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Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
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Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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Abiri A, Bitner BF, Nguyen TV, Pang JC, Roman KM, Vasudev M, Chung DD, Tripathi SH, Harris JC, Kosaraju N, Shih RM, Ko M, Miller JE, Douglas JE, Lee DJ, Eide JG, Kshirsagar RS, Phillips KM, Sedaghat AR, Bergsneider M, Wang MB, Palmer JN, Adappa ND, Hsu FPK, Kuan EC. Clinical and technical factors in endoscopic skull base surgery associated with reconstructive success. Rhinology 2024; 0:3148. [PMID: 38189480 DOI: 10.4193/rhin23.267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
BACKGROUND In this study, we identified key discrete clinical and technical factors that may correlate with primary reconstructive success in endoscopic skull base surgery (ESBS). METHODS ESBS cases with intraoperative cerebrospinal fluid (CSF) leaks at four tertiary academic rhinology programs were retrospectively reviewed. Logistic regression identified factors associated with surgical outcomes by defect subsite (anterior cranial fossa [ACF], suprasellar [SS], purely sellar, posterior cranial fossa [PCF]). RESULTS Of 706 patients (50.4% female), 61.9% had pituitary adenomas, 73.4% had sellar or SS defects, and 20.5% had high-flow intraoperative CSF leaks. The postoperative CSF leak rate was 7.8%. Larger defect size predicted ACF postoperative leaks; use of rigid reconstruction and older age protected against sellar postoperative leaks; and use of dural sealants compared to fibrin glue protected against PCF postoperative leaks. SS postoperative leaks occurred less frequently with the use of dural onlay. Body-mass index, intraoperative CSF leak flow rate, and the use of lumbar drain were not significantly associated with postoperative CSF leak. Meningitis was associated with larger tumors in ACF defects, nondissolvable nasal packing in SS defects, and high-flow intraoperative leaks in PCF defects. Sinus infections were more common in sellar defects with synthetic grafts and nondissolvable nasal packing. CONCLUSIONS Depending on defect subsite, reconstructive success following ESBS may be influenced by factors, such as age, defect size, and the use of rigid reconstruction, dural onlay, and tissue sealants.
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Affiliation(s)
- A Abiri
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - B F Bitner
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - T V Nguyen
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - J C Pang
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - K M Roman
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - M Vasudev
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - D D Chung
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - S H Tripathi
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - J C Harris
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N Kosaraju
- Department of Head and Neck Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R M Shih
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Ko
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - J E Miller
- Department of Head and Neck Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - J E Douglas
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - D J Lee
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - J G Eide
- Department of Otolaryngology-Head and Neck Surgery, Henry Ford Health System, Detroit, MI, USA
| | - R S Kshirsagar
- Department of Head and Neck Surgery, Kaiser Permanente Redwood City Medical Center, Redwood City, CA, USA
| | - K M Phillips
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - A R Sedaghat
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - M Bergsneider
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M B Wang
- Department of Head and Neck Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - J N Palmer
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N D Adappa
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - F P K Hsu
- Department of Neurological Surgery, University of California, Irvine, Orange, CA, USA
| | - E C Kuan
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
- Department of Neurological Surgery, University of California, Irvine, Orange, CA, USA
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Mohammadi E, Behnam B, Mokhtarzadeh A, Rezaee R, Abiri A, Ramezani M, Giesy JP, Sahebkar A. Reproductive Toxicity of Nanoparticles: A Comprehensive Review. Curr Med Chem 2023; 31:CMC-EPUB-133573. [PMID: 37581521 DOI: 10.2174/0929867331666230815101141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/17/2023] [Accepted: 06/23/2023] [Indexed: 08/16/2023]
Abstract
The unique characteristics of nanoparticles (NPs) have captivated scientists in various fields of research. However, their safety profile has not been fully scrutinized. In this regard, the effects of NPs on the reproductive system of animals and humankind have been a matter of concern. In this article, we will review the potential reproductive toxicity of various types of NPs, including carbon nanomaterials, dendrimers, quantum dots, silica, gold, and magnetic nanoparticles, reported in the literature. We also mention some notable cases where NPs have elicited beneficial effects on the reproductive system. This review provides extensive insight into the effects of various NPs on sperm and ovum and the outcomes of their passage through blood-testis and placental barriers and accumulation in the reproductive organs.
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Affiliation(s)
- Elaheh Mohammadi
- Students Research Committee, Faculty of pharmacy, Kerman University of Medical Sciences, Kerman, Iran
- Toxicology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Behzad Behnam
- Students Research Committee, Faculty of pharmacy, Kerman University of Medical Sciences, Kerman, Iran
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
- Herbal and Traditional Medicines Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Extremophile and Productive Microorganisms Research Center, Kerman University of Medical Science, Kerman, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Rezaee
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - John P Giesy
- Toxicology Centre, and Dept. Veterinary Biomedical Sciences, University of Saskatchewan, 10 Campus Drive, Saskatoon, SK S7N 5B4, Canada
- Dept. Environmental Sciences, Baylor University, Waco, TX, USA
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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Mirzaei M, Sharifi I, Mohammad-Rafi F, Anjomshoa M, Abiri A, Moqaddari AH, Nooshadokht M, Raiesi O, Amirheidari B. Antileishmanial effects and drugability characteristics of a heterocyclic copper complex: An in silico, in vitro and molecular study. J Inorg Biochem 2023; 245:112245. [PMID: 37167732 DOI: 10.1016/j.jinorgbio.2023.112245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
Leishmaniasis caused by the protozoan Leishmania presents a severe illness, principally in tropical and subtropical areas. Antileishmanial metal complexes, like Glucantime®️ with proven activity, are routinely studied to probe their potency. We investigated the effects of a Cu (II) homoleptic complex coordinated by two dimethyl-bipyridine ligands against Leishmania major stages in silico and in vitro. The affinity of this heterocyclic Cu (II) complex (CuDMBP) towards a parasitic metacaspase was studied by molecular docking. Key pharmacokinetic and pharmacodynamic properties of the complex were predicted using three web-based tools. CuDMBP was tested for in vitro antileishmanial activities using MTT assay, model murine macrophages, flow cytometry, and quantitative real-time polymerase chain reaction (qPCR). Molecular docking confirmed the tendency between the target macromolecule and the complex. ADMET evaluations highlighted CuDMBP's key pharmacological features, including P-glycoprotein-associated GI absorption and lack of trans-BBB permeability. MTT showed significant inhibitory effects against promastigotes. CuDMBP significantly increased the level of cellular IL-12 expression (p < 0.05), while the upregulation observed in the expression of iNOS was considered not significant (p > 0.05). It decreased the expression of IL-10 significantly (p < 0.05). Findings demonstrated that CuDMBP deserves to be introduced as a leishmanicidal candidate provided further studies are carried out.
