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Article ; Online: In-silico investigation of antibacterial herbal compounds in order to find new antibiotic against Staphylococcus aureus and its resistant subtypes

Fatemeh Abedi Dorcheh / Negar Balmeh / Sahar Sanjari

Informatics in Medicine Unlocked, Vol 28, Iss , Pp 100843- (2022)

2022

Abstract: Introduction: Staphylococcus aureus can cause different diseases. S. aureus resistant strains such as methicillin-resistant strains recently have become a big problem in hospital infections. These strains respond to some current antibiotics, but these ... ...

Abstract	Introduction: Staphylococcus aureus can cause different diseases. S. aureus resistant strains such as methicillin-resistant strains recently have become a big problem in hospital infections. These strains respond to some current antibiotics, but these effects may not last long due to the constant mutations of these bacteria. Therefore, research on other factors, such as herbal compounds, may play a crucial role in inhibition. Hence, in this research, we have tried to find herbal efficient compounds to inhibit S. aureus and Methicillin-Resistant Staphylococcus aureus (MRSA) important proteins and infections. Material and methods: 2000 compounds from 87 medicinal plants were collected from related articles. S. aureus and MRSA important protein structures were obtained from the RCSB PDB database. In addition, the PubChem database was used to achieve the structure of the compounds. Molecular docking analysis of compounds was performed against CrtM(diapophytoene synthase), DNA gyrase, SarA(Staphylococcal Accessory Regulator A), and PBP2a(penicillin-binding protein 2A) proteins which were the most noticeable proteins causing S. aureus and MRSA infections, and finally, the features of top compounds were gained from different databases. Result: The results showed that Berbamine, Galangin, Hypericin, Protohypericin, Pseudohypericin, and Berberine were the best compounds with high binding affinity to each four mentioned proteins with no or minimum side effect. Berbamine had the highest binding affinity to all four proteins. Conclusion: According to the results Mahonia aquifolium, Beberis Vulgaris, Chelidonium majus, Rheum Ribes, Hypericum perforatum, and Hibiscus sabdariffa had the best active compounds against S. aureus important proteins. These medicinal compounds may be effective as antibiotics against S. aureus resistant subtypes because they have no or minimum side effects and are beneficial for health. If it is proven experimentally that the aforementioned herbal compounds are effective on S. aureus, these compounds ...
Keywords	Staphylococcus aureus ; MRSA ; Herbal compounds ; Bioinformatics ; Molecular docking analysis ; Drug discovery ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	540 ; 500
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigation of the mutated antimicrobial peptides to inhibit ACE2, TMPRSS2 and GRP78 receptors of SARS-CoV-2 and angiotensin II type 1 receptor (AT1R) as well as controlling COVID-19 disease.

Abedi Dorcheh, Fatemeh / Balmeh, Negar / Hejazi, Seyed Hossein / Allahyari Fard, Najaf

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–24

Abstract: SARS-CoV-2 is a global problem nowadays. Based on studies, some human receptors are involved in binding to SARS-CoV-2. Thus, the inhibition of these receptors can be effective in the treatment of Covid-19. Because of the proven benefits of antimicrobial ... ...

Abstract	SARS-CoV-2 is a global problem nowadays. Based on studies, some human receptors are involved in binding to SARS-CoV-2. Thus, the inhibition of these receptors can be effective in the treatment of Covid-19. Because of the proven benefits of antimicrobial peptides (AMPs) and the side effects of chemical drugs, they can be known as an alternative to recent medicines. RCSB PDB to obtain PDB id, StraPep and PhytAMP to acquire Bio-AMPs information and 3-D structure, and AlgPred, Toxinpred, TargetAntiAngio, IL-4pred, IL-6pred, ACPred and Hemopred databases were used to find the best score peptide features. HADDOCK 2.2 was used for molecular docking analysis, and UCSF Chimera software version 1.15, SWISS-MODEL and BIOVIA Discovery Studio Visualizer4.5 were used for mutation and structure modeling. Furthermore, MD simulation results were achieved from GROMACS 4.6.5. Based on the obtained results, the Moricin peptide was found to have the best affinity for ACE2. Moreover, Bacteriocin leucocin-A had the highest affinity for GRP78, Cathelicidin-6 had the best affinity for AT1R, and Bacteriocin PlnK had the best binding affinity for TMPRSS2. Additionally, Bacteriocin glycocin F, Bacteriocin lactococcin-G subunit beta and Cathelicidin-6 peptides were the most common compounds among the four receptors. However, these peptides also have some side effects. Consequently, the mutation eliminated the side effects, and MD simulation results indicated that the mutation proved the result of the docking analysis. The effect of AMPs on ACE2, GRP78, TMPRSS2 and AT1R receptors can be a novel treatment for Covid-19.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-12-18
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2292307
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Article: Manipulated bio antimicrobial peptides from probiotic bacteria as proposed drugs for COVID-19 disease.

