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  1. Article ; Online: Evaluation of the FDA-approved kinase inhibitors to uncover the potential repurposing candidates targeting ABC transporters in multidrug-resistant cancer cells: an in silico approach.

    Poustforoosh, Alireza / Moosavi, Fatemeh

    Journal of biomolecular structure & dynamics

    2023  , Page(s) 1–13

    Abstract: Multiple drug resistance (MDR) is characterized by the resistance of cancer cells to a broad spectrum of anticancer drugs. The main mechanism underlying the MDR phenotype is the overexpression of ATP-binding cassette (ABC) transporters by promoting ... ...

    Abstract Multiple drug resistance (MDR) is characterized by the resistance of cancer cells to a broad spectrum of anticancer drugs. The main mechanism underlying the MDR phenotype is the overexpression of ATP-binding cassette (ABC) transporters by promoting active drug efflux from cancer cells. Some small-molecule protein kinase inhibitors have been found to overcome MDR by inhibiting ABC transporters as substrates or modulators. This study investigated the chemical activity of 58 FDA-approved anticancer kinase inhibitors against three multidrug resistance-related proteins. The studied proteins are ATP-Binding Cassette Sub-Family B Member 1 (ABCB1), ATP-Binding Cassette Subfamily C Member 1 (ABCC1), and ATP-binding cassette superfamily G member 2 (ABCG2). The drug-binding domain and ATP binding sites of the proteins were considered the kinase inhibitors' probable target. High-throughput virtual screening and molecular docking were employed to find the hit drugs, and the drugs with the highest binding affinity were further evaluated using the molecular dynamics (MD) simulation. The virtual screening revealed that several kinase inhibitors could be considered potential inhibitors of ABCB1, ABCC1, and ABCG2, among which larotrectinib, entrectinib, and infigratinib showed the highest binding affinity, respectively. Based on the obtained results from MD simulation, these drugs can form strong interactions with the essential residues of the target proteins.
    Language English
    Publishing date 2023-11-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2277848
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Correction: Structure-Based Drug Design for Targeting IRE1: An in Silico Approach for Treatment of Cancer.

    Poustforoosh, Alireza / Faramarz, Sanaz / Nematollahi, Mohammad Hadi / Mahmoodi, Mehdi / Azadpour, Mahdiyeh

    Drug research

    2024  Volume 74, Issue 2, Page(s) e1

    Language English
    Publishing date 2024-01-11
    Publishing country Germany
    Document type Journal Article ; Published Erratum
    ZDB-ID 2703847-6
    ISSN 2194-9387 ; 2194-9379
    ISSN (online) 2194-9387
    ISSN 2194-9379
    DOI 10.1055/a-2235-8845
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Modeling and affinity maturation of an anti-CD20 nanobody: a comprehensive in-silico investigation.

    Poustforoosh, Alireza / Faramarz, Sanaz / Negahdaripour, Manica / Hashemipour, Hassan

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 582

    Abstract: B-cell Non-Hodgkin lymphomas are the malignancies of lymphocytes. CD20 is a membrane protein, which is highly expressed on the cell surface of the B-cells in NHL. Treatments using monoclonal antibodies (mAbs) have resulted in failure in some cases. ... ...

    Abstract B-cell Non-Hodgkin lymphomas are the malignancies of lymphocytes. CD20 is a membrane protein, which is highly expressed on the cell surface of the B-cells in NHL. Treatments using monoclonal antibodies (mAbs) have resulted in failure in some cases. Nanobodies (NBs), single-domain antibodies with low molecular weights and a high specificity in antigen recognition, could be practical alternatives for traditional mAbs with superior characteristics. To design an optimized NB as a candidate CD20 inhibitor with raised binding affinity to CD20, the structure of anti-CD20 NB was optimized to selectively target CD20. The 3D structure of the NB was constructed based on the optimal templates (6C5W and 5JQH), and the key residues were determined by applying a molecular docking study. After identifying the key residues, some mutations were introduced using a rational protocol to improve the binding affinity of the NB to CD20. The rational mutations were conducted using the experimental design (Taguchi method). Six residues (Ser27, Thr28, Phe29, Ile31, Asp99, and Asn100) were selected as the key residues, and five residues were targeted for rational mutation (Trp, Phe, His, Asp, and Tyr). Based on the mutations suggested by the experimental design, two optimized NB structures were constructed. NB2 showed a remarkable binding affinity to CD20 in docking studies with a binding energy of - 853 kcal/mol. The optimized NB was further evaluated using molecular dynamics simulation. The results revealed that CDR1 (complementarity determining regions1) and CDR3 are essential loops for recognizing the antigen. NB2 could be considered as a potential inhibitor of CD20, though experimental evaluations are needed to confirm it.
    MeSH term(s) Antibodies, Monoclonal/pharmacology ; Antigens, CD20/immunology ; B-Lymphocytes ; Molecular Docking Simulation ; Single-Domain Antibodies/pharmacology ; Lymphoma, Non-Hodgkin/immunology ; Lymphoma, Non-Hodgkin/pathology
    Chemical Substances Antibodies, Monoclonal ; Antigens, CD20 ; Single-Domain Antibodies
    Language English
    Publishing date 2023-01-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-27926-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Foretinib, a c-MET receptor tyrosine kinase inhibitor, tackles multidrug resistance in cancer cells by inhibiting ABCB1 and ABCG2 transporters.

