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Article: Cholesterol in Class C GPCRs: Role, Relevance, and Localization.

Isu, Ugochi H / Badiee, Shadi A / Khodadadi, Ehsaneh / Moradi, Mahmoud

2023 Volume 13, Issue 3

Abstract: G-protein coupled receptors (GPCRs), one of the largest superfamilies of cell-surface receptors, are heptahelical integral membrane proteins that play critical roles in virtually every organ system. G-protein-coupled receptors operate in membranes rich ... ...

Abstract	G-protein coupled receptors (GPCRs), one of the largest superfamilies of cell-surface receptors, are heptahelical integral membrane proteins that play critical roles in virtually every organ system. G-protein-coupled receptors operate in membranes rich in cholesterol, with an imbalance in cholesterol level within the vicinity of GPCR transmembrane domains affecting the structure and/or function of many GPCRs, a phenomenon that has been linked to several diseases. These effects of cholesterol could result in indirect changes by altering the mechanical properties of the lipid environment or direct changes by binding to specific sites on the protein. There are a number of studies and reviews on how cholesterol modulates class A GPCRs; however, this area of study is yet to be explored for class C GPCRs, which are characterized by a large extracellular region and often form constitutive dimers. This review highlights specific sites of interaction, functions, and structural dynamics involved in the cholesterol recognition of the class C GPCRs. We summarize recent data from some typical family members to explain the effects of membrane cholesterol on the structural features and functions of class C GPCRs and speculate on their corresponding therapeutic potential.
Language	English
Publishing date	2023-03-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2614641-1
ISSN	2077-0375
ISSN	2077-0375
DOI	10.3390/membranes13030301
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs.

Badiee, Shadi A / Isu, Ugochi H / Khodadadi, Ehsaneh / Moradi, Mahmoud

Membranes

2023 Volume 13, Issue 6

Abstract: Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug ... ...

Abstract	Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the failure of therapeutic interventions and hinders successful treatments. One key mechanism by which multidrug resistance (MDR) proteins carry out their transport function is through alternating access. This mechanism involves intricate conformational changes that enable the binding and transport of substrates across cellular membranes. In this extensive review, we provide an overview of ABC transporters, including their classifications and structural similarities. We focus specifically on well-known mammalian multidrug resistance proteins such as MRP1 and Pgp (MDR1), as well as bacterial counterparts such as Sav1866 and lipid flippase MsbA. By exploring the structural and functional features of these MDR proteins, we shed light on the roles of their nucleotide-binding domains (NBDs) and transmembrane domains (TMDs) in the transport process. Notably, while the structures of NBDs in prokaryotic ABC proteins, such as Sav1866, MsbA, and mammalian Pgp, are identical, MRP1 exhibits distinct characteristics in its NBDs. Our review also emphasizes the importance of two ATP molecules for the formation of an interface between the two binding sites of NBD domains across all these transporters. ATP hydrolysis occurs following substrate transport and is vital for recycling the transporters in subsequent cycles of substrate transportation. Specifically, among the studied transporters, only NBD2 in MRP1 possesses the ability to hydrolyze ATP, while both NBDs of Pgp, Sav1866, and MsbA are capable of carrying out this reaction. Furthermore, we highlight recent advancements in the study of MDR proteins and the alternating access mechanism. We discuss the experimental and computational approaches utilized to investigate the structure and dynamics of MDR proteins, providing valuable insights into their conformational changes and substrate transport. This review not only contributes to an enhanced understanding of multidrug resistance proteins but also holds immense potential for guiding future research and facilitating the development of effective strategies to overcome multidrug resistance, thus improving therapeutic interventions.
Language	English
Publishing date	2023-05-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2614641-1
ISSN	2077-0375
ISSN	2077-0375
DOI	10.3390/membranes13060568
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Article: Natural Products as a Potential Source of Promising Therapeutics for COVID-19 and Viral Diseases.