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Affiliation(s)
- Mohammad Mirzaei
- Pathobiology Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Iraj Sharifi
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Farrokh Mohammad-Rafi
- Pathobiology Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Marzieh Anjomshoa
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Amir Hossain Moqaddari
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Evin, Tehran, Iran
| | - Maryam Nooshadokht
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran; Extremophile and Productive Microorganisms Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| | - Omid Raiesi
- Department of Parasitology, School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran; Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Bagher Amirheidari
- Extremophile and Productive Microorganisms Research Center, Kerman University of Medical Sciences, Kerman, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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Michelle L, Du AT, Abiri A, Kuan EC. Clinical manifestations, management, and outcomes of primary silent sinus syndrome: a systematic review. Rhinology 2023:3080. [PMID: 37219052 DOI: 10.4193/rhin23.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
INTRODUCTION Silent sinus syndrome (SSS) is a rare disorder of the maxillary sinus, which may present with orbital symptoms. Most reports of silent sinus syndrome are limited to small series or case reports. This systematic review comprehensively characterizes the various clinical presentations, management, treatment, and outcomes in patients with SSS. METHODS A systematic literature search of the PubMed, Cochrane, Web of Science, and Scopus databases. Inclusion criteria were studies describing the presentation, management, or treatment of SSS or chronic maxillary atelectasis. RESULTS One hundred fifty-three articles were included in the final review (n=558 patients). Mean age at diagnosis was 38.8 ± 14.1 years, with a relatively even distribution among sexes. Enophthalmos and/or hypoglobus were the most frequent symptoms, along with diplopia, headache, or facial pressure/pain. Most patients (87%) underwent functional endoscopic sinus surgery (FESS), and 23.5% received orbital floor reconstruction. Post-treatment, patients had significant reductions in enophthalmos (2.67 ± 1.39 vs. 0.33 ± 0.75 mm) and hypoglobus (2.22 ± 1.43 vs. 0.23 ± 0.62 mm). Most patients (83.2%) achieved partial or total resolution of clinical symptoms. CONCLUSIONS SSS has a variable clinical presentation, with enophthalmos and hypoglobus being most common. FESS with or without orbital reconstruction are effective treatments to address the underlying pathology and structural deficits.
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Affiliation(s)
- L Michelle
- Department of Otolaryngology - Head and Neck Surgery, University of California Irvine Medical Center, Orange, CA, USA
| | - A T Du
- Department of Otolaryngology - Head and Neck Surgery, University of California Irvine Medical Center, Orange, CA, USA
| | - A Abiri
- Department of Otolaryngology - Head and Neck Surgery, University of California Irvine Medical Center, Orange, CA, USA
| | - E C Kuan
- Department of Otolaryngology - Head and Neck Surgery, University of California Irvine Medical Center, Orange, CA, USA
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Sharififar F, Sharifi F, Mohamadi N, Abiri A, Sharifi I, Harandi MF. Nature-derived alkaloids as a promising bioactive compound in drug discovery to meet global Leishmania needs. LETT DRUG DES DISCOV 2023. [DOI: 10.2174/1570180820666230220141636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Background:
Natural products have been important resources for potential drug development. Among the many classes of natural products, alkaloids have the most therapeutic applications. Treatment of leishmaniasis by chemical drugs remains a challenge because of toxic side effects, limited efficacy, and drug resistance. This review focuses to embrace all researches on leishmanicidal alkaloids over a specific range of time, with special consideration the molecular mechanism of action, and structure-related activity.
Methods:
All publications (in English) from Web of Science, PubMed, Science Direct, Scopus, and Google Scholar from 2000-2021 using a variety of keywords such as natural alkaloids, herbal alkaloids, marine alkaloids along with leishmaniasis were included in the present study. In this summary, the focus is mainly on natural alkaloids of plant, mineral, marine origin, etc., which have empirically demonstrated the antileishmanial effect.
Results:
Fourteen categories of alkaloids with anti-leishmaniasis activity were extracted from the articles. The highest number of alkaloids belonged to isoquinoline, indole, and quinoline alkaloids (21.78%, 20.67%, and 16.48% respectively). This review indicated that the mentioned alkaloids are able to inhibit the proliferation of parasites, the respiratory chain and protein synthesis, arrest the cell cycle, disrupt the mitochondrial membrane integrity, inhibit leishmanial topoisomerase, induce mitochondrial dysfunction, and changes in the parasite morphology.
Discussion:
The present study highlighted antileishmanial alkaloids that are active against different species of Leishmania in vitro and some of them are also active in visceral and cutaneous leishmaniasis models. However, more clinical studies are needed to clarify the anti-leishmanial activity of alkaloids against leishmania in detail.
Conclusion:
Among the reported compounds, two main classes of alkaloids including isoquinoline and indole alkaloids cover a wider range of anti-parasitic compounds, and structure-activity relationships (SAR) studies of these molecular skeletons may be good lead compounds and afford the structural clues to develop novel medicines with more selective therapeutic profiles.
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Affiliation(s)
- Fariba Sharififar
- Herbal and Traditional Medicines Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Sharifi
- Research Center of Tropical and Infectious Diseases Kerman University of Medical Sciences, Kerman, Iran
| | - Neda Mohamadi
- Herbal and Traditional Medicines Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Iraj Sharifi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman,
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Birkenbeuel JL, Abiri A, Nguyen T, Bitner BF, Abello EF, Vasudev M, Hsu FPK, Kuoy E, Kuan EC. Evolution of Radiographic Changes of a Vascularized Pedicled Nasoseptal Flap after Endonasal Endoscopic Skull Base Surgery. AJNR Am J Neuroradiol 2023; 44:171-175. [PMID: 36657948 PMCID: PMC9891332 DOI: 10.3174/ajnr.a7768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 12/06/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND PURPOSE There is active research involving the radiographic appearance of the skull base following reconstruction. The purpose of this study was to describe the radiographic appearance of the vascularized pedicle nasoseptal flap after endoscopic skull base surgery across time. MATERIALS AND METHODS We performed chart and imaging review of all patients with intraoperative nasoseptal flap placement during endoscopic skull base surgery at a tertiary academic skull base surgery program between July 2018 and March 2021. All patients underwent immediate and delayed (>3 months) postoperative MR imaging. Primary outcome variables included flap and pedicle enhancement, flap thickness, and flap adherence to the skull base. RESULTS Sixty-eight patients were included. Flap (P = .003) enhancement significantly increased with time. Mean nasoseptal flap thickness on immediate and delayed postoperative scans was 3.8 and 3.9 mm, respectively (P = .181). The nasoseptal flap adhered entirely to the skull base in 37 (54.4%) and 67 (98.5%) patients on immediate and delayed imaging, respectively (P < .001). CONCLUSIONS Our findings demonstrate heterogeneity of the nasoseptal flap appearance after skull base reconstruction. While it is important for surgeons and radiologists to evaluate variations in flap appearance, the absence of enhancement and lack of adherence to the skull base on immediate postoperative imaging do not appear to predict reconstructive success and healing, with many flaps "self-adjusting" with time.