    Nazari, Somayeh / Mosaffa, Fatemeh / Poustforoosh, Alireza / Mortazavi, Motahareh / Saso, Luciano / Firuzi, Omidreza / Moosavi, Fatemeh

    Toxicology and applied pharmacology

    2024  Volume 484, Page(s) 116866

    Abstract: Background: ABC transporter-mediated multidrug resistance (MDR) remains a major obstacle for cancer pharmacological treatment. Some tyrosine kinase inhibitors (TKIs) have been shown to reverse MDR. The present study was designed to evaluate for the ... ...

    Abstract Background: ABC transporter-mediated multidrug resistance (MDR) remains a major obstacle for cancer pharmacological treatment. Some tyrosine kinase inhibitors (TKIs) have been shown to reverse MDR. The present study was designed to evaluate for the first time whether foretinib, a multitargeted TKI, can circumvent ABCB1 and ABCG2-mediated MDR in treatment-resistant cancer models.
    Methods: Accumulation of fluorescent substrates of ABCB1 and ABCG2 in ABCB1-overexpressing MES-SA/DX5 and ABCG2-overexpressing MCF-7/MX and their parenteral cells was evaluated by flow cytometry. The growth inhibitory activity of single and combination therapy of foretinib and chemotherapeutic drugs on MDR cells was examined by MTT assay. Analysis of combined interaction effects was performed using CalcuSyn software.
    Results: It was firstly proved that foretinib increased the intracellular accumulation of rhodamine 123 and mitoxantrone in MES-SA/DX5 and MCF-7/MX cancer cells, with accumulation ratios of 12 and 2.2 at 25 μM concentration, respectively. However, it did not affect the accumulation of fluorescent substrates in the parental cells. Moreover, foretinib synergistically improved the cytotoxic effects of doxorubicin and mitoxantrone. The means of combination index (CI) values at fraction affected (Fa) values of 0.5, 0.75, and 0.9 were 0.64 ± 0.08 and 0.47 ± 0.09, in MES-SA/DX5 and MCF-7/MX cancer cells, respectively. In silico analysis also suggested that the drug-binding domain of ABCB1 and ABCG2 transporters could be considered as potential target for foretinib.
    Conclusion: Overall, our results suggest that foretinib can target MDR-linked ABCB1 and ABCG2 transporters in clinical cancer therapy.
    MeSH term(s) Humans ; Proto-Oncogene Proteins c-met/pharmacology ; Mitoxantrone/pharmacology ; ATP Binding Cassette Transporter, Subfamily G, Member 2 ; Drug Resistance, Neoplasm ; Drug Resistance, Multiple ; Antineoplastic Agents/therapeutic use ; Neoplasms/drug therapy ; Cell Line, Tumor ; Neoplasm Proteins ; ATP Binding Cassette Transporter, Subfamily B ; Anilides ; Quinolines
    Chemical Substances GSK 1363089 ; Proto-Oncogene Proteins c-met (EC 2.7.10.1) ; Mitoxantrone (BZ114NVM5P) ; ATP Binding Cassette Transporter, Subfamily G, Member 2 ; Antineoplastic Agents ; ABCG2 protein, human ; Neoplasm Proteins ; ABCB1 protein, human ; ATP Binding Cassette Transporter, Subfamily B ; Anilides ; Quinolines
    Language English
    Publishing date 2024-02-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 204477-8
    ISSN 1096-0333 ; 0041-008X
    ISSN (online) 1096-0333
    ISSN 0041-008X
    DOI 10.1016/j.taap.2024.116866
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Tracing the pathways and mechanisms involved in the anti-breast cancer activity of glycyrrhizin using bioinformatics tools and computational methods.

    Poustforoosh, Alireza / Faramarz, Sanaz / Negahdaripour, Manica / Tüzün, Burak / Hashemipour, Hassan

    Journal of biomolecular structure & dynamics

    2023  Volume 42, Issue 2, Page(s) 819–833

    Abstract: A complete investigation to understand the pathways that could be affected by glycyrrhizin (licorice), as anti-breast cancer (BC) agent, has not been performed to date. This study aims to investigate the pathways involved in the anti-cancer activity of ... ...