Bafandeh, Soheila / Khodadadi, Ehsaneh / Ganbarov, Khudaverdi / Asgharzadeh, Mohammad / Köse, Şükran / Samadi Kafil, Hossein

Evidence-based complementary and alternative medicine : eCAM

2023 Volume 2023, Page(s) 5525165

Abstract: Background: A global pandemic has recently been observed due to the new coronavirus disease, caused by SARS-CoV-2. Since there are currently no antiviral medicines to combat the highly contagious and lethal COVID-19 infection, identifying natural ... ...

Abstract	Background: A global pandemic has recently been observed due to the new coronavirus disease, caused by SARS-CoV-2. Since there are currently no antiviral medicines to combat the highly contagious and lethal COVID-19 infection, identifying natural sources that can either be viricidal or boost the immune system and aid in the fight against the disease can be an essential therapeutic support. Methods: This review was conducted based on published papers related to the herbal therapy of COVID-19 by search on databases including PubMed and Scopus with herbal, COVID-19, SARS-CoV-2, and therapy keywords. Results: To combat this condition, people may benefit from the therapeutic properties of medicinal plants, such as increasing their immune system or providing an antiviral impact. As a result, SARS-CoV-2 infection death rates can be reduced. Various traditional medicinal plants and their bioactive components, such as COVID-19, are summarized in this article to assist in gathering and debating techniques for combating microbial diseases in general and boosting our immune system in particular. Conclusion: The immune system benefits from natural products and many of these play a role in activating antibody creation, maturation of immune cells, and stimulation of innate and adaptive immune responses. The lack of particular antivirals for SARS-CoV-2 means that apitherapy might be a viable option for reducing the hazards associated with COVID-19 in the absence of specific antivirals.
Language	English
Publishing date	2023-04-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2171158-6
ISSN	1741-4288 ; 1741-427X
ISSN (online)	1741-4288
ISSN	1741-427X
DOI	10.1155/2023/5525165
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Article ; Online: Induction of proteome changes involved in the cloning of mcr-1 and mcr-2 genes in Escherichia coli DH5-α strain to evaluate colistin resistance.

Feizi, Hadi / Alizadeh, Maryam / Azimi, Hadi / Khodadadi, Ehsaneh / Kamounah, Fadhil S / Ganbarov, Khudaverdi / Ghotaslou, Reza / Rezaee, Mohammad Ahangarzadeh / Kafil, Hossein Samadi

Journal of global antimicrobial resistance

2023 Volume 36, Page(s) 151–159

Abstract: Objectives: Plasmid genes, termed mobile colistin resistance-1 (mcr-1) and mobile colistin resistance-2 (mcr-2), are associated with resistance to colistin in Escherichia coli (E. coli). These mcr genes result in a range of protein modifications ... ...

Abstract	Objectives: Plasmid genes, termed mobile colistin resistance-1 (mcr-1) and mobile colistin resistance-2 (mcr-2), are associated with resistance to colistin in Escherichia coli (E. coli). These mcr genes result in a range of protein modifications contributing to colistin resistance. This study aims to discern the proteomic characteristics of E. coli-carrying mcr-1 and mcr-2 genes. Furthermore, it evaluates the expression levels of various proteins under different conditions (with and without colistin). Methods: Plasmid extraction was performed using an alkaline lysis-based plasmid extraction kit, whereas polymerase chain reaction was used to detect the presence of mcr-1 and mcr-2 plasmids. The E. coli DH5α strain served as the competent cell for accepting and transforming mcr-1 and mcr-2 plasmids. We assessed proteomic alterations in the E. coli DH5α strain both with and without colistin in the growth medium. Proteomic data were analysed using mass spectrometry. Results: The findings revealed significant protein changes in the E. coli DH5α strain following cloning of mcr-1 and mcr-2 plasmids. Of the 20 proteins in the DH5α strain, expression in 8 was suppressed following transformation. In the presence of colistin in the culture medium, 39 new proteins were expressed following transformation with mcr-1 and mcr-2 plasmids. The proteins with altered expression play various roles. Conclusion: The results of this study highlight numerous protein alterations in E. coli resulting from mcr-1 and mcr-2-mediated resistance to colistin. This understanding can shed light on the resistance mechanism. Additionally, the proteomic variations observed in the presence and absence of colistin might indicate potential adverse effects of indiscriminate antibiotic exposure on treatment efficacy and heightened pathogenicity of microorganisms.
MeSH term(s)	Colistin/pharmacology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Proteome ; Proteomics ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Cloning, Molecular
Chemical Substances	Colistin (Z67X93HJG1) ; Proteome ; Escherichia coli Proteins ; Anti-Bacterial Agents
Language	English
Publishing date	2023-12-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2710046-7
ISSN	2213-7173 ; 2213-7173
ISSN (online)	2213-7173
ISSN	2213-7173
DOI	10.1016/j.jgar.2023.12.018
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Article ; Online: Current Advances in DNA Methylation Analysis Methods.