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Affiliation(s)
- J L Birkenbeuel
- From the Departments of Otolaryngology-Head and Neck Surgery (J.L.B., A.A., T.N., B.F.B., E.F.A., M.V., E.C.K.)
| | - A Abiri
- From the Departments of Otolaryngology-Head and Neck Surgery (J.L.B., A.A., T.N., B.F.B., E.F.A., M.V., E.C.K.)
| | - T Nguyen
- From the Departments of Otolaryngology-Head and Neck Surgery (J.L.B., A.A., T.N., B.F.B., E.F.A., M.V., E.C.K.)
| | - B F Bitner
- From the Departments of Otolaryngology-Head and Neck Surgery (J.L.B., A.A., T.N., B.F.B., E.F.A., M.V., E.C.K.)
| | - E F Abello
- From the Departments of Otolaryngology-Head and Neck Surgery (J.L.B., A.A., T.N., B.F.B., E.F.A., M.V., E.C.K.)
| | - M Vasudev
- From the Departments of Otolaryngology-Head and Neck Surgery (J.L.B., A.A., T.N., B.F.B., E.F.A., M.V., E.C.K.)
| | - F P K Hsu
- Neurological Surgery (F.P.K.H., E.C.K.)
| | - E Kuoy
- Radiology (E.K.), Division of Neuroradiology, University of California, Irvine, Irvine, California
| | - E C Kuan
- From the Departments of Otolaryngology-Head and Neck Surgery (J.L.B., A.A., T.N., B.F.B., E.F.A., M.V., E.C.K.)
- Neurological Surgery (F.P.K.H., E.C.K.)
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Marashi H, Beihaghi M, Chaboksavar M, Khaksar S, Tehrani H, Abiri A. In silico analysis and in planta production of recombinant ccl21/IL1β protein and characterization of its in vitro anti-tumor and immunogenic activity. PLoS One 2022; 17:e0261101. [PMID: 36037155 PMCID: PMC9423642 DOI: 10.1371/journal.pone.0261101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
CCL21 has an essential role in anti-tumor immune activity. Epitopes of IL1β have adjuvant activity without causing inflammatory responses. CCR7 and its ligands play a vital role in the immune balance; specifically, in transport of T lymphocytes and antigen-presenting cells such as dendritic cells to the lymph nodes. This study aimed to produce epitopes of CCL21 and IL1β as a recombinant protein and characterize its in vitro anti-tumor and immunogenic activity. A codon-optimized ccl21/IL1β gene was designed and synthesized from human genes. Stability and binding affinity of CCL21/IL1β protein and CCR7 receptor were examined through in silico analyses. The construct was introduced into N. tabacum to produce this recombinant protein and the structure and function of CCL21/IL1β were examined. Purified protein from transgenic leaves generated a strong signal in SDS PAGE and western blotting assays. FTIR measurement and MALDI-TOF/TOF mass spectrography showed that ccl21/IL-1β was correctly expressed in tobacco plants. Potential activity of purified CCL21/IL1β in stimulating the proliferation and migration of MCF7 cancer cell line was investigated using the wound healing method. The results demonstrated a decrease in survival rate and metastasization of cancer cells in the presence of CCL21/IL1β, and IC50 of CCL21 on MCF7 cells was less than that of non-recombinant protein. Agarose assay on PBMCsCCR7+ showed that CCL21/IL1β has biological activity and there is a distinguishable difference between chemokinetic (CCL21) and chemotactic (FBS) movements. Overall, the results suggest that CCL21/IL1β could be considered an effective adjuvant in future in vivo and clinical tests.
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Affiliation(s)
- Hasan Marashi
- College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maria Beihaghi
- College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Biology, Kavian Institute of Higher Education, Mashhad, Iran
- School of Science and Technology, The University of Georgia, Tbilisi, Georgia
- * E-mail:
| | - Masoud Chaboksavar
- Department of Biology, Kavian Institute of Higher Education, Mashhad, Iran
| | - Samad Khaksar
- School of Science and Technology, The University of Georgia, Tbilisi, Georgia
| | - Homan Tehrani
- Department of Paediatric, School of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
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Abstract
Guanine-rich DNA and RNA sequences can fold into noncanonical nucleic acid structures called G-quadruplexes (G4s). Since the discovery that these structures may act as scaffolds for the binding of specific ligands, G4s aroused the attention of a growing number of scientists. The versatile roles of G4 structures in viral replication, transcription, and translation suggest direct applications in therapy or diagnostics. G4-interacting molecules (proteins or small molecules) may also affect the balance between latent and lytic phases, and increasing evidence reveals that G4s are implicated in generally suppressing viral processes, such as replication, transcription, translation, or reverse transcription. In this review, we focus on the discovery of G4s in viruses and the role of G4 ligands in the antiviral drug discovery process. After assessing the role of viral G4s, we argue that host G4s participate in immune modulation, viral tumorigenesis, cellular pathways involved in virus maturation, and DNA integration of viral genomes, which can be potentially employed for antiviral therapeutics. Furthermore, we scrutinize the impediments and shortcomings in the process of studying G4 ligands and drug discovery. Finally, some unanswered questions regarding viral G4s are highlighted for prospective future projects. SIGNIFICANCE STATEMENT: G-quadruplexes (G4s) are noncanonical nucleic acid structures that have gained increasing recognition during the last few decades. First identified as relevant targets in oncology, their importance in virology is now increasingly clear. A number of G-quadruplex ligands are known: viral transcription and replication are the main targets of these ligands. Both viral and cellular G4s may be targeted; this review embraces the different aspects of G-quadruplexes in both host and viral contexts.
