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Frigerio G, Donadoni E, Siani P, Vertemara J, Motta S, Bonati L, Gioia LD, Valentin CD. Mechanism of RGD-conjugated nanodevice binding to its target protein integrin α Vβ 3 by atomistic molecular dynamics and machine learning. NANOSCALE 2024; 16:4063-4081. [PMID: 38334981 DOI: 10.1039/d3nr05123d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Active targeting strategies have been proposed to enhance the selective uptake of nanoparticles (NPs) by diseased cells, and recent experimental findings have proven the effectiveness of this approach. However, no mechanistic studies have yet revealed the atomistic details of the interactions between ligand-activated NPs and integrins. As a case study, here we investigate, by means of advanced molecular dynamics simulations (MD) and machine learning methods (namely equilibrium MD, binding free energy calculations and training of self-organized maps), the interaction of a cyclic-RGD-conjugated PEGylated TiO2 NP (the nanodevice) with the extracellular segment of integrin αVβ3 (the target), the latter experimentally well-known to be over-expressed in several solid tumors. Firstly, we proved that the cyclic-RGD ligand binding to the integrin pocket is established and kept stable even in the presence of the cumbersome realistic model of the nanodevice. In this respect, the unsupervised machine learning analysis allowed a detailed comparison of the ligand/integrin binding in the presence and in the absence of the nanodevice, which unveiled differences in the chemical features. Then, we discovered that unbound cyclic RGDs conjugated to the NP largely contribute to the interactions between the nanodevice and the integrin. Finally, by increasing the density of cyclic RGDs on the PEGylated TiO2 NP, we observed a proportional enhancement of the nanodevice/target binding. All these findings can be exploited to achieve an improved targeting selectivity and cellular uptake, and thus a more successful clinical outcome.
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Affiliation(s)
- Giulia Frigerio
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Edoardo Donadoni
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Stefano Motta
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Laura Bonati
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Luca De Gioia
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
- BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, Italy
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2
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Vakhrushev AV, Gruzdev DA, Demin AM, Levit GL, Krasnov VP. Synthesis of Novel Carborane-Containing Derivatives of RGD Peptide. Molecules 2023; 28:molecules28083467. [PMID: 37110700 PMCID: PMC10143838 DOI: 10.3390/molecules28083467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Short peptides containing the Arg-Gly-Asp (RGD) fragment can selectively bind to integrins on the surface of tumor cells and are attractive transport molecules for the targeted delivery of therapeutic and diagnostic agents to tumors (for example, glioblastoma). We have demonstrated the possibility of obtaining the N- and C-protected RGD peptide containing 3-amino-closo-carborane and a glutaric acid residue as a linker fragment. The resulting carboranyl derivatives of the protected RGD peptide are of interest as starting compounds in the synthesis of unprotected or selectively protected peptides, as well as building blocks for preparation of boron-containing derivatives of the RGD peptide of a more complex structure.
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Affiliation(s)
- Alexander V Vakhrushev
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), 620108 Ekaterinburg, Russia
| | - Dmitry A Gruzdev
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), 620108 Ekaterinburg, Russia
| | - Alexander M Demin
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), 620108 Ekaterinburg, Russia
| | - Galina L Levit
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), 620108 Ekaterinburg, Russia
| | - Victor P Krasnov
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), 620108 Ekaterinburg, Russia
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3
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Wu Y, Wang Y, Yang Z, Teng C, Guo Z. Evaluation of 99m Tc-3PRGD 2 SPECT imaging on angiogenesis in animal models of lung cancer. Thorac Cancer 2022; 13:3025-3031. [PMID: 36104010 PMCID: PMC9626327 DOI: 10.1111/1759-7714.14655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The main purpose of the study was to evaluate the activity and selectivity of 99m Tc-3PRGD2 SPECT/CT and 18 F-FDG PET-CT in order to detect the neovascularization of A549 cell subcutaneously transplanted tumors, and clarify the relationship among tumor vasculature, hypoxia and cell proliferation in the tumor microenvironment. METHODS We established a subcutaneous tumor model, and used 99m Tc-3PRGD2 SPECT/CT and 18 F-FDG PET-CT when the average tumor size reached 0.3-0.5 cm3 . The mice were anesthetized and sacrificed and the tumors were completely removed for frozen section analysis. We subsequently evaluated the status of neovascularization, hypoxia, as well as cell proliferation via immunofluorescence staining (IF) by detecting CD31, pimonidazole and EdU, respectively. RESULTS There was a significant positive correlation (r = 0.88, p < 0.05) between the microvascular density (41.20 ± 18.60) and tumor to nontumor ratio (T/M), which was based on the value of 99m Tc-3PRGD2 (4.20 ± 1.33); meanwhile, no significance (r = -0.16, p > 0.05) was found between the T/M and hypoxic area (116.71 ± 9.36). Neovascular proliferation was particularly vigorous in the parenchymal region of the tumor, while the cells around the cavity were generally hypoxic. 99m TC-3PRGD2 SPECT/CT was more specific than 18 F-FDG PET-CT in detecting malignant tumors. CONCLUSION Both 99m TC-3PRGD2 and 18 F-FDG PET-CT can be used for the detection of malignant tumors, but the specificity and accuracy of 99m TC-3PRGD2 are better. The subcutaneous tumors showed a heterogeneous microenvironment as a result of neovascularization, a high proliferation rate of cancer cells as well as subsequent hypoxia, while most of the hypoxic areas appeared around the cavities of the vessels.