Khodadadi, Ehsan / Fahmideh, Leila / Khodadadi, Ehsaneh / Dao, Sounkalo / Yousefi, Mehdi / Taghizadeh, Sepehr / Asgharzadeh, Mohammad / Yousefi, Bahman / Kafil, Hossein Samadi

BioMed research international

2021 Volume 2021, Page(s) 8827516

Abstract: DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the ... ...

Abstract	DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following the use of microarray hybridization technology. The new generation of sequencing platforms now allows the preparation of genomic maps of DNA methylation at the single-open level. This review includes the majority of methods available to date, introducing the most widely used methods, the bisulfite treatment, biological identification, and chemical cutting along with their advantages and disadvantages. The techniques are then scrutinized according to their robustness, high throughput capabilities, and cost.
MeSH term(s)	DNA Methylation ; Epigenesis, Genetic ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; Sulfites/chemistry
Chemical Substances	Sulfites ; hydrogen sulfite (OJ9787WBLU)
Language	English
Publishing date	2021-03-20
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2021/8827516
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Article ; Online: Comparing proteome changes involved in biofilm formation by Streptococcus mutans after exposure to sucrose and starch.

Rezaei, Tohid / Kamounah, Fadhil S / Khodadadi, Ehsaneh / Mehramouz, Bahareh / Gholizadeh, Pourya / Yousefi, Leila / Ganbarov, Khudaverdi / Ghotaslou, Reza / Yousefi, Mehdi / Asgharzadeh, Mohammad / Eslami, Hosein / Taghizadeh, Sepehr / Pirzadeh, Tahereh / Kafil, Hossein Samadi

Biotechnology and applied biochemistry

2023 Volume 70, Issue 3, Page(s) 1320–1331

Abstract: Streptococcus mutans is a main organism of tooth infections including tooth decay and periodontitis. The aim of this study was to assess the influence of sucrose and starch on biofilm formation and proteome profile of S. mutans ATCC 35668 strain. The ... ...