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Affiliation(s)
- Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Marc Lavigne
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Masoud Rezaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Sanaz Nikzad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Peyman Zare
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Jean-Louis Mergny
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Hamid-Reza Rahimi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
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10
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Mirzaei M, Nadushan AS, Nooshadokht M, Abiri A, Anjomshoa M, Sharifi I, Amirheidari B. In silico and in vitro inhibitory potential of an organometallic Cu (II) complex on Leishmania major stages. Ann Parasitol 2021; 67:45-54. [PMID: 34021979 DOI: 10.17420/ap6701.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Leishmaniosis results in a serious complication, principally in the tropical and subtropical areas. Metalcored complexes, like meglumine antimoniate (MA) have proven antileishmanial activity. Similarly, in this research, we investigated the effects of Cu (II) dimethoxy bipyridine (CuDMOBP) against Leishmania major stages in silico and in vitro. Molecular docking analysis was carried out on the complex and a protozoan metacaspase. The complex's antipromastigote and its cytotoxicity towards macrophages were assayed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method to calculate relative Inhibitory Concentration 50% (IC50), Cytotoxic Concentration 50% (CC50), and Selectivity Index (SI). Expression of TNF-α and IL-10 in intracellular amastigotes and induction of apoptosis was also investigated using quantitative real-time PCR. The complex interacted effectively with four amino acid residues including lysine (Lys171), histidine (His193), arginine (Arg44 and Arg243) of the targeted metacaspase. This indicates a potential affinity between the target macromolecule and the complex. MTT results showed significant in vitro inhibitory effects against promastigotes. Reduction in cellular expression of IL-10 and TNF-α was also significant, p<0.05 and p<0.005, respectively. CuDMOBP showed powerful in vitro anti-leishmanial activity and could be introduced as a new leishmanicidal candidate.
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Affiliation(s)
- Mohammad Mirzaei
- Pathobiology Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Abbasali Salimi Nadushan
- Pathobiology Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nooshadokht
- Pathobiology Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran.,Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Marzieh Anjomshoa
- Pharmaceutics Research Center, Insitute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Iraj Sharifi
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Bagher Amirheidari
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
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11
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Mahdevar E, Safavi A, Abiri A, Kefayat A, Hejazi SH, Miresmaeili SM, Iranpur Mobarakeh V. Exploring the cancer-testis antigen BORIS to design a novel multi-epitope vaccine against breast cancer based on immunoinformatics approaches. J Biomol Struct Dyn 2021; 40:6363-6380. [PMID: 33599191 DOI: 10.1080/07391102.2021.1883111] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recently, cancer immunotherapy has gained lots of attention to replace the current chemoradiation approaches and multi-epitope cancer vaccines are manifesting as the next generation of cancer immunotherapy. Therefore, in this study, we used multiple immunoinformatics approaches along with other computational approaches to design a novel multi-epitope vaccine against breast cancer. The most immunogenic regions of the BORIS cancer-testis antigen were selected according to the binding affinity to MHC-I and II molecules as well as containing multiple cytotoxic T lymphocyte (CTL) epitopes by multiple immunoinformatics servers. The selected regions were linked together by GPGPG linker. Also, a T helper epitope (PADRE) and the TLR-4/MD-2 agonist (L7/L12 ribosomal protein from mycobacterium) were incorporated by A(EAAAK)3A linker to form the final vaccine construct. Then, its physicochemical properties, cleavage sites, TAP transport efficiency, B cell epitopes, IFN-γ inducing epitopes and population coverage were predicted. The final vaccine construct was reverse translated, codon-optimized and inserted into pcDNA3.1 to form the DNA vaccine. The final vaccine construct was a stable, immunogenic and non-allergenic protein that contained numerous CTL epitopes, IFN-γ inducing epitopes and several linear and conformational B cell epitopes. Also, the final vaccine construct formed stable and significant interactions with TLR-4/MD-2 complex according to molecular docking and dynamics simulations. Moreover, its world population coverage for HLA-I and HLA-II were about 93% and 96%, respectively. Taking together, these preliminary results can be used as an appropriate platform for further experimental investigations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elham Mahdevar
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
| | - Ashkan Safavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Amirhosein Kefayat
- Department of Oncology, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Hossein Hejazi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Mohsen Miresmaeili
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
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12
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Langarizadeh MA, Ranjbar Tavakoli M, Abiri A, Ghasempour A, Rezaei M, Ameri A. A review on function and side effects of systemic corticosteroids used in high-grade COVID-19 to prevent cytokine storms. EXCLI J 2021; 20:339-365. [PMID: 33746666 PMCID: PMC7975631 DOI: 10.17179/excli2020-3196] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/09/2021] [Indexed: 12/13/2022]
Abstract
In December 2019, a cluster of pneumonia caused by a novel coronavirus (2019-nCoV), officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan, Hubei province, China. Cytokine storm is an uncontrolled systemic inflammatory response resulting from the release of large amounts of pro-inflammatory cytokines and chemokines that occurs at phase 3 of viral infection. Such emergence led to the development of many clinical trials to discover efficient drugs and therapeutic protocols to fight with this single-stranded RNA virus. Corticosteroids suppress inflammation of the lungs during the cytokine storm, weaken immune responses, and inhibit the elimination of pathogen. For this reason, in COVID-19 corticosteroid therapy, systemic inhibition of inflammation is observed with a wide range of side effects. The present review discusses the effectiveness of the corticosteroid application in COVID-19 infection and the related side effects of these agents. In summary, a number of corticosteroids, including and especially methylprednisolone and dexamethasone, have demonstrated remarkable efficacy, particularly for COVID-19 patients who underwent mechanical ventilation.