Balmeh, Negar / Mahmoudi, Samira / Fard, Najaf Allahyari

Informatics in medicine unlocked

2021 Volume 23, Page(s) 100515

Abstract: Coronavirus disease 19 (COVID-19) is the latest pandemic resulted from the coronavirus family. Due to the high prevalence of this disease, its high mortality rate, and the lack of effective treatment, the need for affordable and accessible drugs is one ... ...

Abstract	Coronavirus disease 19 (COVID-19) is the latest pandemic resulted from the coronavirus family. Due to the high prevalence of this disease, its high mortality rate, and the lack of effective treatment, the need for affordable and accessible drugs is one of the main challenges in this regard. It has been proved that RdRp, 3CL, Spike, and Nucleocapsid are the most important viral proteins playing vital roles in the processes of proliferation and infection. Therefore, we started studying a wide range of bio-peptides and then conducted molecular docking analyses to investigate their binding affinity for the inhibition of these proteins. After obtaining the best bio-peptides with the highest affinity scores, they were examined for further study and then manipulated to eliminate their side effects. Additionally, the molecular dynamic simulation was performed to validate the structure and interaction stability. The results of this study reveal that glycocin F from
Language	English
Publishing date	2021-01-12
Publishing country	England
Document type	Journal Article
ISSN	2352-9148
ISSN	2352-9148
DOI	10.1016/j.imu.2021.100515
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Computer-aided peptide-based drug design for inositol-requiring enzyme 1

Alireza Ghanbari / Amir Norouzy / Negar Balmeh / Najaf Allahyari Fard / Mohammad Amin Moosavi

Basic & Clinical Cancer Research, Vol 14, Iss

2023 Volume 4

Abstract: Inositol-requiring enzyme 1 (IRE1), an endoplasmic reticulum (ER) transmembrane protein with both kinase and endoribonuclease activities, plays an essential role during ER stress and its subsequent unfolded protein response (UPR). Recent evidence shows ... ...

Abstract	Inositol-requiring enzyme 1 (IRE1), an endoplasmic reticulum (ER) transmembrane protein with both kinase and endoribonuclease activities, plays an essential role during ER stress and its subsequent unfolded protein response (UPR). Recent evidence shows IRE1 signaling contributes to tumorigenesis and cancer progression, pointing to the therapeutic importance of this conserved arm of the UPR. Here, we employed different computational tools to design and predict short peptides with the capability of disrupting IRE1 dimerization/oligomerization, as a strategy for inhibiting its Kinase and RNase activities. A mutation-based peptide library was constructed using mCSM-PPI2 and OSPREY 3.0. The molecular interaction analyses between the designed peptides and IRE1 protein were conducted using the HADDOCK 2.2 online server, followed with molecular dynamics analysis by the GROMACS 2020 package. We then selected short peptide candidates that exhibited high affinity and best predicted physicochemical properties in complex with IRE1. Finally, online servers, such as ToxinPred and AllerTop, were used to identify the best peptide candidates that showed no significant allergenic or cytotoxic properties. These rational designed peptides with the capability of binding to IRE1 oligomerization domain can be considered as potential drug candidates for disrupting IRE1 activity in cancer and related diseases, pending for further validation by in silico and experimental studies.
Keywords	Bioinformatics ; cancer ; drug design ; inositol-requiring enzyme 1 ; short peptides ; Medicine ; R
Subject code	571 ; 540
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Tehran University of Medical Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular docking analysis of H1 and H2 antihistamines groups with l-asparaginase II for reducing allergenicity; an in silico approach

Masoumeh Massah / Negar Balmeh / Kiomars Goodarzi / Najaf Allahyari Fard

Informatics in Medicine Unlocked, Vol 28, Iss , Pp 100865- (2022)

2022

Abstract: Introduction: Cancer is a pervasive disease with different types spreading widely worldwide. Acute lymphoblastic leukemia (ALL) is the bone marrow lymphocyte cancer related to the malignancy of B or T lymphoblast white blood cells. This disease has a ... ...

