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Wang D, Yao H, Ye J, Gao Y, Cong H, Yu B. Metal-Organic Frameworks (MOFs): Classification, Synthesis, Modification, and Biomedical Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404350. [PMID: 39149999 DOI: 10.1002/smll.202404350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/02/2024] [Indexed: 08/17/2024]
Abstract
Metal-organic frameworks (MOFs) are a new variety of solid crystalline porous functional materials. As an extension of inorganic porous materials, it has made important progress in preparation and application. MOFs are widely used in various fields such as gas adsorption storage, drug delivery, sensing, and biological imaging due to their high specific surface area, porosity, adjustable pore size, abundant active sites, and functional modification by introducing groups. In this paper, the types of MOFs are classified, and the synthesis methods and functional modification mechanisms of MOFs materials are summarized. Finally, the application prospects and challenges of metal-organic framework materials in the biomedical field are discussed, hoping to promote their application in multidisciplinary fields.
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Affiliation(s)
- Dayang Wang
- College of Chemistry and Chemical Engineering, College of Life Sciences, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao, 266071, China
| | - Huanchen Yao
- College of Chemistry and Chemical Engineering, College of Life Sciences, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao, 266071, China
| | - Jiashuo Ye
- College of Chemistry and Chemical Engineering, College of Life Sciences, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao, 266071, China
| | - Yan Gao
- College of Chemistry and Chemical Engineering, College of Life Sciences, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao, 266071, China
| | - Hailin Cong
- College of Chemistry and Chemical Engineering, College of Life Sciences, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao, 266071, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao, 266071, China
- School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Bing Yu
- College of Chemistry and Chemical Engineering, College of Life Sciences, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao, 266071, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao, 266071, China
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2
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Uthayabalan S, Lake T, Stathopulos PB. MRS2 missense variation at Asp216 abrogates inhibitory Mg 2+ binding, potentiating cell migration and apoptosis resistance. Protein Sci 2024; 33:e5108. [PMID: 38989547 PMCID: PMC11237551 DOI: 10.1002/pro.5108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/06/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Mitochondrial magnesium (Mg2+) is a crucial modulator of protein stability, enzymatic activity, ATP synthesis, and cell death. Mitochondrial RNA splicing protein 2 (MRS2) is the main Mg2+ channel in the inner mitochondrial membrane that mediates influx into the matrix. Recent cryo-electron microscopy (cryo-EM) human MRS2 structures exhibit minimal conformational changes at high and low Mg2+, yet the regulation of human MRS2 and orthologues by Mg2+ binding to analogous matrix domains has been well established. Further, a missense variation at D216 has been identified associated with malignant melanoma and MRS2 expression and activity is implicated in gastric cancer. Thus, to gain more mechanistic and functional insight into Mg2+ sensing by the human MRS2 matrix domain and the association with proliferative disease, we assessed the structural, biophysical, and functional effects of a D216Q mutant. We show that the D216Q mutation is sufficient to abrogate Mg2+-binding and associated conformational changes including increased α-helicity, stability, and monomerization. Further, we reveal that the MRS2 matrix domains interact with ~μM affinity, which is weakened by up to two orders of magnitude in the presence of Mg2+ for wild-type but unaffected for D216Q. Finally, we demonstrate the importance of Mg2+ sensing by MRS2 to prevent matrix Mg2+ overload as HeLa cells overexpressing MRS2 show enhanced Mg2+ uptake, cell migration, and resistance to apoptosis while MRS2 D216Q robustly potentiates these cancer phenotypes. Collectively, our findings further define the MRS2 matrix domain as a critical Mg2+ sensor that undergoes conformational and assembly changes upon Mg2+ interactions dependent on D216 to temper matrix Mg2+ overload.
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Affiliation(s)
- Sukanthathulse Uthayabalan
- Department of Physiology and Pharmacology, Schulich School of Medicine and DentistryUniversity of Western OntarioLondonOntarioCanada
| | - Taylor Lake
- Department of Physiology and Pharmacology, Schulich School of Medicine and DentistryUniversity of Western OntarioLondonOntarioCanada
| | - Peter B. Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and DentistryUniversity of Western OntarioLondonOntarioCanada
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3
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Januškevičienė I, Petrikaitė V. Exploring doxorubicin transport in 2D and 3D models of MDA-MB-231 sublines: impact of hypoxia and cellular heterogeneity on doxorubicin accumulation in cells. Am J Cancer Res 2024; 14:3584-3599. [PMID: 39113879 PMCID: PMC11301288 DOI: 10.62347/vnwh9165] [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: 05/31/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Triple-negative breast cancer (TNBC) treatment is challenging due to its aggressive nature and heterogeneity of this type of cancer, characterized by various subtypes and intratumoral diversity. Doxorubicin (DOX) plays a crucial role in TNBC chemotherapy reducing the tumor size and improving patient survival. However, decreased drug uptake and increased resistance in specific cell subpopulations reduce the effectiveness of the treatment. This study explored the differences in DOX transport in MDA-MB-231 phenotypic sublines in cell monolayer (2D model) and cell spheroids (3D cultures). Cell spheroids were formed using magnetic 3D Bioprinting method. DOX transport into cells and spheroids was evaluated using fluorescence microscopy after different incubation durations with DOX in normoxia and hypoxia. In hypoxia, DOX transport into cells was 2.5 to 5-fold lower than in normoxia. The subline F5 monolayer-cultured cells exhibited the highest DOX uptake, while subline H2 cells showed the lowest uptake in normoxia and hypoxia. In 3D cultures, DOX transport was up to 2-fold lower in spheroids formed from subline H2 cells. Spheroids from subline D8 and MDA-MB-231 parent cells had the highest DOX uptake. A correlation was observed between the characteristics of the cells and their resistance to anticancer drugs. The results indicate that different cancer cell subpopulations in tumours due to differences in drug uptake could significantly impact treatment efficacy.
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Affiliation(s)
- Indrė Januškevičienė
- Laboratory of Drug Targets Histopathology, Institute of Cardiology, Lithuanian University of Health Sciences Sukilėlių av., LT-50162 Kaunas, Lithuania
| | - Vilma Petrikaitė
- Laboratory of Drug Targets Histopathology, Institute of Cardiology, Lithuanian University of Health Sciences Sukilėlių av., LT-50162 Kaunas, Lithuania
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Mikaelian G, Megariotis G, Theodorou DN. Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment. J Phys Chem B 2024; 128:6291-6307. [PMID: 38899795 PMCID: PMC11228990 DOI: 10.1021/acs.jpcb.4c02213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Berubicin, a chemotherapy medication belonging to the class of anthracyclines, is simulated in double-stranded DNA sequences and cyclodextrins in an aqueous environment via full-atom molecular dynamics simulations on the time scale of microseconds. The drug is studied in both the neutral and protonated states so as to better comprehend the role of its charge in the formed complexes. The noncovalent berubicin-DNA and berubicin-cyclodextrin complexes are investigated in detail, paying special attention to their thermodynamic description by employing the double decoupling method, the solvent balance method, the weighted solvent accessible surface model, and the linear interaction energy method. A novel approach for extracting the desolvation thermodynamics of the binding process is also presented. Both the binding and desolvation Gibbs energies are decomposed into entropic and enthalpic contributions so as to elucidate the nature of complexation and its driving forces. Selected structural and geometrical properties of all the complexes, which are all stable, are analyzed. Both cyclodextrins under consideration are widely utilized for drug delivery purposes, and a comparative investigation between their bound states with berubicin is carried out.
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Affiliation(s)
- Georgios Mikaelian
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
| | - Grigorios Megariotis
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
- School
of Engineering, Department of Mineral Resources Engineering, University of Western Macedonia, 50100 Kozani, Greece
| | - Doros N. Theodorou
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
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5
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Stachowicz-Kuśnierz A, Rychlik P, Korchowiec J, Korchowiec B. Insights into Transfer of Supramolecular Doxorubicin/Congo Red Aggregates through Phospholipid Membranes. Molecules 2024; 29:2567. [PMID: 38893446 PMCID: PMC11173802 DOI: 10.3390/molecules29112567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Doxorubicin (DOX) is a commonly used chemotherapeutic drug, from the anthracycline class, which is genotoxic to neoplastic cells via a DNA intercalation mechanism. It is effective and universal; however, it also causes numerous side effects. The most serious of them are cardiotoxicity and a decrease in the number of myeloid cells. For this reason, targeted DOX delivery systems are desirable, since they would allow lowering the drug dose and therefore limiting systemic side effects. Recently, synthetic dyes, in particular Congo red (CR), have been proposed as possible DOX carriers. CR is a planar molecule, built of a central biphenyl moiety and two substituted naphthalene rings, connected with diazo bonds. In water, it forms elongated ribbon-shaped supramolecular structures, which are able to selectively interact with immune complexes. In our previous studies, we have shown that CR aggregates can intercalate DOX molecules. In this way, they preclude DOX precipitation in water solutions and increase its uptake by MCF7 breast cancer cells. In the present work, we further explore the interactions between DOX, CR, and their aggregates (CR/DOX) with phospholipid membranes. In addition to neutral molecules, the protonated doxorubicin form, DXP, is also studied. Molecular dynamics simulations are employed to study the transfer of CR, DOX, DXP, and their aggregates through POPC bilayers. Interactions of CR, DOX, and CR/DOX with model monolayers are studied with Langmuir trough measurements. This study shows that CR may support the transfer of doxorubicin molecules into the bilayer. Both electrostatic and van der Waals interactions with lipids are important in this respect. The former promote the initial stages of the insertion process, the latter keep guest molecules inside the bilayer.
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Affiliation(s)
- Anna Stachowicz-Kuśnierz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.R.); (J.K.)
| | | | | | - Beata Korchowiec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.R.); (J.K.)
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6
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Gach-Janczak K, Drogosz-Stachowicz J, Janecka A, Wtorek K, Mirowski M. Historical Perspective and Current Trends in Anticancer Drug Development. Cancers (Basel) 2024; 16:1878. [PMID: 38791957 PMCID: PMC11120596 DOI: 10.3390/cancers16101878] [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: 04/16/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Cancer is considered one of the leading causes of death in the 21st century. The intensive search for new anticancer drugs has been actively pursued by chemists and pharmacologists for decades, focusing either on the isolation of compounds with cytotoxic properties from plants or on screening thousands of synthetic molecules. Compounds that could potentially become candidates for new anticancer drugs must have the ability to inhibit proliferation and/or induce apoptosis in cancer cells without causing too much damage to normal cells. Some anticancer compounds were discovered by accident, others as a result of long-term research. In this review, we have presented a brief history of the development of the most important groups of anticancer drugs, pointing to the fact that they all have many side effects.
