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Liu C, Liu C, Bai Y, Wang J, Tian W. Drug Self-Delivery Systems: Molecule Design, Construction Strategy, and Biological Application. Adv Healthc Mater 2022; 12:e2202769. [PMID: 36538727 DOI: 10.1002/adhm.202202769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/29/2022] [Indexed: 02/01/2023]
Abstract
Drug self-delivery systems (DSDSs) offer new ways to create novel drug delivery systems (DDSs). In typical DSDSs, therapeutic reagents are not considered passive cargos but active delivery agents of actionable targets. As an advanced drug delivery strategy, DSDSs with positive cooperativity of both free drugs and nanocarriers exhibit the clear merits of unprecedented drug-loading capacity, minimized systemic toxicity, and flexible preparation of nanoscale deliverables for passive targeted therapy. This review highlights the recent advances and future trends in DSDSs on the basis of two differently constructed structures: covalent and noncovalent bond-based DSDSs. Specifically, various chemical and architectural designs, fabrication strategies, and responsive and functional features are comprehensively discussed for these two types of DSDSs. In addition, additional comments on the current development status of DSDSs and the potential applications of their molecular designs are presented in the corresponding discussion. Finally, the promising potential of DSDSs in biological applications is revealed and the relationship between preliminary molecular design of DSDSs and therapeutic effects of subsequent DSDSs biological applications is clarified.
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Affiliation(s)
- Chengfei Liu
- Shaanxi Key Laboratory of Macromolecular Science and Technology, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Caiping Liu
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi, 710021, China
| | - Yang Bai
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi, 710021, China
| | - Jingxia Wang
- Shaanxi Key Laboratory of Macromolecular Science and Technology, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
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Eurtivong C, Choowongkomon K, Ploypradith P, Ruchirawat S. Molecular docking study of lamellarin analogues and identification of potential inhibitors of HIV-1 integrase strand transfer complex by virtual screening. Heliyon 2019; 5:e02811. [PMID: 31763475 PMCID: PMC6861579 DOI: 10.1016/j.heliyon.2019.e02811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/24/2019] [Accepted: 11/07/2019] [Indexed: 11/25/2022] Open
Abstract
Molecular docking has been applied to elucidate the binding of lamellarin analogues with HIV-1 integrase strand transfer complex (PDB ID: 5U1C). The results suggest hydrogen bond interaction with residue Glu92 is key, and stabilisation by π-π stacking interactions with DNA base is chiefly influential to strand transfer activity. Other residues involved in hydrogen bonding are Cys65, His67, Asp64, Asp116 and chelation with Mg2+ ion was seen for certain analogues. Furthermore, hydrophobic interactions can be accounted for several amino acids including Asp64, Cys65, Asp116, His67, Glu92, Tyr143, Phe121, Gly118, Pro142 and Val72, as well as the DNA base. The molecular docking results are in line with the reported literatures of other inhibitors and strand transfer activity observed previously by Faulkner. We further employed molecular docking simulation to virtually screen and identified 4 novel potential inhibitors of HIV-1 integrase strand transfer complex from a Chembridge diversity collection of 25,132 small molecule compounds; Chembridge ID compound codes: 22850303, 27553460, 24578440 and 27591056. The candidates clearly formed hydrogen bonding interactions with important residues: His67 and Glu92. In addition, hydrophobic interactions were seen with residues similar to interactions with lamellarin analogues. The calculated drug-like scores are suggestive of these compounds to have clinical potential and ADMET predictions implied of their acceptable pharmacokinetic and toxicity profiles.
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Affiliation(s)
- Chatchakorn Eurtivong
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Poonsakdi Ploypradith
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
- Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Somsak Ruchirawat
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
- Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Bangkok, 10210, Thailand
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WEI CAIYI, LIU ZEYU, ZHANG DAWEI, MEI YE. DOCKING OF RALTEGRAVIR TO HIV-1 INTEGRASE STRUCTURE ENSEMBLE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610006201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Docking of the drug raltegravir to HIV-1 integrase (IN) was performed based on the established Relaxed Complex Scheme (RCS) method which accounts for the flexibility of both receptor and ligand in molecular docking. Two representative butterfly-like structures of raltegravir were identified and both of them mimicked the binding mode of 5CITEP with similar ligand-receptor interactions. Furthermore, the results that raltegravir interacted with magnesium by intermediate water molecules indicate the importance of water molecules at the binding site which has always been ignored in the docking studies of IN inhibitors. Taking these water molecules into consideration gives more insight into the design and development of the second generation IN inhibitors.
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Affiliation(s)
- CAIYI WEI
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - ZEYU LIU
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - DAWEI ZHANG
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - YE MEI
- Department of Physics, State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, P. R. China
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Jin Y, Xin R, Tong L, Du L, Li M. Combination Anti-HIV Therapy with the Self-Assemblies of an Asymmetric Bolaamphiphilic Zidovudine/Didanosine Prodrug. Mol Pharm 2011; 8:867-76. [DOI: 10.1021/mp100457d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yiguang Jin
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
- Institute of Pharmacy, Pharmaceutical College of Henan University, Henan 475004, China
| | - Rui Xin
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
- Institute of Pharmacy, Pharmaceutical College of Henan University, Henan 475004, China
| | - Li Tong
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lina Du
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Miao Li
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
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Aubert Y, Chassignol M, Roig V, Mbemba G, Weiss J, Meudal H, Mouscadet JF, Asseline U. Synthesis and anti-HIV-1 integrase activity of modified dinucleotides. Eur J Med Chem 2009; 44:5029-44. [PMID: 19796851 DOI: 10.1016/j.ejmech.2009.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/30/2009] [Accepted: 09/04/2009] [Indexed: 11/18/2022]
Abstract
The synthesis of a series of thirty-eight new modified dinucleotides and dinucleotide conjugate analogues of d-(5')ApC(3') is described. The inhibitory activity of these compounds toward HIV-1 integrase was examined in enzymatic assays using the natural dinucleotide as a reference. Among the compounds, a perylene-dinucleotide conjugate has shown a two micromolar anti-integrase activity due to the presence of both the intercalator and the dinucleotide.