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Affiliation(s)
- Mohammad Amin Langarizadeh
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Ardavan Abiri
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Ghasempour
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Masoud Rezaei
- Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Alieh Ameri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
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13
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Abiri A, Rezaei M, Zeighami MH, Vaezpour Y, Dehghan L, KhorramGhahfarokhi M. Discovery of new TLR7 agonists by a combination of statistical learning-based QSAR, virtual screening, and molecular dynamics. Inform Med Unlocked 2021; 27:100787. [PMID: 34805481 PMCID: PMC8591993 DOI: 10.1016/j.imu.2021.100787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/16/2021] [Accepted: 11/11/2021] [Indexed: 01/31/2023] Open
Abstract
Search for new antiviral medications has surged in the past two years due to the COVID-19 crisis. Toll-like receptor 7 (TLR7) is among one of the most important TLR proteins of innate immunity that is responsible for broad antiviral response and immune system control. TLR7 agonists, as both vaccine adjuvants and immune response modulators, are among the top drug candidates for not only our contemporary viral pandemic but also other diseases. The agonists of TLR7 have been utilized as vaccine adjuvants and antiviral agents. In this study, we hybridized a statistical learning-based QSAR model with molecular docking and molecular dynamics simulation to extract new antiviral drugs by drug repurposing of the DrugBank database. First, we manually curated a dataset consisting of TLR7 agonists. The molecular descriptors of these compounds were extracted, and feature engineering was done to restrict the number of features to 45. We applied a statistically inspired modification of the partial least squares (SIMPLS) method to build our QSAR model. In the next stage, the DrugBank database was virtually screened structurally using molecular docking, and the top compounds for the guanosine binding site of TLR were identified. The result of molecular docking was again screened by the ligand-based approach of QSAR to eliminate compounds that do not display strong EC50 values by the previously trained model. We then subjected the final results to molecular dynamics simulation and compared our compounds with imiquimod (an FDA-approved TLR7 agonist) and compound 1 (the most active compound against TLR7 in vitro, EC50 = 0.2 nM). Our results evidently demonstrate that cephalosporins and nucleotide analogues (especially acyclic nucleotide analogues such as adefovir and cidofovir) are computationally potent agonists of TLR7. We finally reviewed some publications about cephalosporins that, just like pieces of a puzzle, completed our conclusion.
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Affiliation(s)
- Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran,Corresponding author
| | - Masoud Rezaei
- Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran,Corresponding author
| | - Mohammad Hossein Zeighami
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Younes Vaezpour
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Leili Dehghan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Maedeh KhorramGhahfarokhi
- Faculty of Pharmacy and Pharmaceutical Sciences, Kerman University of Medical Sciences, Kerman, Iran
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14
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Safavi A, Kefayat A, Mahdevar E, Abiri A, Ghahremani F. Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches. Vaccine 2020; 38:7612-7628. [PMID: 33082015 PMCID: PMC7546226 DOI: 10.1016/j.vaccine.2020.10.016] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 causes a severe respiratory disease called COVID-19. Currently, global health is facing its devastating outbreak. However, there is no vaccine available against this virus up to now. In this study, a novel multi-epitope vaccine against SARS-CoV-2 was designed to provoke both innate and adaptive immune responses. The immunodominant regions of six non-structural proteins (nsp7, nsp8, nsp9, nsp10, nsp12 and nsp14) of SARS-CoV-2 were selected by multiple immunoinformatic tools to provoke T cell immune response. Also, immunodominant fragment of the functional region of SARS-CoV-2 spike (400-510 residues) protein was selected for inducing neutralizing antibodies production. The selected regions' sequences were connected to each other by furin-sensitive linker (RVRR). Moreover, the functional region of β-defensin as a well-known agonist for the TLR-4/MD complex was added at the N-terminus of the vaccine using (EAAAK)3 linker. Also, a CD4 + T-helper epitope, PADRE, was used at the C-terminal of the vaccine by GPGPG and A(EAAAK)2A linkers to form the final vaccine construct. The physicochemical properties, allergenicity, antigenicity, functionality and population coverage of the final vaccine construct were analyzed. The final vaccine construct was an immunogenic, non-allergen and unfunctional protein which contained multiple CD8 + and CD4 + overlapping epitopes, IFN-γ inducing epitopes, linear and conformational B cell epitopes. It could form stable and significant interactions with TLR-4/MD according to molecular docking and dynamics simulations. Global population coverage of the vaccine for HLA-I and II were estimated 96.2% and 97.1%, respectively. At last, the final vaccine construct was reverse translated to design the DNA vaccine. Although the designed vaccine exhibited high efficacy in silico, further experimental validation is necessary.
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Affiliation(s)
- Ashkan Safavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Amirhosein Kefayat
- Department of Oncology, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Mahdevar
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Ghahremani
- Department of Medical Physics and Radiotherapy, Arak School of Paramedicine, Arak University of Medical Sciences, Arak, Iran.
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15
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Langarizadeh MA, Abiri A, Ghasemshirazi S, Foroutan N, Khodadadi A, Faghih-Mirzaei E. Phlorotannins as HIV Vpu inhibitors, an in silico virtual screening study of marine natural products. Biotechnol Appl Biochem 2020; 68:918-926. [PMID: 32860447 DOI: 10.1002/bab.2014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/26/2020] [Indexed: 12/22/2022]
Abstract
The importance of new effective treatment methodologies for human immunodeficiency virus (HIV) is undeniable for the medical society. Viral protein U (Vpu), one of the disparaged accessory proteins of HIV, is responsible for the dissemination of viral particles, and HIV mutants lacking Vpu protein have remarkably reduced pathogenicity. Here, we explored the marine natural products to find the leading structures which can potentially inhibit the activity of Vpu in silico. To fulfill this goal, we set up a virtual screening based on molecular docking to evaluate the binding capacity of different marine products to Vpu. For validation, we used molecular dynamics simulation and monitored the root mean square deviation value and binding interactions. The results were intriguing when we realized that the hit compounds (phlorotannins) had previously been identified as reverse transcriptase and HIV protease inhibitors. This research inaugurates a new road to combat HIV by multifaceted mode of action of these marine natural products without putting the normal cells in jeopardy (with their safe toxicological profile).
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Affiliation(s)
- Mohammad Amin Langarizadeh
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Saeid Ghasemshirazi
- Department of Computer Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Nazanin Foroutan
- Pharmaceutics Research Center, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Arash Khodadadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Ehsan Faghih-Mirzaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
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16
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Safaei M, Mobini GR, Abiri A, Shojaeian A. Synthetic biology in various cellular and molecular fields: applications, limitations, and perspective. Mol Biol Rep 2020; 47:6207-6216. [PMID: 32507922 DOI: 10.1007/s11033-020-05565-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/28/2020] [Indexed: 01/10/2023]
Abstract
Synthetic biology breakthroughs have facilitated genetic circuit engineering to program cells through novel biological functions, dynamic gene expressions, as well as logic controls. SynBio can also participate in the rapid development of new treatments required for the human lifestyle. Moreover, these technologies are applied in the development of innovative therapeutic, diagnostic, as well as discovery-related methods within a wide range of cellular and molecular applications. In the present review study, SynBio applications in various cellular and molecular fields such as novel strategies for cancer therapy, biosensing, metabolic engineering, protein engineering, and tissue engineering were highlighted and summarized. The major safety and regulatory concerns about synthetic biology will be the environmental release, legal concerns, and risks of the engineered organisms. The final sections focused on limitations to SynBio.