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Affiliation(s)
- Katarzyna Gach-Janczak
- Department of Biomolecular Chemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (K.G.-J.); (A.J.); (K.W.)
| | | | - Anna Janecka
- Department of Biomolecular Chemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (K.G.-J.); (A.J.); (K.W.)
| | - Karol Wtorek
- Department of Biomolecular Chemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (K.G.-J.); (A.J.); (K.W.)
| | - Marek Mirowski
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
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Abumansour H, Abusara OH, Khalil W, Abul-Futouh H, Ibrahim AIM, Harb MK, Abulebdah DH, Ismail WH. Biological evaluation of levofloxacin and its thionated derivatives: antioxidant activity, aldehyde dehydrogenase enzyme inhibition, and cytotoxicity on A549 cell line. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03075-x. [PMID: 38613572 DOI: 10.1007/s00210-024-03075-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/28/2024] [Indexed: 04/15/2024]
Abstract
Levofloxacin (LVX) is among the fluoroquinolones antibiotics that has also been studied in vitro and in vivo for its anticancer effects. In this study, we used LVX and novel LVX thionated derivatives; compounds 2 and 3, to evaluate their antioxidant activity, aldehyde dehydrogenase (ALDH) enzymes activity inhibition, and anticancer activity. Combination treatments with doxorubicin (DOX) were investigated as well. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay was used to determine the antioxidant activity. The NADH fluorescence spectrophotometric activity assay was used to determine the ALDH inhibitory effects. Resazurin dye method was applied for cell viability assays. Molecular Operating Environment software was used for the molecular docking experiments. Compared to ascorbic acid, DPPH assay showed that compound 3 had the highest antioxidant activity among the tested compounds with approximately 35% scavenging activity. On ALDH enzymes, compound 3 showed a significant ALDH activity inhibition compared to compound 2 at 200 µM. The IC50 values for the tested compounds were approximately 100 µM on A549 cell line, a non-small cell lung cancer (NSCLC) cell line. However, significant enhancement of cytotoxicity and reduction of IC50 values were observed by combining DOX and synergism was achieved with LVX with a combination index value of 0.4. The molecular docking test showed a minimum binding energy with a good affinity for compound 3 towards ALDH enzymes. Thionated LVX derivatives, may be repurposed for NSCLC therapy in combination with DOX, taking into account the antioxidant activity, ALDH activity inhibition, and the molecular docking results of compound 3.
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Affiliation(s)
- Hamza Abumansour
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan.
| | - Osama H Abusara
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
| | - Wiam Khalil
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman, 11942, Jordan
| | - Hassan Abul-Futouh
- Department of Chemistry, Faculty of Science, The Hashemite University, P.O. Box 330127, Zarqa, 13133, Jordan
| | - Ali I M Ibrahim
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
| | - Mohammad K Harb
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
| | - Dina H Abulebdah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
| | - Worood H Ismail
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
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Hu J, Zhu BY, Niu ZX. Catalysts of Healing: A Symphony of Synthesis and Clinical Artistry in Small-Molecule Agents for Breast Cancer Alleviation. Molecules 2024; 29:1166. [PMID: 38474678 DOI: 10.3390/molecules29051166] [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: 01/11/2024] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Breast cancer, characterized by its molecular intricacy, has witnessed a surge in targeted therapeutics owing to the rise of small-molecule drugs. These entities, derived from cutting-edge synthetic routes, often encompassing multistage reactions and chiral synthesis, target a spectrum of oncogenic pathways. Their mechanisms of action range from modulating hormone receptor signaling and inhibiting kinase activity, to impeding DNA damage repair mechanisms. Clinical applications of these drugs have resulted in enhanced patient survival rates, reduction in disease recurrence, and improved overall therapeutic indices. Notably, certain molecules have showcased efficacy in drug-resistant breast cancer phenotypes, highlighting their potential in addressing treatment challenges. The evolution and approval of small-molecule drugs have ushered in a new era for breast cancer therapeutics. Their tailored synthetic pathways and defined mechanisms of action have augmented the precision and efficacy of treatment regimens, paving the way for improved patient outcomes in the face of this pervasive malignancy. The present review embarks on a detailed exploration of small-molecule drugs that have secured regulatory approval for breast cancer treatment, emphasizing their clinical applications, synthetic pathways, and distinct mechanisms of action.
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Affiliation(s)
- Jing Hu
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Bi-Yue Zhu
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
- Department of Pharmacy, Children's Hospital of Chongqing Medical University, Chongqing 400015, China
| | - Zhen-Xi Niu
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
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9
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Sodomaco S, Gómez S, Giovannini T, Cappelli C. Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces. J Phys Chem A 2023; 127:10282-10294. [PMID: 37993110 DOI: 10.1021/acs.jpca.3c05560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.
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Affiliation(s)
- Sveva Sodomaco
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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Jawad B, Adhikari P, Podgornik R, Ching WY. Impact of BA.1, BA.2, and BA.4/BA.5 Omicron mutations on therapeutic monoclonal antibodies. Comput Biol Med 2023; 167:107576. [PMID: 37871435 DOI: 10.1016/j.compbiomed.2023.107576] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 10/01/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
The emergence of Omicron SARS-CoV-2 subvariants (BA.1, BA.2, BA.4, and BA.5), with an unprecedented number of mutations in their receptor-binding domain (RBD) of the spike-protein, has fueled a resurgence of COVID-19 infections, posing a major challenge to the efficacy of existing vaccines and monoclonal antibody (mAb) therapeutics. We conducted a systematic molecular dynamics (MD) simulation to investigate how the RBD mutations of these subvariants affect the interactions with broad mAbs including AstraZeneca (COV2-2196 and COV2-2130), Brii Biosciences (BRII-196), Celltrion (CT-P59), Eli Lilly (LY-CoV555 and LY-CoV016), Regeneron (REGN10933 and REGN10987), Vir Biotechnology (S309), and S2X259. Our results show a complete loss of binding for COV2-2196, BRII-196, CT-P59, and LY-CoV555 with all Omicron RBDs. Additionally, REGN10987 totally loses its binding with BA.1, but retains a partial binding with BA.2 and BA.4/5. The binding reduction is significant for LY-CoV016 and REGN10933 but moderate for COV2-2130. S309 and S2X259 retain their binding with BA.1 but exhibit decreased binding with other subvariants. We introduce a mutational escape map for each mAb to identify the key RBD sites and the corresponding critical mutations. Overall, our findings suggest that the majority of therapeutic mAbs have diminished or missing activity against Omicron subvariants, indicating the urgent need for a new therapeutic mAb with a better design.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States; Department of Applied Sciences, University of Technology, Baghdad, 10066, Iraq.
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States
| | - Rudolf Podgornik
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing, 100049, China; CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100090, China; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States
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Ali I, Iqbal MN, Ibrahim M, Haq IU, Alonazi WB, Siddiqi AR. Computational exploration of novel ROCK2 inhibitors for cardiovascular disease management; insights from high-throughput virtual screening, molecular docking, DFT and MD simulation. PLoS One 2023; 18:e0294511. [PMID: 37972144 PMCID: PMC10653426 DOI: 10.1371/journal.pone.0294511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Cardiovascular disorders are the world's major cause of death nowadays. To treat cardiovascular diseases especially coronary artery diseases and hypertension, researchers found potential ROCK2 (Rho-associated coiled-coil-containing protein kinase 2) target due to its substantial role in NO-cGMP and RhoA/ROCK pathway. Available drugs for ROCK2 are less effective and some of them depict side effects. Therefore, a set of novel compounds were screened that can potentially inhibit the activity of ROCK2 and help to treat cardiovascular diseases by employing In-silico techniques. In this study, we undertook ligand based virtual screening of 50 million compound's library, to that purpose shape and features (contain functional groups) based pharmacophore query was modelled and validated by Area Under Curve graph (AUC). 2000 best hits were screened for Lipinski's rule of 5 compliance. Subsequently, these selected compounds were docked into the binding site of ROCK2 to gain insights into the interactions between hit compounds and the target protein. Based on binding affinity and RMSD scores, a final cohort of 15 compounds were chosen which were further refined by pharmacokinetics, ADMET and bioactivity scores. 2 potential hits were screened using density functional theory, revealing remarkable biological and chemical activity. Potential inhibitors (F847-0007 and 9543495) underwent rigorous examination through MD Simulations and MMGBSA analysis, elucidating their stability and strong binding affinities. Results of current study unveil the potential of identified novel hits as promising lead compounds for ROCK2 associated with cardiovascular diseases. These findings will further investigate via In-vitro and In-vivo studies to develop novel druglike molecules against ROCK2.
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Affiliation(s)
- Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad, Pakistan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Islamabad, Pakistan
| | - Muhammad Nasir Iqbal
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
- Programa de Pós-Graduação em Inovação Tecnológica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Wadi B. Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad, Pakistan
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12
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Su GA, Wadsworth OJ, Muller HS, Archer WR, Hetts SW, Schulz MD. Polymer-nucleobase composites for chemotherapy drug capture. J Mater Chem B 2023; 11:8449-8455. [PMID: 37580990 DOI: 10.1039/d3tb00819c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Intravenous chemotherapy (e.g., doxorubicin (DOX)) is standard treatment for many cancers but also leads to side effects due to off-target toxicity. To address this challenge, devices for removing off-target chemotherapy agents from the bloodstream have been developed, but the efficacy of such devices relies on the ability of the underlying materials to specifically sequester small-molecule drugs. Anion-exchange materials, genomic DNA, and DNA-functionalized iron oxide particles have all been explored as drug-capture materials, but cost, specificity, batch-to-batch variation, and immunogenicity concerns persist as challenges. Here, we report a new class of fully synthetic drug-capture materials. We copolymerized methacrylic acid and ethylene glycol dimethacrylate in the presence of several nucleobases and derivatives (adenine, cytosine, xanthine, and thymine) to yield a crosslinked resin with nucleobases integrated into the material. These materials demonstrated effective DOX capture: up to 27 mg of DOX per g of material over 20 minutes from a phosphate-buffered saline solution with an initial concentration of 0.05 mg mL-1 of DOX. These materials use only the individual nucleobases for DOX capture and exhibit competitive capture efficacy compared to previous materials that used genomic DNA, making this approach more cost-effective and reducing potential immunological concerns.
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Affiliation(s)
- Gillian A Su
- Department of Chemistry and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Ophelia J Wadsworth
- Department of Chemistry and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA 24061, USA.
| | - H Suzanne Muller
- Department of Chemistry and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA 24061, USA.
| | - William R Archer
- Department of Chemistry and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Steven W Hetts
- Departments of Radiology, Biomedical Imaging, and Neurological Surgery, University of California, San Francisco, CA 94143-0628, USA
| | - Michael D Schulz
- Department of Chemistry and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA 24061, USA.