    Abstract A complete investigation to understand the pathways that could be affected by glycyrrhizin (licorice), as anti-breast cancer (BC) agent, has not been performed to date. This study aims to investigate the pathways involved in the anti-cancer activity of glycyrrhizin against BC. For this purpose, the target genes of glycyrrhizin were obtained from the ChEMBL database. The BC-associated genes for three types of BC (breast carcinoma, malignant neoplasm of breast, and triple-negative breast neoplasms) were retrieved from DisGeNET. The target genes of glycyrrhizin and the BC-associated genes were compared, and the genes with disease specificity index (DSI) > 0.6 were selected for further evaluation using
    MeSH term(s) Humans ; Female ; Glycyrrhizic Acid/pharmacology ; Gene Expression Profiling/methods ; Molecular Docking Simulation ; Gene Expression Regulation, Neoplastic ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Triple Negative Breast Neoplasms/genetics ; Computational Biology/methods
    Chemical Substances Glycyrrhizic Acid (6FO62043WK)
    Language English
    Publishing date 2023-04-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2196347
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Investigation on the mechanisms by which the herbal remedies induce anti-prostate cancer activity: uncovering the most practical natural compound.

    Poustforoosh, Alireza / Faramarz, Sanaz / Negahdaripour, Manica / Tüzün, Burak / Hashemipour, Hassan

    Journal of biomolecular structure & dynamics

    2023  Volume 42, Issue 7, Page(s) 3349–3362

    Abstract: Prostate cancer (PCa) is one of the most reported cancers among men worldwide. Targeting the essential proteins associated with PCa could be a promising method for cancer treatment. Traditional and herbal remedies (HRs) are the most practical approaches ... ...

    Abstract Prostate cancer (PCa) is one of the most reported cancers among men worldwide. Targeting the essential proteins associated with PCa could be a promising method for cancer treatment. Traditional and herbal remedies (HRs) are the most practical approaches for PCa treatment. Here, the proteins and enzymes associated with PCa were determined based on the information obtained from the DisGeNET database. The proteins with a gene-disease association (GDA) score greater than 0.7 and the genes that have a disease specificity index (DSI) = 1 were selected as the target proteins. 28 HRs with anti-PCa activity as a traditional treatment for PCa were chosen as potential bioactive compounds. More than 500 compound-protein complexes were screened to find the top-ranked bioactives. The results were further evaluated using the molecular dynamics (MD) simulation and binding free energy calculations. The outcomes revealed that procyanidin B2 3,3'-di-O-gallate (B2G2), the most active ingredient of grape seed extract (GSE), can act as an agonist for PTEN. PTEN has a key role in suppressing PCa cells by applying phosphatase activity and inhibiting cell proliferation. B2G2 exhibited a considerable binding affinity to PTEN (11.643 kcal/mol). The MD results indicated that B2G2 could stabilize the key residues of the phosphatase domain of PTEN and increase its activity. Based on the obtained results, the active ingredient of GSE, B2G2, could play an agonist role and effectively increase the phosphatase activity of PTEN. The grape seed extract is a useful nutrition that can be used in men's diets to inhibit PCa in their bodies.Communicated by Ramaswamy H. Sarma.
    MeSH term(s) Male ; Humans ; Grape Seed Extract ; Apoptosis ; Prostatic Neoplasms/drug therapy ; Prostatic Neoplasms/genetics ; Cell Proliferation ; Phosphoric Monoester Hydrolases
    Chemical Substances Grape Seed Extract ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
    Language English
    Publishing date 2023-05-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2213344
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: [No title information]

    Poustforoosh, Alireza / Faramarz, Sanaz / Nematollahi, Mohammad Hadi / Mahmoodi, Mehdi / Azadpour, Mahdiyeh

    Drug Research

    2024  Volume 74, Issue 02, Page(s) e1–e1

    Language English
    Publishing date 2024-01-11
    Publisher Georg Thieme Verlag
    Publishing place Stuttgart ; New York
    Document type Article
    ZDB-ID 2703847-6
    ISSN 2194-9387 ; 2194-9379
    ISSN (online) 2194-9387
    ISSN 2194-9379
    DOI 10.1055/a-2235-8845
    Database Thieme publisher's database

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  8. Article: Comparison of Protective Effects of Phenolic Acids on Protein Glycation of BSA Supported by In Vitro and Docking Studies.

    Rashedinia, Marzieh / Rasti Arbabi, Zeinab / Sabet, Razieh / Emami, Leila / Poustforoosh, Alireza / Sabahi, Zahra

    Biochemistry research international

    2023  Volume 2023, Page(s) 9984618

    Abstract: Several diabetic complications are associated with forming advanced glycation end products (AGEs). Different chemical and natural compounds are able to prevent the development of these products. In this study, glycosylation was induced as a model by ... ...