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Affiliation(s)
- Yongkun Wu
- Department of Thoracic SurgeryThe Affiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
| | - Yufei Wang
- Department of Thoracic SurgeryThe Affiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
| | - Zheng Yang
- Department of Thoracic SurgeryThe Affiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
| | - Chuanhui Teng
- Department of Thoracic SurgeryThe Affiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
| | - Zhanlin Guo
- Department of Thoracic SurgeryThe Affiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
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4
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Bose D, Roy L, Chatterjee S. Peptide therapeutics in the management of metastatic cancers. RSC Adv 2022; 12:21353-21373. [PMID: 35975072 PMCID: PMC9345020 DOI: 10.1039/d2ra02062a] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/26/2022] [Indexed: 11/21/2022] Open
Abstract
Cancer remains a leading health concern threatening lives of millions of patients worldwide. Peptide-based drugs provide a valuable alternative to chemotherapeutics as they are highly specific, cheap, less toxic and easier to synthesize compared to other drugs. In this review, we have discussed various modes in which peptides are being used to curb cancer. Our review highlights specially the various anti-metastatic peptide-based agents developed by targeting a plethora of cellular factors. Herein we have given a special focus on integrins as targets for peptide drugs, as these molecules play key roles in metastatic progression. The review also discusses use of peptides as anti-cancer vaccines and their efficiency as drug-delivery tools. We hope this work will give the reader a clear idea of the mechanisms of peptide-based anti-cancer therapeutics and encourage the development of superior drugs in the future.
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Affiliation(s)
- Debopriya Bose
- Department of Biophysics Bose Institute Unified Academic Campus EN 80, Sector V, Bidhan Nagar Kolkata 700091 WB India
| | - Laboni Roy
- Department of Biophysics Bose Institute Unified Academic Campus EN 80, Sector V, Bidhan Nagar Kolkata 700091 WB India
| | - Subhrangsu Chatterjee
- Department of Biophysics Bose Institute Unified Academic Campus EN 80, Sector V, Bidhan Nagar Kolkata 700091 WB India
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Paul B, Gaonkar RH, Dutta D, Dasi R, Mukherjee B, Ganguly S, Das SK. Inhibitory potential of iRGD peptide-conjugated garcinol-loaded biodegradable nanoparticles in rat colorectal carcinoma. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2022; 134:112714. [DOI: 10.1016/j.msec.2022.112714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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6
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Ma Y, Qu X, Liu C, Xu Q, Tu K. Metal-Organic Frameworks and Their Composites Towards Biomedical Applications. Front Mol Biosci 2022; 8:805228. [PMID: 34993235 PMCID: PMC8724581 DOI: 10.3389/fmolb.2021.805228] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/22/2021] [Indexed: 01/10/2023] Open
Abstract
Owing to their unique features, including high cargo loading, biodegradability, and tailorability, metal–organic frameworks (MOFs) and their composites have attracted increasing attention in various fields. In this review, application strategies of MOFs and their composites in nanomedicine with emphasis on their functions are presented, from drug delivery, therapeutic agents for different diseases, and imaging contrast agents to sensor nanoreactors. Applications of MOF derivatives in nanomedicine are also introduced. Besides, we summarize different functionalities related to MOFs, which include targeting strategy, biomimetic modification, responsive moieties, and other functional decorations. Finally, challenges and prospects are highlighted about MOFs in future applications.