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13
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Lee JH, Yang SB, Lee JH, Lim H, Lee S, Kang TB, Lim JH, Kim YJ, Park J. Doxorubicin covalently conjugated heparin displays anti-cancer activity as a self-assembled nanoparticle with a low-anticoagulant effect. Carbohydr Polym 2023; 314:120930. [PMID: 37173028 DOI: 10.1016/j.carbpol.2023.120930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 05/15/2023]
Abstract
Heparin is a glycosaminoglycans (GAGs) member and well-known FDA-approved anticoagulant that has been widely used in the clinic for 100 years. It has also been evaluated in various fields for further clinical applications, such as in anti-cancer or anti-inflammatory therapy beyond its anticoagulant effect. Here, we sought to utilize heparin molecules as drug carriers by directly conjugating the anticancer drug doxorubicin to the carboxyl group of unfractionated heparin. Given the molecular action of doxorubicin in intercalating DNA, it is expected to be less effective when structurally combined with other molecules. However, by utilizing doxorubicin molecules to produce reactive oxygen species (ROS), we found that the heparin-doxorubicin conjugates have significant cytotoxic ability to kill CT26 tumor cells with low anticoagulant activity. Several doxorubicin molecules were bound to heparin to provide sufficient cytotoxic capability and self-assembly ability due to their amphiphilic properties. The self-assembled formation of these nanoparticles was demonstrated through DLS, SEM and TEM. The cytotoxic ROS-generating doxorubicin-conjugated heparins could inhibit tumor growth and metastasis in CT26-bearing Balb/c animal models. Our results demonstrate that this cytotoxic doxorubicin-based heparin conjugate can significantly inhibit tumor growth and metastasis, thus showing promise as a potential new anti-cancer therapeutic.
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Affiliation(s)
- Jae-Hyeon Lee
- Department of Biomedical Chemistry, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea
| | - Seong-Bin Yang
- Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
| | - Jun-Hyuck Lee
- Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
| | - Hansol Lim
- Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
| | - Seokwoo Lee
- College of Pharmacy, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Tae-Bong Kang
- Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
| | - Ji-Hong Lim
- Department of Biomedical Chemistry, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
| | - Young Jun Kim
- Department of Biomedical Chemistry, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea
| | - Jooho Park
- Department of Biomedical Chemistry, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea.
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14
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Piorecka K, Kurjata J, Gostynski B, Kazmierski S, Stanczyk WA, Marcinkowska M, Janaszewska A, Klajnert-Maculewicz B. Is acriflavine an efficient co-drug in chemotherapy? RSC Adv 2023; 13:21421-21431. [PMID: 37465576 PMCID: PMC10350790 DOI: 10.1039/d3ra02608f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Cancer is a global health problem being the second worldwide cause of deaths right after cardiovascular diseases. The main methods of cancer treatment involve surgery, radiation and chemotherapy with an emphasis on the latter. Thus development of nanochemistry and nanomedicine in a search for more effective and safer cancer treatment is an important area of current research. Below, we present interaction of doxorubicin and acriflavine and the cytotoxicity of these drug nano-complexes towards cervical cancer (HeLa) cells. Experimental results obtained from NMR measurements and fluorescence spectroscopy show that the drugs' interaction was due to van der Waals forces, formation of hydrogen bonds and π-π stacking. Quantum molecular simulations confirmed the experimental results with regard to existing π-π stacking. Additionally it was shown that, at the level of theory applied (DFT, triple zeta basis set), the stacking interactions comprise the most preferable interactions (the lowest ΔG ca. -12 kcal mol-1) both between the molecules forming the acriflavine system and between the other component - another drug (doxorubicin) dimer. Biological tests performed on HeLa cells showed high cytotoxicity of the complexes, comparable to free drugs (ACF and DOX), both after 24 and 48 hours of incubation. For non-cancerous cells, a statistically significant difference in the cytotoxicity of drugs and complexes was observed in the case of a short incubation period. The results of the uptake study showed significantly more efficient cellular uptake of acriflavine than doxorubicin, whether administered alone or in combination with an anthracycline. The mechanism determining the selective uptake of acriflavine and ACF : DOX complexes towards non-cancer and cancer cells should be better understood in the future, as it may be of key importance in the design of complexes with toxic anti-cancer drugs.
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Affiliation(s)
- Kinga Piorecka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Jan Kurjata
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Bartłomiej Gostynski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Slawomir Kazmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Wlodzimierz A Stanczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Monika Marcinkowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz 141/143 Pomorska St. 90-236 Lodz Poland
| | - Anna Janaszewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz 141/143 Pomorska St. 90-236 Lodz Poland
| | - Barbara Klajnert-Maculewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz 141/143 Pomorska St. 90-236 Lodz Poland
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15
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Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
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Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
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16
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Yang SB, Lee DN, Lee JH, Seo M, Shin DW, Lee S, Lee YH, Park J. Design and Evaluation of a Carrier-Free Prodrug-Based Palmitic-DEVD-Doxorubicin Conjugate for Targeted Cancer Therapy. Bioconjug Chem 2023; 34:333-344. [PMID: 36735902 DOI: 10.1021/acs.bioconjchem.2c00490] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the development of new drugs, typical polymer- or macromolecule-based nanocarriers suffer from manufacturing process complexity, unwanted systematic toxicity, and low loading capacity. However, carrier-free nanomedicines have made outstanding progress in drug delivery and pharmacokinetics, demonstrating most of the advantages associated with nanoparticles when applied in targeted anticancer therapy. Here, to overcome the problems of nanocarriers and conventional cytotoxic drugs, we developed a novel, carrier-free, self-assembled prodrug consisting of a hydrophobic palmitic (16-carbon chain n-hexadecane chain) moiety and hydrophilic group (or moiety) which is included in a caspase-3-specific cleavable peptide (Asp-Glu-Val-Asp, DEVD) and a cytotoxic drug (doxorubicin, DOX). The amphiphilic conjugate, the palmitic-DEVD-DOX, has the ability to self-assemble into nanoparticles in saline without the need for any carriers or nanoformulations. Additionally, the inclusion of doxorubicin is in its prodrug form and the apoptosis-specific DEVD peptide lead to the reduced side effects of doxorubicin in normal tissue. Furthermore, the carrier-free palmitic-DEVD-DOX nanoparticles could passively accumulate in the tumor tissues of tumor-bearing mice due to an enhanced permeation and retention (EPR) effect. As a result, the palmitic-DEVD-DOX conjugate showed an enhanced therapeutic effect compared with the unmodified DEVD-DOX conjugate. Therefore, this carrier-free palmitic-DEVD-DOX prodrug has great therapeutic potential to treat solid tumors, overcoming the problems of conventional chemotherapy and nanoparticles.
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Affiliation(s)
- Seong-Bin Yang
- Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
| | - Dong-Nyeong Lee
- Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
| | - Jun-Hyuck Lee
- Department of Biomedical Chemistry, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea
| | - Minho Seo
- Department of Biomedical Chemistry, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea
| | - Dong Wook Shin
- College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea
| | - Seokwoo Lee
- College of Pharmacy, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 28119, Republic of Korea.,Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jooho Park
- Department of Applied Life Science, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea.,Department of Biomedical Chemistry, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea
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17
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Gómez S, Lafiosca P, Egidi F, Giovannini T, Cappelli C. UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA. J Chem Inf Model 2023; 63:1208-1217. [PMID: 36745496 PMCID: PMC9976284 DOI: 10.1021/acs.jcim.2c01495] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomolecular receptors. The extraction of information at the molecular level from experimental RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramolecular system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/molecular mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with experimental data, thus confirming the reliability of the computational protocol.
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Affiliation(s)
- Sara Gómez
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy,E-mail:
| | - Piero Lafiosca
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Franco Egidi
- Software
for Chemistry and Materials BV, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Tommaso Giovannini
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy,E-mail:
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18
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Goodman J, Attwood D, Kiely J, Coladas Mato P, Luxton R. Modeling Peptide Nucleic Acid Binding Enthalpies Using MM-GBSA. J Phys Chem B 2022; 126:9528-9538. [PMID: 36375178 PMCID: PMC9706560 DOI: 10.1021/acs.jpcb.2c05547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The binding enthalpies of peptide nucleic acid (PNA) homoduplexes were predicted using a molecular mechanics generalized Born surface area approach. Using the nucleic acid nearest-neighbor model, these were decomposed into sequence parameters which could replicate the enthalpies from thermal melting experiments with a mean error of 8.7%. These results present the first systematic computational investigation into the relationship between sequence and binding energy for PNA homoduplexes and identified a stabilizing helix initiation enthalpy not observed for nucleic acids with phosphoribose backbones.
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Affiliation(s)
- Jack Goodman
- University
of the West of England, BristolBS16 1QY, U.K.,
| | - David Attwood
- University
of the West of England, BristolBS16 1QY, U.K.
| | - Janice Kiely
- University
of the West of England, BristolBS16 1QY, U.K.
| | | | - Richard Luxton
- University
of the West of England, BristolBS16 1QY, U.K.
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19
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Programmable Assembly of Multivalent DNA‐Protein Superstructures for Tumor Imaging and Targeted Therapy. Angew Chem Int Ed Engl 2022; 61:e202211505. [DOI: 10.1002/anie.202211505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/07/2022]
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20
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Xu Z, Shi T, Mo F, Yu W, Shen Y, Jiang Q, Wang F, Liu X. Programmable Assembly of Multivalent DNA‐Protein Superstructures for Tumor Imaging and Targeted Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhen Xu
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Tianhui Shi
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Fengye Mo
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Wenqian Yu
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Yu Shen
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Qunying Jiang
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Fuan Wang
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Xiaoqing Liu
- Wuhan University College of Chemistry and Molecular Sciences No. 299 Bayi Road, Wuchang District 430072 Wuhan CHINA
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21
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Ching WY, Adhikari P, Jawad B, Podgornik R. Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex. Int J Mol Sci 2022; 23:10091. [PMID: 36077490 PMCID: PMC9456519 DOI: 10.3390/ijms231710091] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.
