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Kalhor H, Sadeghi S, Abolhasani H, Kalhor R, Rahimi H. Repurposing of the approved small molecule drugs in order to inhibit SARS-CoV-2 S protein and human ACE2 interaction through virtual screening approaches. J Biomol Struct Dyn 2022; 40:1299-1315. [PMID: 32969333 PMCID: PMC7576931 DOI: 10.1080/07391102.2020.1824816] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/12/2020] [Indexed: 12/19/2022]
Abstract
Most recently, the new coronavirus (SARS-CoV-2) has been recognized as a pandemic by the World Health Organization (WHO) while this virus shares substantial similarity with SARS-CoV. So far, no definitive vaccine or drug has been developed to cure Covid-19 disease, since many important aspects about Covid-19 such as pathogenesis and proliferation pathways are still unclear. It was proven that human ACE2 is the main receptor for the entry of Covid-19 into lower respiratory tract epithelial cells through interaction with SARS-CoV-2 S protein. Based on this observation, it is expected that the virus infection can be inhibited if protein-protein interaction is prevented. In this study, using structure-based virtual screening of FDA databases, several lead drugs were discovered based on the ACE2-binding pocket of SARS-CoV-2 S protein. Then, binding affinity, binding modes, critical interactions, and pharmaceutical properties of the lead drugs were evaluated. Among the previously approved drugs, Diammonium Glycyrrhizinate, Digitoxin, Ivermectin, Rapamycin, Rifaximin, and Amphotericin B represented the most desirable features, and can be possible candidates for Covid-19 therapies. Furthermore, molecular dynamics (MD) simulation was accomplished for three S protein/drug complexes with the highest binding affinity and best conformation and binding free energies were also computed with the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Results demonstrated the stable binding of these compounds to the S protein; however, in order to confirm the curative effect of these drugs, clinical trials must be done.
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Affiliation(s)
- Hourieh Kalhor
- Cellular and Molecular Research Center, Qom
University of Medical Sciences, Qom,
Iran
- Molecular Medicine Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran,
Iran
| | - Solmaz Sadeghi
- Department of Medical Biotechnology, School of
Advanced Technologies in Medicine, Tehran University of Medical Sciences,
Tehran, Iran
| | - Hoda Abolhasani
- Cellular and Molecular Research Center, Qom
University of Medical Sciences, Qom,
Iran
- Spiritual Health Research Center, Qom
University of Medical Sciences, Qom,
Iran
- Department of Pharmacology, School of
Medicine, Qom University of Medical Sciences, Qom,
Iran
| | - Reyhaneh Kalhor
- Cellular and Molecular Research Center, Qom
University of Medical Sciences, Qom,
Iran
- Department of Genetics, Colleague of Sciences,
Kazerun branch, Islamic Azad University, Kazerun,
Iran
| | - Hamzeh Rahimi
- Molecular Medicine Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran,
Iran
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Abstract
SummaryFungizone, the deoxycholate complex of Amphotericin B, is widely used in tissue culture media as a precaution against contamination. However, a number of reports indicate that the polyenes are toxic to certain mammalian cell lines at relatively low concentrations and can potentiate the effects of other chemicals. The effects of Fungizone on the growth of cultured V79 Chinese hamster lung fibroblasts were determined: growth was inhibited at concentrations above 10μg/ml (ID50 = 13μg/ml), but Fungizone did not affect cell growth when present at the concentration recommended for use in tissue culture media (2μg/ml). This concentration of Fungizone was found to significantly increase the growth inhibitory effects of four toxicants with different modes of action; however, this effect is not considered sufficient to invalidate the inclusion of Fungizone in media used in cytotoxicity tests on cultured V79 cells.
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Affiliation(s)
- Steven A. Horner
- Department of Human Morphology, University of Nottingham. Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Minesh K. Shah
- Department of Human Morphology, University of Nottingham. Queen's Medical Centre, Nottingham NG7 2UH, UK
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St Georgiev V. Opportunistic/nosocomial infections. Treatment and developmental therapeutics. I. Cryptococcosis. Med Res Rev 1993; 13:493-506. [PMID: 8361256 DOI: 10.1002/med.2610130405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- V St Georgiev
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
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Malewicz B, Momsen M, Jenkin HM. Combined effect of acyclovir and amphotericin B on the replication of pseudorabies virus in BHK-21 cells. Antimicrob Agents Chemother 1983; 23:119-24. [PMID: 6299180 PMCID: PMC184628 DOI: 10.1128/aac.23.1.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Acyclovir, known as an antiherpetic agent, showed an inhibitory effect on the propagation of pseudorabies virus in BHK-21 cells. The antiviral effect of acyclovir was observed by plaque reduction, as well as by the inhibition of the virus-stimulated uptake of thymidine by BHK-21 cells. Amphotericin B potentiated the antiviral activity of acyclovir. The optimal concentrations of polyene antibiotic expressing the potentiating effect were lower than required for the induction of K+ leakage from the cells. There was no evident amphotericin B-induced stimulation of thymidine incorporation into infected BHK-21 cells. The model presented may be useful to study the potentiation phenomenon of polyene macrolide antibiotics.