Abstract	Streptococcus mutans is a main organism of tooth infections including tooth decay and periodontitis. The aim of this study was to assess the influence of sucrose and starch on biofilm formation and proteome profile of S. mutans ATCC 35668 strain. The biofilm formation was assessed by microtiter plating method. Changes in bacterial proteins after exposure to sucrose and starch carbohydrates were analyzed using matrix-assisted laser desorption/ionization mass spectrometry. The biofilm formation of S. mutans was increased to 391.76% in 1% sucrose concentration, 165.76% in 1% starch, and 264.27% in the 0.5% sucrose plus 0.5% starch in comparison to biofilm formation in the media without sugars. The abundance of glutamines, adenylate kinase, and 50S ribosomal protein L29 was increased under exposure to sucrose. Upregulation of lactate utilization protein C, 5-hydroxybenzimidazole synthase BzaA, and 50S ribosomal protein L16 was formed under starch exposure. Ribosome-recycling factor, peptide chain release factor 1, and peptide methionine sulfoxide reductase MsrB were upregulated under exposure to sucrose in combination with starch. The results demonstrated that the carbohydrates increase microbial pathogenicity. In addition, sucrose and starch carbohydrates can induce biofilm formation of S. mutans via various mechanisms such as changes in the expression of special proteins.
MeSH term(s)	Starch/pharmacology ; Starch/metabolism ; Sucrose/pharmacology ; Sucrose/metabolism ; Streptococcus mutans ; Proteome/metabolism ; Biofilms
Chemical Substances	Starch (9005-25-8) ; Sucrose (57-50-1) ; Proteome
Language	English
Publishing date	2023-01-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	883433-7
ISSN	1470-8744 ; 0885-4513
ISSN (online)	1470-8744
ISSN	0885-4513
DOI	10.1002/bab.2442
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Article ; Online: A critical review of novel antibiotic resistance prevention approaches with a focus on postbiotics.

Ozma, Mahdi Asghari / Moaddab, Seyyed Reza / Hosseini, Hedayat / Khodadadi, Ehsaneh / Ghotaslou, Reza / Asgharzadeh, Mohammad / Abbasi, Amin / Kamounah, Fadhil S / Aghebati Maleki, Leili / Ganbarov, Khudaverdi / Samadi Kafil, Hossein

Critical reviews in food science and nutrition

2023 , Page(s) 1–19

Abstract: Antibiotic resistance is a significant public health issue, causing illnesses that were once easily treatable with antibiotics to develop into dangerous infections, leading to substantial disability and even death. To help fight this growing threat, ... ...

Abstract	Antibiotic resistance is a significant public health issue, causing illnesses that were once easily treatable with antibiotics to develop into dangerous infections, leading to substantial disability and even death. To help fight this growing threat, scientists are developing new methods and techniques that play a crucial role in treating infections and preventing the inappropriate use of antibiotics. These effective therapeutic methods include phage therapies, quorum-sensing inhibitors, immunotherapeutics, predatory bacteria, antimicrobial adjuvants, haemofiltration, nanoantibiotics, microbiota transplantation, plant-derived antimicrobials, RNA therapy, vaccine development, and probiotics. As a result of the activity of probiotics in the intestine, compounds derived from the structure and metabolism of these bacteria are obtained, called postbiotics, which include multiple agents with various therapeutic applications, especially antimicrobial effects, by using different mechanisms. These compounds have been chosen in particular because they don't promote the spread of antibiotic resistance and don't include substances that can increase antibiotic resistance. This manuscript provides an overview of the novel approaches to preventing antibiotic resistance with emphasis on the various postbiotic metabolites derived from the gut beneficial microbes, their activities, recent related progressions in the food and medical fields, as well as concisely giving an insight into the new concept of postbiotics as "hyperpostbiotic".
Language	English
Publishing date	2023-05-19
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1037504-1
ISSN	1549-7852 ; 1040-8398
ISSN (online)	1549-7852
ISSN	1040-8398
DOI	10.1080/10408398.2023.2214818
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Article ; Online: Current Advances in DNA Methylation Analysis Methods

Ehsan Khodadadi / Leila Fahmideh / Ehsaneh Khodadadi / Sounkalo Dao / Mehdi Yousefi / Sepehr Taghizadeh / Mohammad Asgharzadeh / Bahman Yousefi / Hossein Samadi Kafil

BioMed Research International, Vol

2021 Volume 2021

Abstract	DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following the use of microarray hybridization technology. The new generation of sequencing platforms now allows the preparation of genomic maps of DNA methylation at the single-open level. This review includes the majority of methods available to date, introducing the most widely used methods, the bisulfite treatment, biological identification, and chemical cutting along with their advantages and disadvantages. The techniques are then scrutinized according to their robustness, high throughput capabilities, and cost.
Keywords	Medicine ; R
Subject code	310
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
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Article: A Comprehensive Study on the Antimicrobial Properties of Resveratrol as an Alternative Therapy.