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Affiliation(s)
- Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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22
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Banerjee J, Hasan SN, Samanta S, Giri B, Bag BG, Dash SK. Self-Assembled Maslinic Acid Attenuates Doxorobucin Induced Cytotoxicity via Nrf2 Signaling Pathway: An In Vitro and In Silico Study in Human Healthy Cells. Cell Biochem Biophys 2022; 80:563-578. [PMID: 35849306 DOI: 10.1007/s12013-022-01083-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/03/2022] [Indexed: 11/03/2022]
Abstract
The clinical applications of some well-known chemotherapeutic drugs for cancer treatment have been restricted nowadays owing to their adverse effects on many physiological systems. In this experimental study, maslinic acid (MA) isolated from Olea europaea (Olive) fruit extract was used to mitigate the cytotoxicity induced by Doxorubicin (DOX) in human healthy peripheral blood mononuclear cells (hPBMCs). Self-assembled maslinic acid (SA-MA) was obtained in ethanol-water mixture (35.5 mM: 4:1 v/v). The morphology of SA-MA was analyzed by various physicochemical characterization techniques, which revealed its micro-metric vesicular architecture as well as nano-vesicular appearances. In this study, treatment of hPBMCs with DOX has been found to generate severe intracellular oxidative stress, which was significantly mitigated after pre-treatment with SA-MA. Alteration of hPBMC morphologies after DOX treatment was also restored notably by pre-treatment with SA-MA. Furthermore, pentoxifylline (TNF-α inhibitor) and indomethacin (COX-2 inhibitor) were used to investigate the responsible pathway by which SA-MA protected hPBMCs from DOX-induced cellular stress. Restoration of hPBMC viability above 92% in both cases confirmed that SA-MA protected the cells by inhibiting inflammatory pathways generated by DOX treatment. Subsequently, in molecular docking study, it was also evaluated that MA could successfully bind with the pocket region of Keap1, while Nrf2 was capable of upregulating cytoprotecting genes.
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Affiliation(s)
- Jhimli Banerjee
- Department of Physiology, University of Gour Banga, Malda, West Bengal, 732103, India
| | - Sk Nurul Hasan
- Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Sovan Samanta
- Department of Physiology, University of Gour Banga, Malda, West Bengal, 732103, India
| | - Biplab Giri
- Department of Physiology, University of Gour Banga, Malda, West Bengal, 732103, India
| | - Braja Gopal Bag
- Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Sandeep Kumar Dash
- Department of Physiology, University of Gour Banga, Malda, West Bengal, 732103, India.
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23
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Shedding Light on the Drug-Target Prediction of the Anti-Inflammatory Peptide TnP with Bioinformatics Tools. Pharmaceuticals (Basel) 2022; 15:ph15080994. [PMID: 36015142 PMCID: PMC9412873 DOI: 10.3390/ph15080994] [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: 06/13/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Peptide–protein interactions are involved in various fundamental cellular functions, and their identification is crucial for designing efficacious peptide therapeutics. Drug–target interactions can be inferred by in silico prediction using bioinformatics and computational tools. We patented the TnP family of synthetic cyclic peptides, which is in the preclinical stage of developmental studies for chronic inflammatory diseases such as multiple sclerosis. In an experimental autoimmune enceph-alomyelitis model, we found that TnP controls neuroinflammation and prevents demyelination due to its capacity to cross the blood–brain barrier and to act in the central nervous system blocking the migration of inflammatory cells responsible for neuronal degeneration. Therefore, the identification of potential targets for TnP is the objective of this research. In this study, we used bioinformatics and computational approaches, as well as bioactivity databases, to evaluate TnP–target prediction for proteins that were not experimentally tested, specifically predicting the 3D structure of TnP and its biochemical characteristics, TnP–target protein binding and docking properties, and dynamics of TnP competition for the protein/receptor complex interaction, construction of a network of con-nectivity and interactions between molecules as a result of TnP blockade, and analysis of similarities with bioactive molecules. Based on our results, integrins were identified as important key proteins and considered responsible to regulate TnP-governed pharmacological effects. This comprehensive in silico study will help to understand how TnP induces its anti-inflammatory effects and will also facilitate the identification of possible side effects, as it shows its link with multiple biologically important targets in humans.
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24
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Congo Red as a Supramolecular Carrier System for Doxorubicin: An Approach to Understanding the Mechanism of Action. Int J Mol Sci 2022; 23:ijms23168935. [PMID: 36012200 PMCID: PMC9408855 DOI: 10.3390/ijms23168935] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
The uptake and distribution of doxorubicin in the MCF7 line of breast-cancer cells were monitored by Raman measurements. It was demonstrated that bioavailability of doxorubicin can be significantly enhanced by applying Congo red. To understand the mechanism of doxorubicin delivery by Congo red supramolecular carriers, additional monolayer measurements and molecular dynamics simulations on model membranes were undertaken. Acting as molecular scissors, Congo red particles cut doxorubicin aggregates and incorporated them into small-sized Congo red clusters. The mixed doxorubicin/Congo red clusters were adsorbed to the hydrophilic part of the model membrane. Such behavior promoted transfer through the membrane.
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25
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Doxorubicin-Based Hybrid Compounds as Potential Anticancer Agents: A Review. Molecules 2022; 27:molecules27144478. [PMID: 35889350 PMCID: PMC9318127 DOI: 10.3390/molecules27144478] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
The scarcity of novel and effective therapeutics for the treatment of cancer is a pressing and alarming issue that needs to be prioritized. The number of cancer cases and deaths are increasing at a rapid rate worldwide. Doxorubicin, an anticancer agent, is currently used to treat several types of cancer. It disrupts myriad processes such as histone eviction, ceramide overproduction, DNA-adduct formation, reactive oxygen species generation, Ca2+, and iron hemostasis regulation. However, its use is limited by factors such as drug resistance, toxicity, and congestive heart failure reported in some patients. The combination of doxorubicin with other chemotherapeutic agents has been reported as an effective treatment option for cancer with few side effects. Thus, the hybridization of doxorubicin and other chemotherapeutic drugs is regarded as a promising approach that can lead to effective anticancer agents. This review gives an update on hybrid compounds containing the scaffolds of doxorubicin and its derivatives with potent chemotherapeutic effects.
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26
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Exner KS, Ivanova A. A doxorubicin-peptide-gold nanoparticle conjugate as a functionalized drug delivery system: exploring the limits. Phys Chem Chem Phys 2022; 24:14985-14992. [PMID: 35687051 DOI: 10.1039/d2cp00707j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Efficient transport of pharmaceuticals to malignant cells in the human body often requires the application of drug-delivery systems (DDSs) consisting of several building blocks, each of them bearing a specific function. While nanoparticles are promising as potential carrier moieties, biomolecules may add to the efficient delivery by binding several drug molecules simultaneously. In this contribution, we apply a combination of atomistic molecular dynamics simulations and density functional theory calculations to characterize a multi-component DDS for the transport of the anthracycline antibiotic doxorubicin (DOX), comprising a gold nanoparticle (NP) and a drug-binding peptide (DBP) grafted on the NP surface. We have shown previously that the DDS can stabilize one DOX per DBP. However, by increasing the drug load to a 2 : 1 DOX : DBP ratio the two drug molecules compete for the available adsorption sites, which may cause spontaneous dissociation of one DOX molecule. We identify the chain length of the DBP as a limiting factor for the drug-loading capacity and provide important guidelines for further optimization of multi-component functionalized DDSs.
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Affiliation(s)
- Kai S Exner
- Sofia University, Faculty of Chemistry and Pharmacy, Department of Physical Chemistry, 1 James Bourchier blvd., 1164 Sofia, Bulgaria. .,Cluster of Excellence RESOLV, Bochum, Germany
| | - Anela Ivanova
- Sofia University, Faculty of Chemistry and Pharmacy, Department of Physical Chemistry, 1 James Bourchier blvd., 1164 Sofia, Bulgaria.
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27
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Lysophosphatidic acid protects cervical cancer HeLa cells from apoptosis induced by doxorubicin hydrochloride. Oncol Lett 2022; 24:267. [PMID: 35782896 PMCID: PMC9247665 DOI: 10.3892/ol.2022.13387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/27/2022] [Indexed: 11/11/2022] Open
Abstract
Cervical cancer is one of the most common types of gynecological tumors. Lysophosphatidic acid (LPA), as a bioactive lipid medium, plays an important role in numerous physiological and pathophysiological processes, including the stimulation of cell migration and tumor cell invasion. LPA is increased in the plasma of patients with cervical cancer. Doxorubicin hydrochloride (DOX) is used as a first-line drug in the treatment of cervical cancer in clinics, however, the effect and molecular mechanism of LPA on DOX-induced apoptosis in cervical cancer cells remain unclear. Therefore, the present study aimed to explore the effect and underlying molecular mechanism of LPA on DOX-induced apoptosis in cervical cancer cells. HeLa cells were treated as a control group or with LPA (10 µmol/l), DOX (4 µmol/l) or LPA (10 µmol/l) + DOX (4 µmol/l) for 24 h. Using transmission electron microscopy the results demonstrated that LPA reduced cell death and the degree of chromatin aggregation in DOX-induced HeLa cells. Reverse transcription-quantitative PCR demonstrated that LPA significantly downregulated caspase-3 mRNA expression levels in DOX-induced HeLa cells. Moreover, western blotting demonstrated that LPA significantly reduced caspase-3 and cleaved caspase-3 protein expression levels in DOX-induced HeLa, C33A and SiHa cells. Furthermore, flow cytometry demonstrated that LPA may prevent apoptosis in DOX-induced HeLa cells (P<0.05). Using dichloro-dihydro-fluorescein diacetate assay, it was demonstrated that LPA significantly reduced the intracellular ROS levels induced by DOX. In summary, the present study indicated that LPA may protect HeLa cells from apoptosis induced by DOX. These findings have provided experimental evidence that LPA may be a potential therapeutic target for the treatment of cervical cancer.
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28
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Jawad B, Adhikari P, Podgornik R, Ching WY. Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant. J Phys Chem Lett 2022; 13:3915-3921. [PMID: 35481766 PMCID: PMC9063111 DOI: 10.1021/acs.jpclett.2c00423] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The emergence of new SARS-CoV-2 Omicron variant of concern (OV) has exacerbated the COVID-19 pandemic because of a large number of mutations in the spike protein, particularly in the receptor-binding domain (RBD), resulting in highly contagious and/or vaccine-resistant strains. Herein, we present a systematic analysis based on detailed molecular dynamics (MD) simulations in order to understand how the OV RBD mutations affect the ACE2 binding. We show that the OV RBD binds to ACE2 more efficiently and tightly predominantly because of strong electrostatic interactions, thereby promoting increased infectivity and transmissibility compared to other strains. Some of the OV RBD mutations are predicted to affect the antibody neutralization either through their role in the S-protein conformational changes, such as S371L, S373P, and S375F, or through changing its surface charge distribution, such as G339D, N440K, T478K, and E484A. Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.