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Affiliation(s)
- Yana Ma
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
| | - Xianglong Qu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Cui Liu
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
| | - Qiuran Xu
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.,Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, China
| | - Kangsheng Tu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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7
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Fertala A. Three Decades of Research on Recombinant Collagens: Reinventing the Wheel or Developing New Biomedical Products? Bioengineering (Basel) 2020; 7:E155. [PMID: 33276472 PMCID: PMC7712652 DOI: 10.3390/bioengineering7040155] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Collagens provide the building blocks for diverse tissues and organs. Furthermore, these proteins act as signaling molecules that control cell behavior during organ development, growth, and repair. Their long half-life, mechanical strength, ability to assemble into fibrils and networks, biocompatibility, and abundance from readily available discarded animal tissues make collagens an attractive material in biomedicine, drug and food industries, and cosmetic products. About three decades ago, pioneering experiments led to recombinant human collagens' expression, thereby initiating studies on the potential use of these proteins as substitutes for the animal-derived collagens. Since then, scientists have utilized various systems to produce native-like recombinant collagens and their fragments. They also tested these collagens as materials to repair tissues, deliver drugs, and serve as therapeutics. Although many tests demonstrated that recombinant collagens perform as well as their native counterparts, the recombinant collagen technology has not yet been adopted by the biomedical, pharmaceutical, or food industry. This paper highlights recent technologies to produce and utilize recombinant collagens, and it contemplates their prospects and limitations.
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Affiliation(s)
- Andrzej Fertala
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Curtis Building, Room 501, 1015 Walnut Street, Philadelphia, PA 19107, USA
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8
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From biomedicinal to in silico models and back to therapeutics: a review on the advancement of peptidic modeling. Future Med Chem 2019; 11:2313-2331. [PMID: 31581914 DOI: 10.4155/fmc-2018-0365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Bioactive peptides participate in numerous metabolic functions of living organisms and have emerged as potential therapeutics on a diverse range of diseases. Albeit peptide design does not go without challenges, overwhelming advancements on in silico methodologies have increased the scope of peptide-based drug design and discovery to an unprecedented amount. Within an in silico model versus an experimental validation scenario, this review aims to summarize and discuss how different in silico techniques contribute at present to the design of peptide-based molecules. Published in silico results from 2014 to 2018 were selected and discriminated in major methodological groups, allowing a transversal analysis, promoting a landscape vision and asserting its increasing value in drug design.
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9
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Li C, Su M, Yin B, Guo D, Wei S, Kong F, Feng L, Wu R, Sun D. Integrin αvβ3 enhances replication of porcine epidemic diarrhea virus on Vero E6 and porcine intestinal epithelial cells. Vet Microbiol 2019; 237:108400. [PMID: 31585640 DOI: 10.1016/j.vetmic.2019.108400] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 01/12/2023]
Abstract
The entry mechanism of porcine epidemic diarrhea virus (PEDV) remains unclear, especially the virus receptor. Our previous study revealed a potential correlation between integrin αvβ3 and PEDV infection. In the current study, the effect of overexpression, silencing, antibody inhibition, and co-expression with porcine aminopeptidase N (pAPN) of integrin αvβ3 on PEDV infection was investigated and analyzed in African green monkey Vero E6 cells and porcine intestinal epithelial cells (IECs) using the classical strain CV777 and variant strain HM2017 of PEDV. Integrin αvβ3 significantly enhanced the replication of the classical and variant strains of PEDV in Vero E6 cells and IECs. The integrin αv and β3 subunits were both involved in the enhancement of PEDV infection, the Arg-Gly-Asp peptides targeting integrin αvβ3 significantly inhibited replication of PEDV in Vero E6 cells, and co-expression of integrin αvβ3 with pAPN significantly enhanced replication of PEDV in Vero E6 and BHK-21 cells. These results demonstrate that integrin αvβ3 enhances PEDV replication in Vero E6 cells and IECs. These data provide novel insights into the entry mechanism of PEDV.
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Affiliation(s)
- Chunqiu Li
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, PR China
| | - Mingjun Su
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, PR China
| | - Baishuang Yin
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, 132101, PR China
| | - Donghua Guo
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, PR China
| | - Shan Wei
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, PR China
| | - Fanzhi Kong
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, PR China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, PR China
| | - Rui Wu
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, PR China
| | - Dongbo Sun
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, PR China.