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Abstract
The antitumor action of bovine seminal RNAase is studied as a function of the enzyme concentration and of the number of plated cells. With polyoma transformed hamster kidney cells, a 50% inhibition of cell growth is obtained with a 10 micrograms/ml of enzyme, while at this concentration growth of normal cells is very little affected. On the other hand the higher the number of plated cells, the lesser is the effect. The enzyme is found to be very effective also on tumor cells derived from a spontaneous tumor (neuroblastoma) and on cells derived from a chemically induced tumor (glioma). Amphoterycin B which is known to alter the permeability of eukariotic cells, does not affect the resistance of normal cells to the cytotoxic action of the enzyme.
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Fujimoto WY, Starman BJ, Rowe DW. The effect of amphotericin B-deoxycholate on proliferation and protein synthesis in human skin fibroblast cultures. IN VITRO 1978; 14:1003-9. [PMID: 738737 DOI: 10.1007/bf02616214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cultures of adult human skin fibroblasts were grown in the presence of the recommended antifungal dose (3 microgram per ml) of amphotericin B-deoxycholate. A reduction in cell culture growth, measured as DNA content and protein content per culture, was observed. However, radioisotope incorporation into noncollagen protein and, to a lesser extent, collagen protein was enhanced. These effects were due to amphotericin B, not to deoxycholate. These observations were made under several growth conditions and indicate that cell proliferation or isotope-labeling studies in fibroblasts in the presence of amphotericin B-deoxycholate are susceptible to errors in interpretation.
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Fisher PB, Bryson V, Schaffner CP. Polyene macrolide antibiotic cytotoxicity and membrane permeability alterations. I. Comparative effects of four classes of polyene macrolides on mammalian cells. J Cell Physiol 1978; 97:345-51. [PMID: 310437 DOI: 10.1002/jcp.1040970309] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The relationship between polyene macrolide-induced early membrane damage and cytotoxicity in B1 (hamster), B82 (mouse), and RAG (mouse) cells has been investigated. Filipin (FIL) induced the greatest immediate damage, as monitored by 51Cr release, followed by mediocidin (MED), amphotericin B-deoxycholate (Fungizone) (FZ) and pimaricin (PIM). For long term effect, PIM was the least toxic followed by MED, FZ, and FIL as indicated by 24-hour survival, 72-hour viability, and growth rate of cells. In evaluating polyene macrolide-induced permeability alterations and cytotoxicity two types of interactions with mammalian cells were found: (1) cell toxicity at polyene macrolide levels not eliciting immediate membrane permeability changes; and (2) immediate membrane damage without long range toxicity.
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Goldstein NI, Fisher PB. Selection of mouse X hamster hybrids using HAT medium and a polyene antibiotic. IN VITRO 1978; 14:200-6. [PMID: 352913 DOI: 10.1007/bf02618223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the present study we tested the feasibility of utilizing a structurally modified polyene antibiotic, amphotericin B methyl ester (AME), as a half-selection agent for isolating somatic cell hybrids. By using HAT medium supplemented with AME we have isolated interspecific mouse-hamster hybrids from mixed cultures of mouse (TK-C1 ID or HPRT-A9) and hamster (BHK/C 13) cells fused with Sendai virus, lysolecithin or polyethylene glycol. Hybrid cells proliferated and clones were isolated after 2 to 3 weeks growth in three changes of HAT-AME medium and subsequent growth in HAT medium alone. In contrast, genetically deficient parental C1 1D or A9 cells and AME-sensitive BHK/C 13 cells were killed using a similar growth protocol. The described technique is simple, efficient and permits one to use a cell line without a genetic defect in combination with a genetically deficient cell type in hybrid formation.
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Badaracco G, Cassani G. Ribonucleic acid synthesis dependent on exogenous triphosphates in nystatin-treated cells of of Kluyveromyces latis. Antimicrob Agents Chemother 1976; 9:748-53. [PMID: 949173 PMCID: PMC429615 DOI: 10.1128/aac.9.5.748] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Kluyveromyces lactis cells treated with nystatin became permeable to ribonucleoside triphosphates. Although not viable, nystatin-treated cells were capable of sustaining ribonucleic acid synthesis. The system depended on the presence of divalent ions and the four nucleoside triphosphates, and was strongly stimulated by ammonium sulfate. The system utilized endogenous deoxyribonucleic acid as template. Synthesis of ribonucleic acid was associated with the cells and probably occurred internally.