Abedini, Ehsan / Khodadadi, Ehsaneh / Zeinalzadeh, Elham / Moaddab, Seyyed Reza / Asgharzadeh, Mohammad / Mehramouz, Bahareh / Dao, Sounkalo / Samadi Kafil, Hossein

Evidence-based complementary and alternative medicine : eCAM

2021 Volume 2021, Page(s) 8866311

Abstract: Resveratrol is a polyphenolic antioxidant whose possible health benefits include anticarcinogenic, antiaging, and antimicrobial properties that have gained significant attention. The compound is well accepted by individuals and has been commonly used as ... ...

Abstract	Resveratrol is a polyphenolic antioxidant whose possible health benefits include anticarcinogenic, antiaging, and antimicrobial properties that have gained significant attention. The compound is well accepted by individuals and has been commonly used as a nutraceutical in recent decades. Its widespread usage makes it essential to study as a single agent as well as in combination with traditional prescription antibiotics as regards to antimicrobial properties. Resveratrol demonstrates the action of antimicrobials against a remarkable bacterial diversity, viruses, and fungus. This report explains resveratrol as an all-natural antimicrobial representative. It may modify the bacterial virulence qualities resulting in decreased toxic substance production, biofilm inhibition, motility reduction, and quorum sensing disturbance. Moreover, in conjunction with standard antibiotics, resveratrol improves aminoglycoside efficacy versus
Language	English
Publishing date	2021-03-16
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2171158-6
ISSN	1741-4288 ; 1741-427X
ISSN (online)	1741-4288
ISSN	1741-427X
DOI	10.1155/2021/8866311
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Article ; Online: Bacterial Proteomics and its Application in Pathogenesis Studies.

Ozma, Mahdi Asghari / Khodadadi, Ehsaneh / Rezaee, Mohammad Ahangarzadeh / Asgharzadeh, Mohammad / Aghazadeh, Mohammad / Zeinalzadeh, Elham / Ganbarov, Khudaverdi / Kafil, Hossein Samadi

Current pharmaceutical biotechnology

2021 Volume 23, Issue 10, Page(s) 1245–1256

Abstract: Bacteria build their structures by implementing several macromolecules such as proteins, polysaccharides, phospholipids, and nucleic acids, which preserve their lives and play an essential role in their pathogenesis. There are two genomic and proteomic ... ...

Abstract	Bacteria build their structures by implementing several macromolecules such as proteins, polysaccharides, phospholipids, and nucleic acids, which preserve their lives and play an essential role in their pathogenesis. There are two genomic and proteomic methods to study various macromolecules of bacteria, which are complementary methods and provide comprehensive information. Proteomic approaches are used to identify proteins and their cell applications. Furthermore, macromolecules are utilized to study bacteria's structures and functions. These proteinbased methods provide comprehensive information about the cells, such as the external structures, internal compositions, post-translational modifications, and mechanisms of particular actions, including biofilm formation, antibiotic resistance, and adaptation to the environment, promoting bacterial pathogenesis. These methods use various devices such as MALDI-TOF MS, LC-MS, and two-dimensional electrophoresis, which are valuable tools for studying different structural and functional proteins of the bacteria and their mechanisms of pathogenesis, causing rapid, easy, and accurate diagnosis of the infections.
MeSH term(s)	Bacteria ; Drug Resistance, Microbial ; Proteomics/methods ; Tandem Mass Spectrometry
Language	English
Publishing date	2021-09-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2132197-8
ISSN	1873-4316 ; 1389-2010
ISSN (online)	1873-4316
ISSN	1389-2010
DOI	10.2174/1389201022666210908153234
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