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Affiliation(s)
- Mohsen Safaei
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Gholam-Reza Mobini
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Shojaeian
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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17
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Jodeiryzaer S, Farsimadan M, Abiri A, Sharafshah A, Vaziri H. Association of oestrogen receptor alpha gene SNPs Arg157Ter C>T and Val364Glu T>A with female infertility. Br J Biomed Sci 2020; 77:216-218. [DOI: 10.1080/09674845.2020.1759993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- S Jodeiryzaer
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - M Farsimadan
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - A Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - A Sharafshah
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - H Vaziri
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
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18
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Amjadi Oskouie A, Abiri A. Refining our methodologies for assessing quadruplex DNA ligands; selectivity or an illusion of selectivity? Anal Biochem 2020; 613:113744. [PMID: 32325085 DOI: 10.1016/j.ab.2020.113744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/11/2020] [Accepted: 04/15/2020] [Indexed: 12/21/2022]
Abstract
Regulation of transcription and replication by the tetrad patterns of DNA has drawn the attention of many scientists. In this perspective article, we discuss some disparaged parameters in the study of G-quadruplex structures (G4-tetrads). Besides, the implication of "destabilization as a side-effect" by these ligands on quadruplexes is explained. The lack of strict control of in vitro cell-free experiments in terms of ionic concentration, pH, epigenetic modifications, (macro)molecular crowding, and solvent effects is evident in many previous studies. The role of these factors in ligands binding and their possible effects in G-quadruplex structures are also represented.
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Affiliation(s)
- Akbar Amjadi Oskouie
- Department of Biology, Ardabil Branch, Islamic Azad University, Ardabil, Iran; Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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19
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Rashidipour N, Karami-Mohajeri S, Mandegary A, Mohammadinejad R, Wong A, Mohit M, Salehi J, Ashrafizadeh M, Najafi A, Abiri A. Where ferroptosis inhibitors and paraquat detoxification mechanisms intersect, exploring possible treatment strategies. Toxicology 2020; 433-434:152407. [PMID: 32061663 DOI: 10.1016/j.tox.2020.152407] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022]
Abstract
Paraquat (PQ) is a fast-acting and effective herbicide that is used throughout the world to eliminate weeds. Over the past years, PQ was considered one of the most popular poisoning substances for suicide, and PQ poisoning accounts for about one-third of suicides around the world. Poisoning with PQ may cause multiorgan failure, pulmonary fibrosis, and ultimately death. Exposure to PQ results in the accumulation of PQ in the lungs, causing severe damage and, eventually, fibrosis. Until now, no effective antidote has been found to treat poisoning with PQ. In general, the toxicity of PQ is due to the formation of high energy oxygen free radicals and the peroxidation of unsaturated lipids in the cell. Ferroptosis is the result of the loss of glutathione peroxidase 4 (GPX4) activity that transforms iron-dependent lipid hydroperoxides to lipid alcohols, which are inert in the biological environment. Impaired iron metabolism and lipid peroxidation are increasingly known as the driving agents of ferroptosis. The contribution of ferroptosis to the development of cell death during poisoning with PQ has not yet been addressed. There is growing evidence about the relationship between PQ poisoning and ferroptosis. This raises the possibility of using ferroptosis inhibitors for the treatment of PQ poisoning. In this hypothesis-driven review article, we elaborated how ferroptosis inhibitors might circumvent the toxicity induced by PQ and may be potentially useful for the treatment of PQ toxicity.
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Affiliation(s)
- Niloofar Rashidipour
- Department of Anesthesiology, Faculty of Allied Medical Sciences, Kerman University of Medical Sciences, Kerman, Iran; Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.
| | - Somayyeh Karami-Mohajeri
- Department of Toxicology and Pharmacology, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Mandegary
- Department of Toxicology and Pharmacology, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran; Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.
| | - Anselm Wong
- Victorian Poisons Information Centre, Emergency Department and Austin Toxicology Unit, Austin Health, Victoria, Australia; Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia; Centre for Integrated Critical Care, Department of Medicine and Radiology, Melbourne Medical School, University of Melbourne, Victoria, Australia
| | - Melika Mohit
- Department of Laboratory Sciences, Sirjan Faculty of Medical Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Jafar Salehi
- Department of Anesthesiology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Amir Najafi
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran; Department of Toxicology and Pharmacology, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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20
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Moshafi MH, Ghasemshirazi S, Abiri A. The art of suicidal molecular seduction for targeting drug resistance. Med Hypotheses 2020; 140:109676. [PMID: 32203818 DOI: 10.1016/j.mehy.2020.109676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/29/2020] [Accepted: 03/14/2020] [Indexed: 12/11/2022]
Abstract
The development of drug resistance is one of the most significant challenges of the current century in the pharmaceutical industry. Superinfections, cancer chemoresistance, and resistance observed in many non-infectious diseases are nullifying the efforts and monetary supplies, put in the advent of new drug molecules. Millions of people die because of this drug resistance developed gradually through extensive use of the drugs. Inherently, some drugs are less prone to become ineffective by drug resistance than others. Covalent inhibitors bind to their targets via a biologically permanent bound with their cognate receptor and therefore display more potent inhibiting characteristics. Suicide inhibitors or mechanism-based inhibitors are one of the covalent inhibitors, which require a pre-activation step by their targeting enzyme. This step accrues their selectivity and specificity with respect to other covalent inhibitors. After that pre-activation step, they produce an analogue of the transition state of the catalytic enzyme, which is practically incapable of dissociating from the enzyme. Suicide inhibitors, due to their high intrinsic affinity toward the related enzyme, are resistant to many mechanisms involved in the development of drug resistance and can be regarded as one of the enemies of this scientific hurdle. These inhibitors compete even with monoclonal antibodies in terms of their cost-effectiveness and efficacy.