    Abstract Several diabetic complications are associated with forming advanced glycation end products (AGEs). Different chemical and natural compounds are able to prevent the development of these products. In this study, glycosylation was induced as a model by incubating bovine serum albumin (BSA) with glucose. Consequently, BSA was treated with glucose and different concentrations (1.25, 2.5, and 5
    Language English
    Publishing date 2023-07-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2566725-7
    ISSN 2090-2255 ; 2090-2247
    ISSN (online) 2090-2255
    ISSN 2090-2247
    DOI 10.1155/2023/9984618
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Antioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish

    Taysi, Mehmet Reşit / Kirici, Muammer / Kirici, Mahinur / Tuzun, Burak / Poustforoosh, Alireza

    Journal of biomolecular structure & dynamics

    2023  Volume 42, Issue 1, Page(s) 163–176

    Abstract: Chlorpyrifos (CPF), which was started to be used in 1965, is a broad spectrum organophosphate insecticide that is used more and more day by day. Commonly used to control pests in farmland and homes, CPF is more toxic to fish than organochlorine compounds. ...

    Abstract Chlorpyrifos (CPF), which was started to be used in 1965, is a broad spectrum organophosphate insecticide that is used more and more day by day. Commonly used to control pests in farmland and homes, CPF is more toxic to fish than organochlorine compounds. CPF poses a serious threat to the health of humans and aquatic organisms. This paper studies the relationship between CPF exposure and antioxidant enzyme activities in gill, kidney and liver tissues of
    MeSH term(s) Humans ; Animals ; Cattle ; Chlorpyrifos ; Antioxidants ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Oxidative Stress ; Insecticides ; Cyprinidae/metabolism ; Fresh Water
    Chemical Substances Chlorpyrifos (JCS58I644W) ; Antioxidants ; Insecticides
    Language English
    Publishing date 2023-03-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2192807
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Structure-Based Drug Design for Targeting IRE1: An in Silico Approach for Treatment of Cancer.

    Poustforoosh, Alireza / Faramarz, Sanaz / Nematollahi, Mohammad Hadi / Mahmoodi, Mehdi / Azadpour, Mahdiyeh

    Drug research

    2023  Volume 74, Issue 2, Page(s) 81–88

    Abstract: Background: Endoplasmic Reticulum (ER) stress and Unfolded Protein Response (UPR) play a key role in cancer progression. The aggregation of incorrectly folded proteins in the ER generates ER stress, which in turn activates the UPR as an adaptive ... ...

    Abstract Background: Endoplasmic Reticulum (ER) stress and Unfolded Protein Response (UPR) play a key role in cancer progression. The aggregation of incorrectly folded proteins in the ER generates ER stress, which in turn activates the UPR as an adaptive mechanism to fix ER proteostasis. Inositol-requiring enzyme 1 (IRE1) is the most evolutionary conserved ER stress sensor, which plays a pro-tumoral role in various cancers. Targeting its' active sites is one of the most practical approaches for the treatment of cancers.
    Objective: In this study, we aimed to use the structure of 4μ8C as a template to produce newly designed compounds as IRE1 inhibitors.
    Methods: Various functional groups were added to the 4μ8C, and their binding affinity to the target sites was assessed by conducting a covalent molecular docking study. The potential of the designed compound for further in vitro and in vivo studies was evaluated using ADMET analysis.
    Results: Based on the obtained results, the addition of hydroxyl groups to 4μ8C enhanced the binding affinity of the designed compound to the target efficiently. Compound 17, which was constructed by the addition of one hydroxyl group to the structure of 4μ8C, can construct a strong covalent bond with Lys907. The outcomes of ADMET analysis indicated that compound 17 could be considered a drug-like molecule.
    Conclusion: Our results revealed that designed compound 17 could inhibit IRE1 activity. Therefore, this designed compound is a remarkable inhibitor of IRE1 and introduces a promising therapeutic strategy for cancer treatment.
    MeSH term(s) Molecular Docking Simulation ; Protein Serine-Threonine Kinases/chemistry ; Protein Serine-Threonine Kinases/genetics ; Protein Serine-Threonine Kinases/metabolism ; Endoplasmic Reticulum Stress ; Unfolded Protein Response ; Neoplasms/drug therapy ; Iohexol/analogs & derivatives
    Chemical Substances compound 17 (31122-84-6) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Iohexol (4419T9MX03)
    Language English
    Publishing date 2023-12-22
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2703847-6
    ISSN 2194-9387 ; 2194-9379
    ISSN (online) 2194-9387
    ISSN 2194-9379
    DOI 10.1055/a-2211-2218
    Database MEDical Literature Analysis and Retrieval System OnLINE

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