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Affiliation(s)
- Yves Aubert
- Centre de Biophysique Moléculaire CNRS UPR 4301, affiliated with the University of Orléans and with INSERM Rue Charles Sadron, 45071 Orléans Cedex 02, France
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Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA). J Mol Model 2008; 15:233-45. [DOI: 10.1007/s00894-008-0399-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 09/06/2008] [Indexed: 11/26/2022]
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Zhu J, Wang J, Cheng MS, Zhang JH. Dinucleotides docking to scorpion polypeptide toxins: a molecular modeling method for protein functional site recognition. Biochem Biophys Res Commun 2008; 378:157-61. [PMID: 18983976 DOI: 10.1016/j.bbrc.2008.10.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 10/17/2008] [Indexed: 11/28/2022]
Abstract
To understand the principles underlying protein folding, many molecular modeling methods are being developed for predicting functional positions. In this work, fully flexible dinucleotides d(pApA), d(pApC), d(pApG), d(pApT), d(pCpA), d(pCpC), d(pCpG), d(pCpT), d(pGpA), d(pGpC), d(pGpG), d(pGpT), d(pTpA), d(pTpC), d(pTpG), and d(pTpT) were first docked onto the surface of scorpion polypeptide toxins (LqhIT2, PDB ID:2I61) and homology modeled ANEPIII. Automated docking was able to identify sites on scorpion polypeptide toxins where favorable nucleotide interactions can occur, and those sites were in agreement with the mutation data of this protein published recently [I. Karbat, R. Kahn, L. Cohen, N. Ilan, N. Gilles, G. Corzo, O. Froy, M. Gur, G. Albrecht, S.H. Heinemann, D. Gordon, M. Gurevitz, The unique pharmacology of the scorpion alpha-like toxin Lqh3 is associated with its flexible C-tail, Febs J 274 (2007) 1918-1931]. Simulation results suggested that dinucleotides docking is a suitable molecular modeling method that could be developed for protein functional site recognition.
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Affiliation(s)
- Jun Zhu
- School of Life Science and Bio-pharmaceutics, Shenyang Pharmaceutical University, P.O. Box 17, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning Province 110016, PR China
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Zhu J, Wang J, Su ZC, Li Q, Cheng MS, Zhang JH. Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Arch Pharm Res 2008; 31:1120-8. [PMID: 18806954 DOI: 10.1007/s12272-001-1278-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 03/20/2008] [Accepted: 04/17/2008] [Indexed: 10/21/2022]
Abstract
Twelve ssDNA aptamers specific for a novel recombinant anti-neuroexcitation peptide (ANEPIII) were identified using the SELEX method from a 79-nucleotide ssDNA pool to purify ANEPIII in a more efficient way. To further understand the binding modes between ssDNA and ANEPIII, fully flexible dinucleotides were docked onto the homology-modeled ANEPIII structure. AutoDocking identified favorable binding sites on ANEPIII for nucleotides, which was valuable for designing more potent ligands.
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Affiliation(s)
- Jun Zhu
- School of Life Science and Bio-pharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
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Abstract
HIV-1 integrase is a protein of Mr 32 000 encoded at the 3'-end of the pol gene. Integration of HIV DNA into the host cell chromosomal DNA apparently occurs by a carefully defined sequence of DNA tailoring (3'-processing (3'P)) and coupling (integration) reactions. Integration of HIV DNA into human DNA represents the biochemical completion of the invasion of the human cell (e.g., T-cell) by HIV. Unlike major successes seen in the development of clinically approved anti-HIV agents against HIV reverse transcriptase and HIV protease, there are no FDA-approved anti-HIV drugs in clinical use where the mechanism of action is inhibition of HIV integrase. This review summarises some key advances in the area of integrase inhibitors with the major focus being on new generation inhibitors. Special emphasis is placed on diketo acids with aromatic and heteroaromatic moieties, diketo acids with nucleobase scaffolds, bis-diketo acids, functionalised naphthyridines and other isosteres of diketo acids. Data pertaining to integrase inhibition and in vitro anti-HIV activity are discussed. Mention is made of drugs in clinical trials, both past (S-1360, L-870,810 and L-870,812 and present (GS-9137 and MK-0518). Other promising drugs, including those from the authors' laboratory, are referred. Resistant mutants arising from key integrase inhibitors and cross-resistance are indicated.
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Affiliation(s)
- Vasu Nair
- Department of Pharmaceutical and Biomedical Sciences, The Center for Drug Discovery, University of Georgia, Athens, GA 30602, USA.
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Meadows DC, Tantillo DJ, Gervay-Hague J. Correlation of Biological Activity with Active Site Binding Modes of Geminal Disulfone HIV-1 Integrase Inhibitors. ChemMedChem 2006; 1:959-64. [PMID: 16952140 DOI: 10.1002/cmdc.200600040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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