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10
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Gocheva G, Ivanova A. A Look at Receptor–Ligand Pairs for Active-Targeting Drug Delivery from Crystallographic and Molecular Dynamics Perspectives. Mol Pharm 2019; 16:3293-3321. [DOI: 10.1021/acs.molpharmaceut.9b00250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gergana Gocheva
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Anela Ivanova
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
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11
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Hamdan F, Bigdeli Z, Balalaie S, Sewald N, Michalek C. Efficient synthesis of novel RGD based peptides and the conjugation of the pyrazine moiety to their N-terminus. NEW J CHEM 2019. [DOI: 10.1039/c8nj04874f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel RGD based peptides (RGDFAKLF and RGDNGRG) were designed and synthesized and were later coupled to the pyrazine moiety at the N-terminus. The IC50 values from the in vitro study of the target peptides using a cell adhesion assay indicated the essential impact of the existence of the pyrazine moiety. Meanwhile, peptide 4 exhibited the best IC50 value.
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Affiliation(s)
- Fatima Hamdan
- Peptide Chemistry Research Center
- K. N. Toosi University of Technology
- Tehran
- Iran
| | - Zahra Bigdeli
- Peptide Chemistry Research Center
- K. N. Toosi University of Technology
- Tehran
- Iran
| | - Saeed Balalaie
- Peptide Chemistry Research Center
- K. N. Toosi University of Technology
- Tehran
- Iran
- Medical Biology Research Center
| | - Norbert Sewald
- Organic and Bioorganic Chemistry
- Department of Chemistry
- Bielefeld University
- D-33615 Bielefeld
- Germany
| | - Carmela Michalek
- Organic and Bioorganic Chemistry
- Department of Chemistry
- Bielefeld University
- D-33615 Bielefeld
- Germany
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12
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Guskova O, Savchenko V, König U, Uhlmann P, Sommer JU. How do immobilised cell-adhesive Arg–Gly–Asp-containing peptides behave at the PAA brush surface? MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1502429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Olga Guskova
- Leibniz Institut für Polymerforschung Dresden e.V., Dresden, Germany
- Dresden Center for Computational Materials Science, Technische Universität Dresden, Dresden, Germany
| | - Vladyslav Savchenko
- Fakultät Umweltwissenschaften, Technische Universität Dresden, Dresden, Germany
| | - Ulla König
- Leibniz Institut für Polymerforschung Dresden e.V., Dresden, Germany
| | - Petra Uhlmann
- Leibniz Institut für Polymerforschung Dresden e.V., Dresden, Germany
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jens-Uwe Sommer
- Leibniz Institut für Polymerforschung Dresden e.V., Dresden, Germany
- Dresden Center for Computational Materials Science, Technische Universität Dresden, Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, Dresden, Germany
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13
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Oglic D, Oatley SA, Macdonald SJF, Mcinally T, Garnett R, Hirst JD, Gärtner T. Active Search for Computer-aided Drug Design. Mol Inform 2018; 37. [PMID: 29388736 DOI: 10.1002/minf.201700130] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/03/2018] [Indexed: 01/08/2023]
Abstract
We consider lead discovery as active search in a space of labelled graphs. In particular, we extend our recent data-driven adaptive Markov chain approach, and evaluate it on a focused drug design problem, where we search for an antagonist of an αv integrin, the target protein that belongs to a group of Arg-Gly-Asp integrin receptors. This group of integrin receptors is thought to play a key role in idiopathic pulmonary fibrosis, a chronic lung disease of significant pharmaceutical interest. As an in silico proxy of the binding affinity, we use a molecular docking score to an experimentally determined αvβ6 protein structure. The search is driven by a probabilistic surrogate of the activity of all molecules from that space. As the process evolves and the algorithm observes the activity scores of the previously designed molecules, the hypothesis of the activity is refined. The algorithm is guaranteed to converge in probability to the best hypothesis from an a priori specified hypothesis space. In our empirical evaluations, the approach achieves a large structural variety of designed molecular structures for which the docking score is better than the desired threshold. Some novel molecules, suggested to be active by the surrogate model, provoke a significant interest from the perspective of medicinal chemistry and warrant prioritization for synthesis. Moreover, the approach discovered 19 out of the 24 active compounds which are known to be active from previous biological assays.
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Affiliation(s)
- Dino Oglic
- School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham, NG8 1BB, United Kingdom.,Institut für Informatik III, Universität Bonn, Römerstraße 164, 53117, Bonn, Germany
| | - Steven A Oatley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Simon J F Macdonald
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Thomas Mcinally
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Roman Garnett
- Department of Computer Science and Engineering Washington University in St. Louis, One Brookings Drive CB 1045, St. Louis, MO, 63130, USA
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Thomas Gärtner
- School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham, NG8 1BB, United Kingdom
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