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Affiliation(s)
- Mohammad Hassan Moshafi
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Saeid Ghasemshirazi
- Department of Computer Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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21
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Pourshojaei Y, Abiri A, Eskandari K, Haghighijoo Z, Edraki N, Asadipour A. Phenoxyethyl Piperidine/Morpholine Derivatives as PAS and CAS Inhibitors of Cholinesterases: Insights for Future Drug Design. Sci Rep 2019; 9:19855. [PMID: 31882733 PMCID: PMC6934599 DOI: 10.1038/s41598-019-56463-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
Acetylcholinesterase (AChE) catalyzes the conversion of Aβ peptide to its aggregated form and the peripheral anionic site (PAS) of AChE is mainly involved in this phenomenon. Also catalytic active site (CAS) of donepezil stimulates the break-down of acetylcholine (ACh) and depletion of ACh in cholinergic synapses are well established in brains of patients with AD. In this study, a set of compounds bearing phenoxyethyl amines were synthesized and their inhibitory activity toward electric eel AChE (eeAChE) and equine butyrylcholinesterase (eqBuChE) were evaluated. Molecular dynamics (MD) was employed to record the binding interactions of best compounds against human cholinesterases (hAChE and hBuChE) as well as donepezil as reference drug. In vitro results revealed that compound 5c is capable of inhibiting eeAChE activity at IC50 of 0.50 µM while no inhibitory activity was found for eqBuChE for up to 100 µM concentrations. Compound 5c, also due to its facile synthesis, small structure and high selectivity for eeAChE would be very interesting candidate in forthcoming studies. The main interacting parts of compound 5c and compound 7c (most potent eeAChE and eqBuChE inhibitors respectively) with receptors which confer selectivity for AChE and BuChE inhibition were identified, discussed, and compared with donepezil’s interactions. Also during MD simulation it was discovered for the first time that binding of substrates like donepezil to dual CAS and PAS or solely CAS region might have a suppressive impact on 4-α-helical bundles near the tryptophan amphiphilic tetramerization (WAT) domain of AChE and residues which are far away from AChE active site. The results proposed that residues involved in donepezil interactions (Trp86 and Phe295) which are located in CAS and mid-gorge are the mediator of conformational changes in whole protein structure.
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Affiliation(s)
- Yaghoub Pourshojaei
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran.,Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Khalil Eskandari
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| | - Zahra Haghighijoo
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ali Asadipour
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
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22
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Haqiqi H, Farsimadan M, Abiri A, Sharafshah A, Vaziri H, Zahiri Z. Association of FSHR missense mutations with female infertility, in silico investigation of their molecular significance and exploration of possible treatments using virtual screening and molecular dynamics. Anal Biochem 2019; 586:113433. [DOI: 10.1016/j.ab.2019.113433] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/12/2019] [Indexed: 11/16/2022]
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23
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Jabbarzadeh Kaboli P, Afzalipour Khoshkbejari M, Mohammadi M, Abiri A, Mokhtarian R, Vazifemand R, Amanollahi S, Yazdi Sani S, Li M, Zhao Y, Wu X, Shen J, Cho CH, Xiao Z. Targets and mechanisms of sulforaphane derivatives obtained from cruciferous plants with special focus on breast cancer - contradictory effects and future perspectives. Biomed Pharmacother 2019; 121:109635. [PMID: 31739165 DOI: 10.1016/j.biopha.2019.109635] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
Breast cancer is the most common type of cancer among women. Therefore, discovery of new and effective drugs with fewer side effects is necessary to treat it. Sulforaphane (SFN) is an organosulfur compound obtained from cruciferous plants, such as broccoli and mustard, and it has the potential to treat breast cancer. Hence, it is vital to find out how SFN targets certain genes and cellular pathways in treating breast cancer. In this review, molecular targets and cellular pathways of SFN are described. Studies have shown SFN inhibits cell proliferation, causes apoptosis, stops cell cycle and has anti-oxidant activities. Increasing reactive oxygen species (ROS) produces oxidative stress, activates inflammatory transcription factors, and these result in inflammation leading to cancer. Increasing anti-oxidant potential of cells and discovering new targets to reduce ROS creation reduces oxidative stress and it eventually reduces cancer risks. In short, SFN effectively affects histone deacetylases involved in chromatin remodeling, gene expression, and Nrf2 anti-oxidant signaling. This review points to the potential of SFN to treat breast cancer as well as the importance of other new cruciferous compounds, derived from and isolated from mustard, to target Keap1 and Akt, two key regulators of cellular homeostasis.
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Affiliation(s)
- Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China; Drug Discovery Research Group, Parham Academy of Biomedical Sciences, The Heritage B-16-10, Selangor, 43300, Malaysia.
| | | | - Mahsa Mohammadi
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Roya Mokhtarian
- Drug Discovery Research Group, Parham Academy of Biomedical Sciences, The Heritage B-16-10, Selangor, 43300, Malaysia
| | - Reza Vazifemand
- Laboratory of Virology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, 43400, Malaysia
| | - Shima Amanollahi
- Drug Discovery Research Group, Parham Academy of Biomedical Sciences, The Heritage B-16-10, Selangor, 43300, Malaysia; School of Mathematical, Physical, and Natural Sciences, University of Florence, Firenze, 50134, Italy
| | - Shaghayegh Yazdi Sani
- Drug Discovery Research Group, Parham Academy of Biomedical Sciences, The Heritage B-16-10, Selangor, 43300, Malaysia
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China.
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24
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Bagheri M, Ghasemshirazi S, Abiri A. Eschatological scrutiny of unprofessional usage of molecular docking; how unreliability in computational methods arises from amateurish mistakes. Biocatalysis and Agricultural Biotechnology 2019. [DOI: 10.1016/j.bcab.2019.101224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Shamsimeymandi R, Pourshojaei Y, Eskandari K, Mohammadi-Khanaposhtani M, Abiri A, Khodadadi A, Langarizadeh A, Sharififar F, Amirheidari B, Akbarzadeh T, Lotfian H, Foroumadi A, Asadipour A. Design, synthesis, biological evaluation, and molecular dynamics of novel cholinesterase inhibitors as anti-Alzheimer's agents. Arch Pharm (Weinheim) 2019; 352:e1800352. [PMID: 31136018 DOI: 10.1002/ardp.201800352] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 11/08/2022]
Abstract
A series of novel chroman-4-one derivatives were designed and synthesized successfully with good to excellent yield (3a-l). In addition, the obtained products were evaluated for their cholinesterase (ChE) inhibitory activities. The results show that among the various synthesized compounds, analogs bearing the piperidinyl ethoxy side chain with 4-hydroxybenzylidene on the 3-positions of chroman-4-one (3l) showed the most potent activity with respect to acetylcholinesterase (anti-AChE activity; IC50 = 1.18 μM). In addition, the structure-activity relationship was studied and the results revealed that the electron-donating groups on the aryl ring of the 3-benzylidene fragment (3k, 3l) resulted in the designed compounds to be more potent ChE inhibitors in comparison with those having electron-withdrawing groups (3h). In this category, the strongest ChE inhibition was found for the compound containing piperidine as cyclic amine, and a hydroxyl group (for AChE, compound 3l) and fluoro group (for butyrylcholinesterase (BuChE, compound 3i) on the para-position of the aryl ring of the benzylidene group. The molecular docking and dynamics studies of the most potent compounds (3i and 3l against BuChE and AChE, respectively) demonstrated remarkable interactions with the binding pockets of the ChE enzymes and confirmed the results obtained through in vitro experiments.