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Affiliation(s)
- Bahaa Jawad
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
- Department
of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Puja Adhikari
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
| | - Rudolf Podgornik
- Wenzhou
Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School
of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
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29
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Azimzadeh M, Aghili Z, Jannat B, Jafari S, Rafizadeh Tafti S, Nasirizadeh N. Nanocomposite of electrochemically reduced graphene oxide and gold nanourchins for electrochemical DNA detection. IET Nanobiotechnol 2022; 16:190-198. [PMID: 35442560 PMCID: PMC9178657 DOI: 10.1049/nbt2.12086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/24/2022] [Accepted: 04/02/2022] [Indexed: 12/19/2022] Open
Abstract
A nanocomposite of graphene oxide and gold nanourchins has been used here to modify the surface of a screen‐printed carbon electrode to enhance the sensitivity of the electrochemical DNA detection system. A specific single‐stranded DNA probe was designed based on the target DNA sequence and was thiolated to be self‐assembled on the surface of the gold nanourchins placed on the modified electrode. Doxorubicin was used as an electrochemical label to detect the DNA hybridisation using differential pulse voltammetry (DPV). The assembling process was confirmed using scanning electron microscopy (SEM) imaging, cyclic voltammetry (CV), and the EIS method. The high sensitivity of the proposed system led to a low detection limit of 0.16 fM and a wide linear range from 0.5 to 950.0 fM. The specificity of the DNA hybridisation and the signalling molecule (haematoxylin) caused very high selectivity towards the target DNA than other non‐specific sequences.
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Affiliation(s)
- Mostafa Azimzadeh
- Halal Research Center of IRI, MOH, Tehran, Iran.,Medical Nanotechnology & Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Stem Cell Biology Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Advanced Medical Sciences and Technologies, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Zahra Aghili
- Food & Drug Control Reference Laboratories Center, FDA, MOH, Tehran, Iran
| | | | - Saeid Jafari
- Department of Textile and Polymer Engineering, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Saeed Rafizadeh Tafti
- Medical Nanotechnology & Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Navid Nasirizadeh
- Halal Research Center of IRI, MOH, Tehran, Iran.,Department of Textile and Polymer Engineering, Yazd Branch, Islamic Azad University, Yazd, Iran
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30
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Bhangu SK, Fernandes S, Beretta GL, Tinelli S, Cassani M, Radziwon A, Wojnilowicz M, Sarpaki S, Pilatis I, Zaffaroni N, Forte G, Caruso F, Ashokkumar M, Cavalieri F. Transforming the Chemical Structure and Bio-Nano Activity of Doxorubicin by Ultrasound for Selective Killing of Cancer Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107964. [PMID: 35100658 DOI: 10.1002/adma.202107964] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Reconfiguring the structure and selectivity of existing chemotherapeutics represents an opportunity for developing novel tumor-selective drugs. Here, as a proof-of-concept, the use of high-frequency sound waves is demonstrated to transform the nonselective anthracycline doxorubicin into a tumor selective drug molecule. The transformed drug self-aggregates in water to form ≈200 nm nanodrugs without requiring organic solvents, chemical agents, or surfactants. The nanodrugs preferentially interact with lipid rafts in the mitochondria of cancer cells. The mitochondrial localization of the nanodrugs plays a key role in inducing reactive oxygen species mediated selective death of breast cancer, colorectal carcinoma, ovarian carcinoma, and drug-resistant cell lines. Only marginal cytotoxicity (80-100% cell viability) toward fibroblasts and cardiomyocytes is observed, even after administration of high doses of the nanodrug (25-40 µg mL-1 ). Penetration, cytotoxicity, and selectivity of the nanodrugs in tumor-mimicking tissues are validated by using a 3D coculture of cancer and healthy cells and 3D cell-collagen constructs in a perfusion bioreactor. The nanodrugs exhibit tropism for lung and limited accumulation in the liver and spleen, as suggested by in vivo biodistribution studies. The results highlight the potential of this approach to transform the structure and bioactivity of anticancer drugs and antibiotics bearing sono-active moieties.
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Affiliation(s)
- Sukhvir Kaur Bhangu
- School of Science, RMIT University, Melbourne, Victoria, 3000, Australia
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
- School of Chemistry, The University of Melbourne, Victoria, 3010, Australia
| | - Soraia Fernandes
- International Clinical Research Center (ICRC), St Anne's University Hospital, Brno, 65691, Czechia
| | - Giovanni Luca Beretta
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, Milan, 20133, Italy
| | - Stella Tinelli
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, Milan, 20133, Italy
| | - Marco Cassani
- International Clinical Research Center (ICRC), St Anne's University Hospital, Brno, 65691, Czechia
| | - Agata Radziwon
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Marcin Wojnilowicz
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Sophia Sarpaki
- BIOEMTECH, 27 Neapoleos st., Lefkippos Attica Technology Park - N.C.S.R. Demokritos, Athens, 15341, Greece
| | - Irinaios Pilatis
- BIOEMTECH, 27 Neapoleos st., Lefkippos Attica Technology Park - N.C.S.R. Demokritos, Athens, 15341, Greece
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, Milan, 20133, Italy
| | - Giancarlo Forte
- International Clinical Research Center (ICRC), St Anne's University Hospital, Brno, 65691, Czechia
| | - Frank Caruso
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | | | - Francesca Cavalieri
- School of Science, RMIT University, Melbourne, Victoria, 3000, Australia
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma "Tor Vergata", via della ricerca scientifica 1, Rome, 00133, Italy
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31
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Evaluating Radioactive Analogs of Doxorubicin to Quantify ChemoFilter Binding and Whole Body PET/MR Drug Biodistribution. J Vasc Interv Radiol 2022; 33:687-694. [DOI: 10.1016/j.jvir.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/20/2022] [Accepted: 03/06/2022] [Indexed: 11/23/2022] Open
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32
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Lafiosca P, Gómez S, Giovannini T, Cappelli C. Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach. J Chem Theory Comput 2022; 18:1765-1779. [PMID: 35184553 PMCID: PMC8908768 DOI: 10.1021/acs.jctc.1c01066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
We report on the
first formulation of a novel polarizable QM/MM
approach, where the density functional tight binding (DFTB) is coupled
to the fluctuating charge (FQ) force field. The resulting method (DFTB/FQ)
is then extended to the linear response within the TD-DFTB framework
and challenged to study absorption spectra of large condensed-phase
systems.
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Affiliation(s)
- Piero Lafiosca
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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33
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Costoya J, Surnar B, Kalathil AA, Kolishetti N, Dhar S. Controlled release nanoplatforms for three commonly used chemotherapeutics. Mol Aspects Med 2022; 83:101043. [PMID: 34920863 PMCID: PMC10074549 DOI: 10.1016/j.mam.2021.101043] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022]
Abstract
In order to combat an evolving, multidimensional disease such as cancer, research has been aimed at synthesizing more efficient and effective versions of popular chemotherapeutic drugs. Despite these efforts, there remains a necessity for the development of suitable delivery vehicles that can both harness the chemotherapeutic effects meanwhile reducing some of the known issues when using these drugs such as unwanted side-effects, acquired drug resistance, and associated difficulties with drug delivery. Synthetic drug discovery approaches focusing on modification of the native structure of these chemotherapeutic drugs often face challenges such as loss of efficacy, as well as a potential worsening of side-effects. Synthetic chemists are then left with increasingly narrow choices for possible chemistry they could implement to achieve the desired therapy. The emergence of targeted therapies using controlled-release nanomaterials can provide many opportunities for conventional chemotherapeutic drugs to be delivered to specific target sites, ultimately leading to reduced side-effects and improved efficacy. Logically, it may prove advantageous to consider nano-delivery systems as a likely candidate for circumventing some of the barriers associated with creating viable drug therapies. In this review, we summarize controlled release nanoformulations of the three most widely used and approved chemotherapeutics, doxorubicin, paclitaxel, and cisplatin as an alternative therapeutic approach against different cancer types.
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Affiliation(s)
- Joel Costoya
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Bapurao Surnar
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Akil A Kalathil
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Nagesh Kolishetti
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
| | - Shanta Dhar
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
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34
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Jawad B, Adhikari P, Cheng K, Podgornik R, Ching WY. Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. Int J Mol Sci 2022; 23:838. [PMID: 35055023 PMCID: PMC8776159 DOI: 10.3390/ijms23020838] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
| | - Kun Cheng
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA;
| | - Rudolf Podgornik
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou 325000, China;
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
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35
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Mozaffari S, Salehi D, Mahdipoor P, Beuttler R, Tiwari R, Aliabadi HM, Parang K. Design and application of hybrid cyclic-linear peptide-doxorubicin conjugates as a strategy to overcome doxorubicin resistance and toxicity. Eur J Med Chem 2021; 226:113836. [PMID: 34537446 DOI: 10.1016/j.ejmech.2021.113836] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/19/2021] [Accepted: 09/05/2021] [Indexed: 12/15/2022]
Abstract
Doxorubicin (Dox) is used for breast cancer, leukemia, and lymphoma treatment as an effective chemotherapeutic agent. However, Dox use is restricted due to inherent and acquired resistance and an 8-fold increase in the risk of potentially fatal cardiotoxicity. Hybrid cyclic-linear peptide [R5K]W7A and linear peptide R5KW7A were conjugated with Dox through a glutarate linker to afford [R5K]W7A-Dox and R5KW7A-Dox conjugates to generate Dox derivatives. Alternatively, [R5K]W7C was conjugated with Dox via a disulfide linker to generate [R5K]W7C-S-S-Dox conjugate, where S-S is a disulfide bond. Comparative antiproliferative assays between conjugates [R5K]W7A-Dox, [R5K]W7C-S-S-Dox, linear R5KW7A-Dox, the corresponding physical mixtures of the peptides, and Dox were performed in normal and cancer cells. [R5K]W7A-Dox conjugate was 2-fold more efficient than R5KW7A-Dox, and [R5K]W7C-S-S-Dox conjugates in inhibiting the cell proliferation of human leukemia cells (CCRF-CEM). Therefore, hybrid cyclic-linear [R5K]W7A-Dox conjugate was selected for further studies and inhibited the cell viability of CCRF-CEM (84%), ovarian adenocarcinoma (SK-OV-3, 39%), and gastric carcinoma (AGS, 73%) at a concentration of 5 μM after 72 h of incubation, which was comparable to Dox (5 μM) efficacy (CCRF-CEM (85%), SK-OV-3 (33%), and AGS (87%)). While [R5K]W7A-Dox had a significant effect on the viability of cancer cells, it exhibited minimal cytotoxicity to normal kidney (LLC-PK1, 5-7%) and heart cells (H9C2, <9%) at concentrations of 5-10 μM (compared to free Dox at 5 μM that reduced the viability of kidney and heart cells by 85% and 44%, respectively). The fluorescence microscopy images were consistent with the cytotoxicity studies, indicating minimal uptake of the cyclic-linear [R5K]W7A-Dox (5 μM) in H9C2 cells. In comparison, Dox (5 μM) showed significant uptake, reduced cell viability, and changed the morphology of the cells after 24 h. [R5K]W7A-Dox showed 16-fold and 9.5-fold higher activity against Dox-resistant cells MDA231R and MES-SA/MX2 (lethal dose for 50% cell death or LC50 of 2.3 and 4.3 μM, respectively) compared to free Dox (LC50 of 36-41 μM, respectively). These data, along with the results obtained from the cell viability tests, indicate comparable efficiency of [R5K]W7A-Dox to free Dox in leukemia, ovarian, and gastric cancer cells, significantly reduced toxicity in normal kidney LLC-PK1 and heart H9C2 cells, and significantly higher efficiency in Dox-resistant cells. A number of endocytosis inhibitors did not affect the cellular uptake of [R5K]W7A-Dox.