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Fisher PB, Goldstein NI, Bryson V, Schaffner CP. Reduced toxicity of amphotericin B methyl ester (AME) vs. amphotericin B and fungizone in tissue culture. IN VITRO 1976; 12:133-40. [PMID: 1248851 DOI: 10.1007/bf02796361] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The comparative toxicities of amphotericin B methyl ester (AME), the parent antibiotic amphotericin B (AB), and the deoxycholate solubilized complex of AB, Fungizone (FZ), toward five cell lines has been determined as measured by early membrane damage (51Cr release), 24 hr survival, 72 hr viability, and growth rate. Cells used were of turtle (TH-1), marsupial (PT K2), human MA 160), rabbit (RK-13) and hamster (BHK-21) origin. AME: (a) caused less membrane damage at 1 hr than AB or FZ; (b) was less toxic than AB or FZ as indicated by 24 hr cell survival and 72 hr cell viability; and (c) was required in higher levels than AB or FZ to reduce the growth rate of all five cell lines. Spectrophotometric analysis of residual polyene levels indicated that AME had good stability in tissue culture medium. Previous studies have indicated that AME has the same in vitro antifungal activity as the parent antibiotic AB (1, 2). These findings suggest that AME may prove to be superior to AB and FZ for use as an antifungal agent in tissue culture systems.
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Amati P, Blasi F, Di Porzio U, Riccio A, Traboni C. Hamster alpha-amanitine-resistant RNA polymerase II able to transcribe polyoma virus genome in somatic cell hybrids. Proc Natl Acad Sci U S A 1975; 72:753-7. [PMID: 164668 PMCID: PMC432395 DOI: 10.1073/pnas.72.2.753] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A hamster cell line resistant to alpha-amanitine has been isolated (alpha-am-r, BHK-T6-G-1). Cell extracts of this mutant have an alpha-amanitine-resistant RNA polymerase II (nucleosidetriphosphate: RNA nucleotidyl-transferase, EC 2.7.7.6) activity as shown by DEAE-cellulose column chromatography. This mutation is dominant in interspecific hybrids with 3T3 mouse cells. In such hybrids polyoma virus can grow with equal efficiency in the presence or absence of the drug, thus indicating that the RNA polymerase of the unsusceptible parental cell can participate in the correct transcription of the viral genome.
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Okunewick JP, Brozovich BJ, Kuhnert PM. Effect of ethidium bromide and fractionated x-irradiation on Rauscher leukemia development. Int J Cancer 1974; 14:617-24. [PMID: 4459278 DOI: 10.1002/ijc.2910140508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Dolberg D, Bissell MJ. Side effects of amphotericin B-deoxycholate (fungizone) and nystatin in chick cells in culture. IN VITRO 1974; 10:26-9. [PMID: 4471176 DOI: 10.1007/bf02615335] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Smith HS, Hackett AJ. The specificity of dimethylbenzylrifampicin as an inhibitor of viral induced transformation. Proc Natl Acad Sci U S A 1974; 71:2770-2. [PMID: 4369359 PMCID: PMC388552 DOI: 10.1073/pnas.71.7.2770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The effect of 2',6'-dimethyl-N(4')-benzyl-N(4')- [desmethyl]rifampicin on viral transformation induced by two unrelated oncogenic viruses was compared. Transformation of Balb/3T3 cells by the small, DNA-containing papova virus simian virus 40 was completely normal under conditions where transformation by the large, RNA-containing oncornavirus murine sarcoma virus was inhibited more than 150-fold. For these experiments a resistant variant of Balb/3T3 was selected that grows well in high concentrations of the drug, is not dependent on the drug for growth, and is probably not blocked at the level of drug uptake. These data show that dimethyl-benzylrifampicin specifically inhibits oncornavirus-induced transformation rather than nonspecifically inhibiting cellular growth or transformation.
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Bissell MJ, Hatie C, Tischler AN, Calvin M. Preferential inhibition of the growth of virus-transformed cells in culture by rifazone-82, a new rifamycin derivative. Proc Natl Acad Sci U S A 1974; 71:2520-4. [PMID: 4366963 PMCID: PMC388491 DOI: 10.1073/pnas.71.6.2520] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rifazone-8(2), a new rifamycin derivative, is shown to preferentially inhibit the growth of virus-transformed chick cells in culture. Macromolecular synthesis and glucose uptake of transformed cells are also appreciably decreased in the presence of low concentrations of rifazone-8(2) where the normal cells appear unaffected. While rifazone-8(2) is shown to be a selective inhibitor of RNA-directed DNA polymerase in vitro, its action on the growth of transformed cells may involve some other mechanism.
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RNA-Directed DNA Polymerase—Properties and Functions in Oncogenic RNA Viruses and Cells1. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s0079-6603(08)60208-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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