by targeting GABAAreceptors. Expert Opin Drug Discov 2011; 6:1187-201. [DOI: 10.1517/17460441.2011.627324] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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95
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Predicting P-glycoprotein-mediated drug transport based on support vector machine and three-dimensional crystal structure of P-glycoprotein. PLoS One 2011; 6:e25815. [PMID: 21991360 PMCID: PMC3186768 DOI: 10.1371/journal.pone.0025815] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/11/2011] [Indexed: 01/16/2023] Open
Abstract
Human P-glycoprotein (P-gp) is an ATP-binding cassette multidrug transporter that confers resistance to a wide range of chemotherapeutic agents in cancer cells by active efflux of the drugs from cells. P-gp also plays a key role in limiting oral absorption and brain penetration and in facilitating biliary and renal elimination of structurally diverse drugs. Thus, identification of drugs or new molecular entities to be P-gp substrates is of vital importance for predicting the pharmacokinetics, efficacy, safety, or tissue levels of drugs or drug candidates. At present, publicly available, reliable in silico models predicting P-gp substrates are scarce. In this study, a support vector machine (SVM) method was developed to predict P-gp substrates and P-gp-substrate interactions, based on a training data set of 197 known P-gp substrates and non-substrates collected from the literature. We showed that the SVM method had a prediction accuracy of approximately 80% on an independent external validation data set of 32 compounds. A homology model of human P-gp based on the X-ray structure of mouse P-gp as a template has been constructed. We showed that molecular docking to the P-gp structures successfully predicted the geometry of P-gp-ligand complexes. Our SVM prediction and the molecular docking methods have been integrated into a free web server (http://pgp.althotas.com), which allows the users to predict whether a given compound is a P-gp substrate and how it binds to and interacts with P-gp. Utilization of such a web server may prove valuable for both rational drug design and screening.
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