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Affiliation(s)
- Saghar Mozaffari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - David Salehi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - Parvin Mahdipoor
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - Richard Beuttler
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - Rakesh Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA.
| | - Hamidreza Montazeri Aliabadi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA.
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA.
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36
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Gonsalves A, Tambe P, Le D, Thakore D, Wadajkar AS, Yang J, Nguyen KT, Menon JU. Synthesis and characterization of a novel pH-responsive drug-releasing nanocomposite hydrogel for skin cancer therapy and wound healing. J Mater Chem B 2021; 9:9533-9546. [PMID: 34757371 PMCID: PMC8725646 DOI: 10.1039/d1tb01934a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Local skin cancer recurrence occurs in ∼12% of the patients post-surgery due to persistent growth of residual cancer cells. Wound infection is another significant complication following surgery. We report a novel in situ-forming nanocomposite hydrogel (NCH) containing PLGA-carboxymethyl chitosan nanoparticles (186 nm) for localized pH-responsive skin cancer therapy and wound healing. This injectable hydrogel, comprising of a citric acid-derived polymer backbone, gelled within 5 minutes, and demonstrated excellent swelling (283% of dry weight) and compressive strengths (∼5.34 MPa). Nanoparticle incorporation did not significantly affect hydrogel properties. The NCH effluents were cytocompatible with human dermal fibroblasts at 500 μg ml-1 concentration and demonstrated pH-dependent drug release and promising therapeutic efficacy against A431 and G361 skin cancer cells in vitro. Significant zones of inhibition were observed in S. aureus and E. coli cultures on NCH treatment, confirming its antibacterial properties. Our studies show that the pH-responsive NCH can be potentially used for adjuvant skin cancer treatment and wound healing.
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Affiliation(s)
- Andrea Gonsalves
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
| | - Pranjali Tambe
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76019, USA
- Department of Biomedical Engineering, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Duong Le
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
| | - Dheeraj Thakore
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76019, USA
- Department of Biomedical Engineering, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aniket S Wadajkar
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76019, USA
- Department of Biomedical Engineering, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jian Yang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Kytai T Nguyen
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76019, USA
- Department of Biomedical Engineering, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jyothi U Menon
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA.
- Department of Chemical Engineering, University of Rhode Island, Kingston, RI 02881, USA
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Computational Study on Potential Novel Anti-Ebola Virus Protein VP35 Natural Compounds. Biomedicines 2021; 9:biomedicines9121796. [PMID: 34944612 PMCID: PMC8698941 DOI: 10.3390/biomedicines9121796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/27/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
Ebola virus (EBOV) is one of the most lethal pathogens that can infect humans. The Ebola viral protein VP35 (EBOV VP35) inhibits host IFN-α/β production by interfering with host immune responses to viral invasion and is thus considered as a plausible drug target. The aim of this study was to identify potential novel lead compounds against EBOV VP35 using computational techniques in drug discovery. The 3D structure of the EBOV VP35 with PDB ID: 3FKE was used for molecular docking studies. An integrated library of 7675 African natural product was pre-filtered using ADMET risk, with a threshold of 7 and, as a result, 1470 ligands were obtained for the downstream molecular docking using AutoDock Vina, after an energy minimization of the protein via GROMACS. Five known inhibitors, namely, amodiaquine, chloroquine, gossypetin, taxifolin and EGCG were used as standard control compounds for this study. The area under the curve (AUC) value, evaluating the docking protocol obtained from the receiver operating characteristic (ROC) curve, generated was 0.72, which was considered to be acceptable. The four identified potential lead compounds of NANPDB4048, NANPDB2412, ZINC000095486250 and NANPDB2476 had binding affinities of −8.2, −8.2, −8.1 and −8.0 kcal/mol, respectively, and were predicted to possess desirable antiviral activity including the inhibition of RNA synthesis and membrane permeability, with the probable activity (Pa) being greater than the probable inactivity (Pi) values. The predicted anti-EBOV inhibition efficiency values (IC50), found using a random forest classifier, ranged from 3.35 to 11.99 μM, while the Ki values ranged from 0.97 to 1.37 μM. The compounds NANPDB4048 and NANPDB2412 had the lowest binding energy of −8.2 kcal/mol, implying a higher binding affinity to EBOV VP35 which was greater than those of the known inhibitors. The compounds were predicted to possess a low toxicity risk and to possess reasonably good pharmacological profiles. Molecular dynamics (MD) simulations of the protein–ligand complexes, lasting 50 ns, and molecular mechanisms Poisson-Boltzmann surface area (MM-PBSA) calculations corroborated the binding affinities of the identified compounds and identified novel critical interacting residues. The antiviral potential of the molecules could be confirmed experimentally, while the scaffolds could be optimized for the design of future novel anti-EBOV chemotherapeutics.
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Ng YM, Coghi P, Ng JPL, Ali F, Wong VKW, Coluccini C. Synthesis and Coordination Properties of a Water-Soluble Material by Cross-Linking Low Molecular Weight Polyethyleneimine with Armed Cyclotriveratrilene. Polymers (Basel) 2021; 13:4133. [PMID: 34883636 PMCID: PMC8659696 DOI: 10.3390/polym13234133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
In this study, a full organic and water-soluble material was synthesized by coupling low molecular weight polyethylenimine (PEI-800) with cyclotriveratrilene (CTV). The water-soluble cross-linked polymer contains hydrophobic holes with a high coordination capability towards different organic drug molecules. The coordinating capability towards hydrophilic drugs (doxorubicin, gatifloxacin and sinomenine) and hydrophobic drugs (camptothecin and celastrol) was analyzed in an aqueous medium by using NMR, UV-Vis and emission spectroscopies. The coordination of drug molecules with the armed CTV unit through hydrophobic interactions was observed. In particular, celastrol exhibited more ionic interactions with the PEI moiety of the hosting system. In the case of doxorubicin, the host-guest detachment was induced by the addition of ammonium chloride, suggesting that the intracellular environment can facilitate the release of the drug molecules.
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Affiliation(s)
- Yoke Mooi Ng
- Institute of New Drug Development, College of Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan;
| | - Paolo Coghi
- School of Pharmacy, Macau University of Science and Technology, Macau 999078, China;
| | - Jerome P. L. Ng
- Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (J.P.L.N.); (V.K.W.W.)
| | - Fayaz Ali
- Department Chemistry, Abbottabad University of Science and Technology, Abbottabad 22010, Pakistan;
| | - Vincent Kam Wai Wong
- Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (J.P.L.N.); (V.K.W.W.)
| | - Carmine Coluccini
- Institute of New Drug Development, College of Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan;
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Karadurmus L, Dogan-Topal B, Kurbanoglu S, Shah A, Ozkan SA. The Interaction between DNA and Three Intercalating Anthracyclines Using Electrochemical DNA Nanobiosensor Based on Metal Nanoparticles Modified Screen-Printed Electrode. MICROMACHINES 2021; 12:mi12111337. [PMID: 34832748 PMCID: PMC8619472 DOI: 10.3390/mi12111337] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
The screen-printed electrodes have gained increasing importance due to their advantages, such as robustness, portability, and easy handling. The manuscript presents the investigation of the interaction between double-strand deoxyribonucleic acid (dsDNA) and three anthracyclines: epirubicin (EPI), idarubicin (IDA), and doxorubicin (DOX) by differential pulse voltammetry on metal nanoparticles modified by screen-printed electrodes. In order to investigate the interaction, the voltammetric signals of dsDNA electroactive bases were used as an indicator. The effect of various metal nanomaterials on the signals of guanine and adenine was evaluated. Moreover, dsDNA/PtNPs/AgNPs/SPE (platinum nanoparticles/silver nanoparticles/screen-printed electrodes) was designed for anthracyclines–dsDNA interaction studies since the layer-by-layer modification strategy of metal nanoparticles increases the surface area. Using the signal of multi-layer calf thymus (ct)-dsDNA, the within-day reproducibility results (RSD%) for guanine and adenine peak currents were found as 0.58% and 0.73%, respectively, and the between-day reproducibility results (RSD%) for guanine and adenine peak currents were found as 1.04% and 1.26%, respectively. The effect of binding time and concentration of three anthracyclines on voltammetric signals of dsDNA bases were also evaluated. The response was examined in the range of 0.3–1.3 ppm EPI, 0.1–1.0 ppm IDA and DOX concentration on dsDNA/PtNPs/AgNPs/SPE. Electrochemical studies proposed that the interaction mechanism between three anthracyclines and dsDNA was an intercalation mode.
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Affiliation(s)
- Leyla Karadurmus
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (L.K.); (S.K.)
- Department of Analytical Chemistry, Faculty of Pharmacy, Adıyaman University, Adıyaman 02040, Turkey
| | - Burcu Dogan-Topal
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (L.K.); (S.K.)
- Correspondence: (B.D.-T.); (S.A.O.)
| | - Sevinc Kurbanoglu
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (L.K.); (S.K.)
| | - Afzal Shah
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Sibel A. Ozkan
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (L.K.); (S.K.)
- Correspondence: (B.D.-T.); (S.A.O.)
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Baral K, Adhikari P, Jawad B, Podgornik R, Ching WY. Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics. Polymers (Basel) 2021; 13:3434. [PMID: 34641249 PMCID: PMC8512769 DOI: 10.3390/polym13193434] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
The structure and properties of the arginine-glycine-aspartate (RGD) sequence of the 1FUV peptide at 0 K and body temperature (310 K) are systematically investigated in a dry and aqueous environment using more accurate ab initio molecular dynamics and density functional theory calculations. The fundamental properties, such as electronic structure, interatomic bonding, partial charge distribution, and dielectric response function at 0 and 310 K are analyzed, comparing them in dry and solvated models. These accurate microscopic parameters determined from highly reliable quantum mechanical calculations are useful to define the range and strength of complex molecular interactions occurring between the RGD peptide and the integrin receptor. The in-depth bonding picture analyzed using a novel quantum mechanical metric, the total bond order (TBO), quantifies the role played by hydrogen bonds in the internal cohesion of the simulated structures. The TBO at 310 K decreases in the dry model but increases in the solvated model. These differences are small but extremely important in the context of conditions prevalent in the human body and relevant for health issues. Our results provide a new level of understanding of the structure and properties of the 1FUV peptide and help in advancing the study of RGD containing other peptides.
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Affiliation(s)
- Khagendra Baral
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (K.B.); (P.A.); (B.J.)
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (K.B.); (P.A.); (B.J.)