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Affiliation(s)
- Reza Shamsimeymandi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Yaghoub Pourshojaei
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran.,Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Khalil Eskandari
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Maryam Mohammadi-Khanaposhtani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Arash Khodadadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Fariba Sharififar
- Department of Pharmacognosy, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Bagher Amirheidari
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Tahmineh Akbarzadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.,Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hania Lotfian
- Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Foroumadi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.,Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Asadipour
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
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26
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Safavi A, Kefayat A, Abiri A, Mahdevar E, Behnia AH, Ghahremani F. In silico analysis of transmembrane protein 31 (TMEM31) antigen to design novel multiepitope peptide and DNA cancer vaccines against melanoma. Mol Immunol 2019; 112:93-102. [PMID: 31079006 DOI: 10.1016/j.molimm.2019.04.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/25/2019] [Accepted: 04/30/2019] [Indexed: 12/18/2022]
Abstract
Multiepitope cancer vaccines are announcing themselves as the future of melanoma treatment. Herein, high immunogenic regions of transmembrane protein 31 (TMEM31) antigen were selected according to cytotoxic T lymphocytes' (CTL) epitopes and major histocompatibility complex (MHC) binding affinity through in silico analyses. The 32-62, 77-105, and 125-165 residues of the TMEM31 were selected as the immunodominant fragments. They were linked together by RVRR and HEYGAEALERAG motifs to improve epitopes separation and presentation. In addition, to activate helper T lymphocytes (HTL), Pan HLA DR-binding epitope (PADRE) peptide sequence and tetanus toxin fragment C (TTFrC) were incorporated into the final construct. Also, the Beta-defensin conserved domain was utilized in the final construct as a novel adjuvant for Toll-like receptor 4/myeloid differentiation factor (TLR4-MD) activation. The CTL epitopes, cleavage sites, post-translational modifications, TAP transport efficiency, and B cells epitopes were predicted for the peptide vaccine. The final construct contained multiple CTL and B cell epitopes. In addition, it showed 93.55% and 99.13% population coverage in the world for HLA I and HLA II, respectively. According to these preliminary results, the multiepitope cancer vaccine can be an appropriate choice for further experimental investigations.
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Affiliation(s)
- Ashkan Safavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Amirhosein Kefayat
- Department of Oncology, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Elham Mahdevar
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
| | - Amir Hossein Behnia
- Department of Biology, Faculty of the Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Fatemeh Ghahremani
- Department of Medical Physics and Radiotherapy, Arak University of Medical Sciences, Arak, Iran
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27
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Pourshojaei Y, Abiri A, Eskandari R, Dourandish F, Eskandari K, Asadipour A. Synthesis, biological evaluation, and computational studies of novel fused six-membered O-containing heterocycles as potential acetylcholinesterase inhibitors. Comput Biol Chem 2019; 80:249-258. [PMID: 31029750 DOI: 10.1016/j.compbiolchem.2019.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/09/2019] [Accepted: 04/06/2019] [Indexed: 12/15/2022]
Abstract
An efficient, borax-catalyzed protocol for the synthesis of novel 4-aryl-substituted-4H-pyran derivatives fused to α-pyrone ring in a one-pot is described. By this achievement, some novel 4-aryl substituted 4H-pyrans fused to the α-pyrone ring as potential acetylcholinesterase inhibitors (AChEIs) with good to excellent yields are obtained from a one-pot three-component reaction between various aryl aldehydes, 4-hydroxy-6-methyl-2H-pyran-2-one and malononitrile. The method is a facile, inexpensive, practical and highly efficient one to obtain target compounds. The chemical structures of all compounds were characterized by FT-IR, FT-13CNMR and FT-1HNMR, MS spectroscopy and also elemental analyses data. Furthermore, the purity of all novel compounds was checked by HPLC. In addition, both molecular modelling studies and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMETox) prediction nominated all compounds as good acetylcholinesterase inhibitors to the potential treatment of Alzheimer, Parkinson and Autism diseases that among them compound 4f showed the best activity against acetylcholinesterase enzyme.
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Affiliation(s)
- Yaghoub Pourshojaei
- Department of Medicinal Chemistry, Faculty of Pharmacy & Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran; Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy & Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Razieh Eskandari
- Department of Computer Engineering, Faculty of Engineering and Technology, Shahrekord University, Shahrekord, Iran
| | - Fatemeh Dourandish
- Department of Medicinal Chemistry, Faculty of Pharmacy & Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Khalil Eskandari
- Department of Medicinal Chemistry, Faculty of Pharmacy & Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| | - Ali Asadipour
- Department of Medicinal Chemistry, Faculty of Pharmacy & Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
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28
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Abiri A. Plerixafor and related macrocyclic amines are potential drug candidates in treatment of malaria by "filling the flap" region of plasmepsin enzymes. Med Hypotheses 2018; 118:68-73. [PMID: 30037618 DOI: 10.1016/j.mehy.2018.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/24/2018] [Accepted: 06/19/2018] [Indexed: 11/30/2022]
Abstract
Death by Plasmodium falsiparum, the leading cause of malaria, is going to remain a major obstacle among the infectious diseases. Plasmepsin aspartic proteases are key proteins in the pathogenesis of plasmodium species which break down the hemoglobin and exploit it as a source of amino acids. These enzymes are one of the favorite targeting agents for medicinal chemists to design new drugs. Plasmepsin proteins show a "flap" region in their N-terminal domain, predisposing them to a good "filler" drug with an exceptional affinity to this enzyme. Plerixafor (Mozobil®, AMD3100), a CXCR4 antagonist with a bicyclam ring, historically discovered as an impurity in a mixture which had anti-HIV properties, is now a FDA approved drug for mobilizing haematopoietic stem cells in cancer patients. In this hypothesis, we focused on the similarity of the structure of plerixafor and its analogues with heme functional group of hemoglobin, the main substrate of plasmepsin, and also with some other recent azamacrocyclic compounds demonstrating antimalarial activity, to test whether these compounds are capable of exhibiting antimalarial activity by inhibiting plasmepsin or not. A preliminary in silico docking study was used to evaluate this hypothesis and docking results indicated that macrocyclic cyclams and cyclens can reliably act as potent lead drug or central pharmacophore in developing new plasmepsin inhibitors as compared with previously designed plasmepsin II inhibitors.
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Affiliation(s)
- Ardavan Abiri
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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