Abstract	Introduction: Cancer is a pervasive disease with different types spreading widely worldwide. Acute lymphoblastic leukemia (ALL) is the bone marrow lymphocyte cancer related to the malignancy of B or T lymphoblast white blood cells. This disease has a rapid progression and can be fatal within several months without treatment. The use of l-asparaginase II is the most important treatment with specific side effects that can provoke allergic reactions, such as anaphylaxis. The purpose of this study was to evaluate the possibility of using l-asparaginase II and antihistamine without the antihistamine interfering with the l-asparaginase II ligand. Methods: The UniProt and RCSB PDB databases were used to access ansB gene and l-asparaginase crystallographic structure information. Allergome, Allermatch, and SDAP databases were used to examine epitope's allergenicity and predict protein allergenicity. Using DrugBank and ChEMBL, 47H1 and 8H2 approved antihistamines were achieved. The 3D structures were obtained from the PubChem database. Also, molecular docking analysis was performed in the Molegro 6.0 software. Results: The primary epitope responsible for the allergenicity of the l-asparaginase II enzyme with two possible areas of allergenic was introduced. The results showed that among all H1 and H2 antihistamines, Betazole (−64.0225 kcal/mol) had a better binding affinity than other antihistamines to the l-asparaginase II enzyme (−64.5873 kcal/mol). Other antihistamines may interfere with l-asparaginase 2-asparagine activity. Conclusion: It can be stated that drugs with higher binding affinity than asparagine can have a negative effect on l-asparaginase II enzyme function. Betazole was identified as a suitable drug for allergy control with an appropriate binding affinity to asparagine, and therefore, it can have a minimal drug interaction with the l-asparaginase II enzyme.
Keywords	Acute lymphoblastic leukemia ; l-asparaginase II ; Betazole ; Molecular docking analysis ; Allergy ; Computer applications to medicine. Medical informatics ; R858-859.7
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Manipulated bio antimicrobial peptides from probiotic bacteria as proposed drugs for COVID-19 disease

Negar Balmeh / Samira Mahmoudi / Najaf Allahyari Fard

Informatics in Medicine Unlocked, Vol 23, Iss , Pp 100515- (2021)

2021

Abstract	Coronavirus disease 19 (COVID-19) is the latest pandemic resulted from the coronavirus family. Due to the high prevalence of this disease, its high mortality rate, and the lack of effective treatment, the need for affordable and accessible drugs is one of the main challenges in this regard. It has been proved that RdRp, 3CL, Spike, and Nucleocapsid are the most important viral proteins playing vital roles in the processes of proliferation and infection. Therefore, we started studying a wide range of bio-peptides and then conducted molecular docking analyses to investigate their binding affinity for the inhibition of these proteins. After obtaining the best bio-peptides with the highest affinity scores, they were examined for further study and then manipulated to eliminate their side effects. Additionally, the molecular dynamic simulation was performed to validate the structure and interaction stability. The results of this study reveal that glycocin F from Lactococcus lactis and lactococcine G from Lactobacillus plantarum had the high affinities to bind to the viral proteins, and the manipulation of their sequence also led to the side effects’ elimination. In addition, in some cases, their affinities to attach the SARS-CoV-2 proteins have increased. It seems that these two drugs which were discovered and designed, are optimal for treating the COVID-19 infection. However, experimental and pre-clinical studies are necessary to assay their therapeutic effects.
Keywords	COVID-19 ; Probiotic bacteria ; Drug discovery ; Bio antimicrobial peptides ; Bioinformatics ; Drug designing ; Computer applications to medicine. Medical informatics ; R858-859.7
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors.

Balmeh, Negar / Mahmoudi, Samira / Mohammadi, Niloofar / Karabedianhajiabadi, Anasik

Informatics in medicine unlocked

2020 Volume 20, Page(s) 100407

Abstract: The SARS-CoV-2 causes severe pulmonary infectious disease with an exponential spread-ability. In the present research, we have tried to look into the molecular cause of disease, dealing with the development and spread of the coronavirus disease 2019 ( ... ...

Abstract	The SARS-CoV-2 causes severe pulmonary infectious disease with an exponential spread-ability. In the present research, we have tried to look into the molecular cause of disease, dealing with the development and spread of the coronavirus disease 2019 (COVID-19). Therefore, different approaches have investigated against disease development and infection in this research; First, We identified hsa-miR-1307-3p out of 1872 pooled microRNAs, as the best miRNA, with the highest affinity to SARS-CoV-2 genome and its related cell signaling pathways. Second, the findings presented that this miRNA had a considerable role in PI3K/Act, endocytosis, and type 2 diabetes, moreover, it may play a critical role in the prevention of GRP78 production and the virus entering, proliferation and development. Third, nearly 1033 medicinal herbal compounds were collected and docked with ACE2, TMPRSS2, GRP78, and AT1R receptors, which were the most noticeable receptors in causing the COVID-19. Among them, there were three common compounds including berbamine, hypericin, and hesperidin, which were more effective and appropriate to prevent the COVID-19 infection. Also, it was revealed some of these chemical compounds which had a greater affinity for AT1R receptor inhibitors can be suitable therapeutic targets for inhibiting AT1R and preventing the adverse side effects of this receptor. According to the result, clinical assessment of these three herbal compounds and hsa-miR-1307-3p may have significant outcomes for the prevention, control, and treatment of COVID-19 infection.
Keywords	covid19
Language	English
Publishing date	2020-08-07
Publishing country	England
Document type	Journal Article
ISSN	2352-9148
ISSN	2352-9148
DOI	10.1016/j.imu.2020.100407
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Novel Drug Discovery to Combat COVID-19 by Repressing Important Virus Proteins Involved in Pathogenesis Using Medicinal Herbal Compounds.