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (K.B.); (P.A.); (B.J.)
| | - Rudolf Podgornik
- School of Physical Sciences, Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China;
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou 325000, China
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (K.B.); (P.A.); (B.J.)
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Jawad B, Adhikari P, Podgornik R, Ching WY. Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. J Chem Inf Model 2021; 61:4425-4441. [PMID: 34428371 PMCID: PMC8409146 DOI: 10.1021/acs.jcim.1c00560] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Indexed: 12/12/2022]
Abstract
The spike protein of SARS-CoV-2 binds to the ACE2 receptor via its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analyses at molecular, amino acid (AA), and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex for SARS-CoV and SARS-CoV-2 with its Alpha and Beta variants. Our study uses the molecular dynamics (MD) simulations with the molecular mechanics generalized Born surface area (MM-GBSA) method to predict the binding free energy (BFE) and to determine the actual interacting AAs, as well as two ab initio quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q493, Y505, Q498, N501, T500, N487, Y449, F486, K417, Y489, F456, Y495, and L455 have been identified as hotspots in SARS-CoV-2 RBD, while those in ACE2 are K353, K31, D30, D355, H34, D38, Q24, T27, Y83, Y41, and E35. RBD with Alpha and Beta variants has slightly different interacting AAs due to N501Y mutation. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q493, Q498, N501, F486, K417, and F456 in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. RBD with the Alpha variant binds with ACE2 stronger than the wild-type RBD or Beta. In the Beta variant, K417N reduces the binding, E484K slightly enhances it, and N501Y significantly increases it as in Alpha. The DFT results reveal that N487, Q493, Y449, T500, G496, G446, and G502 in RBD of SARS2 form pairs via specific hydrogen bonding with Q24, H34, E35, D38, Y41, Q42, and K353 in ACE2.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy,
University of Missouri-Kansas City, Kansas City, Missouri
64110, United States
| | - Puja Adhikari
- Department of Physics and Astronomy,
University of Missouri-Kansas City, Kansas City, Missouri
64110, United States
| | - Rudolf Podgornik
- Wenzhou Institute of the University of
Chinese Academy of Sciences, Wenzhou, Zhejiang 325000,
China
- School of Physical Sciences and Kavli Institute of
Theoretical Science, University of Chinese Academy of Sciences,
Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics,
Institute of Physics, Chinese Academy of Sciences, Beijing
100090, China
- Department of Physics, Faculty of Mathematics and
Physics, University of Ljubljana, SI-1000 Ljubljana,
Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy,
University of Missouri-Kansas City, Kansas City, Missouri
64110, United States
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Firestein R, Marcinkiewicz C, Nie L, Chua HK, Velazquez Quesada I, Torelli M, Sternberg M, Gligorijevic B, Shenderova O, Schirhagl R, Feuerstein GZ. Pharmacodynamic Studies of Fluorescent Diamond Carriers of Doxorubicin in Liver Cancer Cells and Colorectal Cancer Organoids. Nanotechnol Sci Appl 2021; 14:139-159. [PMID: 34522092 PMCID: PMC8434926 DOI: 10.2147/nsa.s321725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/14/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND We recently reported on preferential deposition of bare fluorescent diamond particles FDP-NV-700/800nm (FDP-NV) in the liver following intravenous administration to rats. The pharmacokinetics of FDP-NV in that species indicated short residency in the circulation by rapid clearance by the liver. Retention of FDP-NV in the liver was not associated with any pathology. These observations suggested that cancer therapeutics, such as doxorubicin, linked to FDP-NV, could potentially serve for anti-cancer treatment while sparing toxicities of peripheral organs. PURPOSE To generate proof-of-concept (POC) and detail mechanisms of action of doxorubicin-coated FDP-NV-700/800nm (FDP-DOX) as a prospective chemotherapeutic for metastatic liver cancer. METHODS FDP-DOX was generated by adsorption chemistry. Experimental design included concentration and time-dependent efficacy studies as compared with naïve (baren) FDP-NV in in vitro liver cancer cells models. Uptake of FDP-NV and FDP-DOX by HepG-2, Hep-3B and hCRC organoids were demonstrated by flow-cytometry and fluorescent microscopy. FDP-DOX pharmacodynamic effects included metabolic as well as cell death biomarkers Annexin V, TUNEL and LDH leakage. DOX desorpted from FDP-DOX was assessed by confocal microscopy and chemical assay of cells fractions. RESULTS FDP-DOX efficacy was dose- and time-dependent and manifested in both liver cancer cell lines and human CRC organoids. FDP-DOX was rapidly internalized into cancer cells/organoids leading to cancer growth inhibition and apoptosis. FDP-DOX disrupted cell membrane integrity as evident by LDH release and suppressing mitochondrial metabolic pathways (AlamarBlue assay). Access of free DOX to the nuclei was confirmed by direct UV-Visible fluorescent assay and confocal microscopy of DOX fluorescence. CONCLUSION The rapid uptake and profound cancer inhibition observed using FDP-DOX in clinically relevant cancer models, highlight FDP-DOX promise for cancer chemotherapeutics. We also conclude that the in vitro data justify further investment in in vivo POC studies.
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Affiliation(s)
- Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia,Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Cezary Marcinkiewicz
- Debina Diagnostics Inc., Newtown Square, PA, USA,College of Engineering, Department of Bioengineering, Temple University, Philadelphia, PA, USA
| | - Linyan Nie
- Groningen University, Groningen, 9727, the Netherlands
| | - Hui Kheng Chua
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia,Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Ines Velazquez Quesada
- College of Engineering, Department of Bioengineering, Temple University, Philadelphia, PA, USA
| | - Marco Torelli
- Adámas Nanotechnologies, Inc., Raleigh, NC, 27617, USA
| | | | - Bojana Gligorijevic
- College of Engineering, Department of Bioengineering, Temple University, Philadelphia, PA, USA
| | | | | | - Giora Z Feuerstein
- Debina Diagnostics Inc., Newtown Square, PA, USA,Correspondence: Giora Z Feuerstein Debina Diagnostics Inc., 33 Bishop Hollow Road, Newtown Square, PA, 19073, USATel +4842221575 Email
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Kumar S, Nair MS. Deciphering the interaction of flavones with calf thymus DNA and octamer DNA sequence (CCAATTGG) 2. RSC Adv 2021; 11:29354-29371. [PMID: 35479565 PMCID: PMC9040621 DOI: 10.1039/d1ra04101k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/22/2021] [Indexed: 01/18/2023] Open
Abstract
We investigated the interaction of three flavone compounds, baicalein, chrysin and flavone with calf thymus DNA and octamer DNA sequence (CCAATTGG)2. The binding mechanisms of the flavone compounds with both DNA were unveiled using biophysical, thermodynamic and molecular modelling techniques. Absorption and fluorescence titrations confirm the formation of the DNA complexes along with the extent of interaction. Absorption data proposed an intercalation mode of binding. Fluorescence displacement assays using ethidium bromide and Hoechst 33258 data supports a partial intercalation. Potassium iodide quenching substantiated this finding. Circular dichroism data revealed major structural changes on binding with flavones which can arise from intercalation partially or in a tilted arrangement. Analysis of the effect of ionic strength on complex formation eliminated the role of electrostatic interaction in the binding. Differential scanning calorimetric data showed substantial changes in the melting temperatures of complexes and predicted the DNA–baicalein complex as the most stable one. Molecular modelling showcased that the complexes are located near the AT rich region. Docking analysis with different sequences showed that the flavone compounds intercalated with base pairs only with d(CGATCG)2. Binding of flavones induce conformational changes in double stranded DNA.![]()
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Affiliation(s)
- Shailendra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee Uttarakhand-247667 India +91-1332-273560 +91-1332-285790
| | - Maya S Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee Uttarakhand-247667 India +91-1332-273560 +91-1332-285790
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Rotkrua P, Lohlamoh W, Watcharapo P, Soontornworajit B. A molecular hybrid comprising AS1411 and PDGF-BB aptamer, cholesterol, and doxorubicin for inhibiting proliferation of SW480 cells. J Mol Recognit 2021; 34:e2926. [PMID: 34258818 DOI: 10.1002/jmr.2926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
Cancer treatment commonly relies on chemotherapy. This treatment faces many challenges, including treatment specificity and undesired side effects. To address these, a Dox-loaded Chol-aptamer molecular hybrid (Dox-CAH) was developed. This multivalent interaction system combines the key function of each integrated species: doxorubicin, cholesterol, and two aptamers binding to nucleolin and platelet-derived growth factor BB (PDGF-BB). The study has four stages: preparation of CAH via oligonucleotide hybridization, intercalation of doxorubicin into CAH, verification of CAH binding on SW480 by fluorescence microscopy and flow cytometry, and investigation of effect of Dox-CAH on SW480 proliferation. CAH was successfully prepared, as confirmed by electrophoresis. Flow cytometry and fluorescence microscopy demonstrated CAH binding to SW480, due to the presence of the AS1411 aptamer. This molecular hybrid exhibited specific binding because it did not bind to CCD 841 CoN. CAH binding to PDGF-BB compromises its function, as shown by enzyme-linked immunosorbent assay (ELISA) and cell assay. The DNA duplex in this molecular hybrid reduces the cytotoxicity of the Dox-CAH. Binding and the reduction of Dox-CAH toxicity may improve treatment specificity and minimize side effects. Dox-CAH is a model for more effective anticancer therapy, allowing incorporation of chemotherapeutic drugs and recognition elements.
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Affiliation(s)
- Pichayanoot Rotkrua
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Walaiporn Lohlamoh
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Paphada Watcharapo
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Pathumthani, Thailand
| | - Boonchoy Soontornworajit
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Pathumthani, Thailand
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Elkayal R, Motawea A, Reicha FM, Elmezayyen AS. Novel electro self-assembled DNA nanospheres as a drug delivery system for atenolol. NANOTECHNOLOGY 2021; 32:255602. [PMID: 33797397 DOI: 10.1088/1361-6528/abd727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
We describe new method for preparing DNA nanospheres for a self-assembled atenolol@DNA (core/shell) drug delivery system. In this paper, we propose the electrochemical transformation of an alkaline polyelectrolyte solution of DNA into DNA nanospheres. We successfully electrosynthesized DNA nanospheres that were stable for at least 2 months at 4 °C. UV-visible spectra of the prepared nanospheres revealed a peak ranging from 372 to 392 nm depending on the DNA concentration and from 361 to 398.3 nm depending on the electrospherization time. This result, confirmed with size distribution curves worked out from transmission electron microscopy (TEM) images, showed that increasing electrospherization time (6, 12 and 24 h) induces an increase in the average size of DNA nanospheres (48, 65.5 and 117 nm, respectively). In addition, the average size of DNA nanospheres becomes larger (37.8, 48 and 76.5 nm) with increasing DNA concentration (0.05, 0.1 and 0.2 wt%, respectively). Also, the affinity of DNA chains for the surrounding solvent molecules changed from favorable to bad with concomitant extreme reduction in the zeta potential from -31 mV to -17 mV. Principally, the attractive and hydrophobic interactions tend to compact the DNA chain into a globule, as confirmed by Fourier transform infrared spectroscopy (FTIR) and TEM. To advance possible applications, we successfully electro self-assembled an atenolol@DNA drug delivery system. Our findings showed that electrospherization as a cost-benefit technique could be effectively employed for sustained drug release. This delivery system achieved a high entrapment efficiency of 68.03 ± 2.7% and a moderate drug-loading efficiency of 3.73%. The FTIR spectra verified the absence of any chemical interaction between the drug and the DNA during the electrospherization process. X-ray diffraction analysis indicated noteworthy lessening in atenolol crystallinity. The present findings could aid the effectiveness of electrospherized DNA for use in various other pharmaceutical and biomedical applications.