Mahmoudi, Samira / Balmeh, Negar / Mohammadi, Niloofar / Sadeghian-Rizi, Tahereh

Avicenna journal of medical biotechnology

2021 Volume 13, Issue 3, Page(s) 107–115

Abstract: Background: The cause of COVID-19 global pandemic is SARS-CoV-2. Given the outbreak of this disease, it is so important to find a treatment. One strategy to cope with COVID-19 is to use the active ingredients of medicinal plants. In this study, the ... ...

Abstract	Background: The cause of COVID-19 global pandemic is SARS-CoV-2. Given the outbreak of this disease, it is so important to find a treatment. One strategy to cope with COVID-19 is to use the active ingredients of medicinal plants. In this study, the effect of active substances was surveyed in inhibiting four important druggable targets, including S protein, 3CLpro, RdRp, and N protein. RdRp controls the replication of SARS-CoV-2 and is crucial for its life cycle. 3CLpro is the main protease of the virus and could be another therapeutic target. Moreover, N protein and S protein are responsible for SARS-CoV-2 assembly and attaching, respectively. Methods: The 3D structures of herbal active ingredients were prepared and docked with the mentioned SARS-CoV-2 proteins to obtain their affinity. Then, available antiviral drugs introduced in other investigations were docked using similar tools and compared with the results of this study. Finally, other properties of natural compounds were uncovered for drug designing. Results: The outcomes of the study revealed that Linarin, Amentoflavone, (-)-Catechin Gallate and Hypericin from Conclusion: In addition to having high affinity, these herb active ingredients have antioxidant, vasoprotective, anticarcinogenic, and antiviral properties. Therefore, they can be used as extremely safe therapeutic compounds in drug design studies to control COVID-19.
Language	English
Publishing date	2021-08-17
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2520683-7
ISSN	2008-4625 ; 2008-2835
ISSN (online)	2008-4625
ISSN	2008-2835
DOI	10.18502/ajmb.v13i3.6370
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors

Negar Balmeh / Samira Mahmoudi / Niloofar Mohammadi / Anasik Karabedianhajiabadi

Informatics in Medicine Unlocked, Vol 20, Iss , Pp 100407- (2020)

2020

Abstract	The SARS-CoV-2 causes severe pulmonary infectious disease with an exponential spread-ability. In the present research, we have tried to look into the molecular cause of disease, dealing with the development and spread of the coronavirus disease 2019 (COVID-19). Therefore, different approaches have investigated against disease development and infection in this research; First, We identified hsa-miR-1307-3p out of 1872 pooled microRNAs, as the best miRNA, with the highest affinity to SARS-CoV-2 genome and its related cell signaling pathways. Second, the findings presented that this miRNA had a considerable role in PI3K/Act, endocytosis, and type 2 diabetes, moreover, it may play a critical role in the prevention of GRP78 production and the virus entering, proliferation and development. Third, nearly 1033 medicinal herbal compounds were collected and docked with ACE2, TMPRSS2, GRP78, and AT1R receptors, which were the most noticeable receptors in causing the COVID-19. Among them, there were three common compounds including berbamine, hypericin, and hesperidin, which were more effective and appropriate to prevent the COVID-19 infection. Also, it was revealed some of these chemical compounds which had a greater affinity for AT1R receptor inhibitors can be suitable therapeutic targets for inhibiting AT1R and preventing the adverse side effects of this receptor. According to the result, clinical assessment of these three herbal compounds and hsa-miR-1307-3p may have significant outcomes for the prevention, control, and treatment of COVID-19 infection.
Keywords	COVID-19 receptor blockers ; SARS-CoV-2 ; miRNAs ; Medicinal herbal compounds ; Bioinformatics ; Therapeutic targets ; Computer applications to medicine. Medical informatics ; R858-859.7
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors

Balmeh, Negar / Mahmoudi, Samira / Mohammadi, Niloofar / Karabedianhajiabadi, Anasik

Informatics in Medicine Unlocked

2020 Volume 20, Page(s) 100407

Keywords	covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ISSN	2352-9148
DOI	10.1016/j.imu.2020.100407
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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