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Affiliation(s)
- Rehab Elkayal
- Biological Advanced Materials, Physics Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Amira Motawea
- Department of Pharmaceutics, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Fikry M Reicha
- Biological Advanced Materials, Physics Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Ayman S Elmezayyen
- Biological Advanced Materials, Physics Department, Faculty of Science, Mansoura University, Mansoura, Egypt
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Pal S, Paul S. An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA. Phys Chem Chem Phys 2021; 23:3361-3376. [PMID: 33502401 DOI: 10.1039/d0cp05210h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The stability of c-KIT G-quadruplex DNA via ligands has been a significant concern in the growing field of cancer therapy. Thus, it is very important to understand the mechanism behind the high binding affinity of the small drug molecules on the c-KIT G-quadruplex DNA. In this study, we have investigated the binding mode and pathway of the APTO-253 ligand on the c-KIT G-quadruplex DNA employing a total of 10 μs all atom molecular dynamics simulations and further 8.82 μs simulations via the umbrella sampling method using both OL15 and BSC1 latest force fields for DNA structures. From the cluster structure analysis, mainly three binding pathways i.e., top, bottom and side loop stacking modes are identified. Moreover, RMSD, RMSF and 2D-RMSD values indicate that the c-KIT G-quadruplex DNA and APTO-253 molecules are stable throughout the simulation run. Furthermore, the number of hydrogen bonds in each tetrad and the distance between the two central K+ cations confirm that the c-KIT G-quadruplex DNA maintains its conformation in the process of complex formation with the APTO-253 ligand. The binding free energies and the minimum values in the potential of mean forces suggest that the binding processes are energetically favorable. Furthermore, we have found that the bottom stacking mode is the most favorable binding mode among all the three modes for the OL15 force field. However, for the BSC1 force field, both the top and bottom binding modes of the APTO-253 ligand in c-KIT G-quadruplex DNA are comparable to each other. To investigate the driving force for the complex formation, we have noticed that the van der Waals (vdW) and π-π stacking interactions are mainly responsible. Our detailed studies provide useful information for the discovery of novel drugs in the field of stabilization of G-quadruplex DNAs.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
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Sangpheak K, Waraho-Zhmayev D, Haonoo K, Torpaiboon S, Teacharsripaiboon T, Rungrotmongkol T, Poo-Arporn RP. Investigation of interactions between binding residues and solubility of grafted humanized anti-VEGF IgG antibodies expressed as full-length format in the cytoplasm of a novel engineered E. coli SHuffle strain. RSC Adv 2021; 11:6035-6048. [PMID: 35423148 PMCID: PMC8694825 DOI: 10.1039/d0ra08534k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/25/2021] [Indexed: 12/29/2022] Open
Abstract
Monoclonal antibodies (mAbs) are one of the fastest-growing areas of biopharmaceutical industry and have been widely used for a broad spectrum of diseases. Meanwhile, the immunogenicity of non-human derived antibodies can generate side effects by inducing the human immune response to produce human anti-mouse-immunoglobulin antibody (HAMA). In this work, we aim to reduce the immunogenicity of muMAb A.4.6.1 by substitute human sequences for murine sequences. Humanized antibodies are constructed by grafting, specificity determining residues (SDR), complementary determining regions (CDR), and chimeric region of muMAb A.4.6.1, onto variable domain of Trastuzumab (Herceptin). The interactions between grafted antibodies and their target, Vascular endothelial growth factor (VEGF), were theoretically investigated by molecular dynamics simulation in order to evaluate the antibodies-antigen binding behavior. The obtained protein-protein interactions and calculated binding free energy suggested that the SDR-VEGF complex presented a significantly greater binding affinity, number of contact and total number of H-bonds compared to CDR and chimeric mAbs, significantly. Moreover, the Camsol program predicted that the solubility of SDR mAb exhibits the greatest solubility. This result was supported by performing a western blot analysis of the grafted mAbs with soluble and insoluble fractions in order to evaluate their solubility, in which SDR was found to have a much lower amount of insoluble proteins. Consequently, the enhanced binding affinity and solubility of the designed SDR was achieved by the single S106D mutation using computational methods. With the aim of low immunogenicity, high solubility, and high affinity, this SDR humanized antibody was expected to have greater efficacy than murine or chimeric antibodies for future use in humans.
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Affiliation(s)
- Kanyani Sangpheak
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi 10140 Bangkok Thailand
| | - Dujduan Waraho-Zhmayev
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi 10140 Bangkok Thailand
| | - Korakod Haonoo
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi 10140 Bangkok Thailand
| | - Sarun Torpaiboon
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi 10140 Bangkok Thailand
| | - Tarin Teacharsripaiboon
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi 10140 Bangkok Thailand
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University 10330 Bangkok Thailand.,Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University 10330 Bangkok Thailand
| | - Rungtiva P Poo-Arporn
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi 10140 Bangkok Thailand
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Khan S, Fakhar Z, Ahmad A. Targeting ebola virus VP40 protein through novel inhibitors: exploring the structural and dynamic perspectives on molecular landscapes. J Mol Model 2021; 27:49. [PMID: 33495861 DOI: 10.1007/s00894-021-04682-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 01/17/2021] [Indexed: 11/27/2022]
Abstract
Ebola filovirus (EBOV) is one of the deadliest known infectious agents, and a cause of Western African epidemics from 2013 to 2016. The virus has infected nearly 3000 humans and almost 1900 have died. In the past few years, various small molecules have been discovered to display efficiency against EBOV and some of them have progressed towards clinical trials. Even though continuous attempts have been made to find antiEBOV therapeutics, no potential drugs are yet approved against this viral infection. The development of small antiviral inhibitors has gained tremendous attention in the attempt to overcome EVD. With this background, we seek to offer molecular insights into EBOV VP40 protein inhibition, using all atom molecular mechanics methodology and binding free energy calculations. We have selected five novel reported inhibitors against VP40 protein, namely Comp1, Comp2, Comp3, Comp4, and Comp5, and explored their binding against the same target. It was evident from the analysis that all the inhibitors displayed stability in complex with VP40 protein; however, Comp1 exhibited enhanced stability and compactness. Comp1 unveiled favorable binding, which accounted for positive correlation motions in the active site residues. Likewise, Comp1 revealed the most promising binding (ΔGbind - 40.3504 kcal/mol) as compared to the other four inhibitors, which disclosed relatively less favorable ΔGbind. The highest binding energy of Comp1 to VP40 protein can be primarily endorsed to the upsurge in van der Waals energy by ΔEvdW - 37.1609 kcal/mol and Coulomb energy by ΔEele - 52.7332 kcal/mol. Also, the hydrogen bond network is robust in Comp1-VP40 complex, with four hydrogen bonds, whilst it is less in other inhibitors. The outcomes from this report may assist in the advancement of novel VP40 inhibitors with high selectivity and potency for EVD therapeutics.
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Affiliation(s)
- Shama Khan
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Zeynab Fakhar
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Aijaz Ahmad
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg, 2193, South Africa.
- Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, 2193, South Africa.
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Kumar A, Patel S, Bhatkar D, Sarode SC, Sharma NK. A novel method to detect intracellular metabolite alterations in MCF-7 cells by doxorubicin induced cell death. Metabolomics 2021; 17:3. [PMID: 33389242 DOI: 10.1007/s11306-020-01755-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Metabolic reprogramming within cancer cells has been recognized as a potential barrier to chemotherapy. Additionally, metabolic tumor heterogeneity is the one of factors behind discernible hallmarks such as drug resistance, relapse of the tumor and the formation of secondary tumors. METHODS In this paper, cell-based assays including PI/annexin V staining and immunoblot assay were performed to show the apoptotic cell death in MCF-7 cells treated with DOX. Further, MCF-7 cells were lysed in a hypotonic buffer and the whole cell lysate was purified by a novel and specifically designed metabolite (~ 100 to 1000 Da) fractionation system called vertical tube gel electrophoresis (VTGE). Further, purified intracellular metabolites were subjected to identification by LC-HRMS technique. RESULTS Cleaved PARP 1 in MCF-7 cells treated with DOX was observed in the present study. Concomitantly, data showed the absence of active caspase 3 in MCF-7 cells. Novel findings are to identify key intracellular metabolites assisted by VTGE system that include lipid (CDP-DG, phytosphingosine, dodecanamide), non-lipid (N-acetyl-D-glucosamine, N1-acetylspermidine and gamma-L-glutamyl-L-cysteine) and tripeptide metabolites in MCF-7 cells treated by DOX. Interestingly, we reported the first evidence of doxorubicinone, an aglycone form of DOX in MCF-7 cells that are potentially linked to the mechanism of cell death in MCF-7 cells. CONCLUSION This paper reported novel methods and processes that involve VTGE system based purification of hypotonically lysed novel intracellular metabolites of MCF-7 cells treated by DOX. Here, these identified intracellular metabolites corroborate to caspase 3 independent and mitochondria induced apoptotic cell death in MCF-7 cells. Finally, these findings validate a proof of concept on the applications of novel VTGE assisted purification and analysis of intracellular metabolites from various cell culture models.
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Affiliation(s)
- Ajay Kumar
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Sheetal Patel
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Devyani Bhatkar
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Sachin C Sarode
- Department of Oral Pathology and Microbiology, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, India
| | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India.
- Cancer and Translational Research Lab, Department of Biotechnology, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y Patil Vidyapeeth Pune, Pune, MH, 411033, India.
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Keshavarz F. Molecular level insights into the direct health impacts of some organic aerosol components. NEW J CHEM 2021. [DOI: 10.1039/d1nj00231g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quantum chemistry and biomodeling indicate that the studied organic aerosol components cannot directly cause oxidative stress or mutagenicity/carcinogenicity.
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Affiliation(s)
- Fatemeh Keshavarz
- Institute for Atmospheric and Earth System Research
- Faculty of Science
- University of Helsinki
- FI-00014 Helsinki
- Finland
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