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Article ; Online: Missense mutations in spike protein of SARS-CoV-2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor.

Mahmood, Tousif Bin / Hossan, Mohammad Imran / Mahmud, Shafi / Shimu, Mst Sharmin Sultana / Alam, Md Jahidul / Bhuyan, Md Mahfuzur Rahman / Emran, Talha Bin

Immunity, inflammation and disease

2022 Volume 10, Issue 9, Page(s) e683

Abstract: Introduction: Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID-19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ... ...

Abstract	Introduction: Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID-19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. Methods: In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS-CoV-2 delta variant performing different computational analysis. Results: From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. Conclusions: Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS-CoV-2 delta variant.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/genetics ; Humans ; Molecular Docking Simulation ; Mutation, Missense ; Peptidyl-Dipeptidase A/metabolism ; Protein Binding ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Viral Structures/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-08-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2740382-8
ISSN	2050-4527 ; 2050-4527
ISSN (online)	2050-4527
ISSN	2050-4527
DOI	10.1002/iid3.683
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia.

Mahmood, Tousif Bin / Saha, Ayan / Hossan, Mohammad Imran / Mizan, Shagufta / Arman, S M Abu Sufian / Chowdhury, Afrin Sultana

Current research in microbial sciences

2021 Volume 2, Page(s) 100065

Abstract: Counts for SARS-CoV-2 associated infections and fatalities are on the rise globally even in regions which contained the spread momentarily. The pattern of infections has been found to be controlled by the distinctive selection pressures exerted by ... ...

Abstract	Counts for SARS-CoV-2 associated infections and fatalities are on the rise globally even in regions which contained the spread momentarily. The pattern of infections has been found to be controlled by the distinctive selection pressures exerted by fluctuating environmental nature and hosts. A total of 410 whole-genome sequences submitted by the South Asian countries were retrieved from the GISAID database and analyzed to assess the impact and pattern of mutations in this region. Most common and frequent mutations in the South Asian countries are 241C >
Language	English
Publishing date	2021-08-24
Publishing country	Netherlands
Document type	Journal Article
ISSN	2666-5174
ISSN (online)	2666-5174
DOI	10.1016/j.crmicr.2021.100065
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Evaluation of the susceptibility and fatality of lung cancer patients towards the COVID-19 infection: A systemic approach through analyzing the ACE2, CXCL10 and their co-expressed genes.

Mahmood, Tousif Bin / Chowdhury, Afrin Sultana / Hossain, Mohammad Uzzal / Hasan, Mehedee / Mizan, Shagufta / Aakil, Md Mezbah-Ul-Islam / Hossan, Mohammad Imran

Current research in microbial sciences

2021 Volume 2, Page(s) 100022

Abstract: Coronavirus disease-2019 (COVID-19) is a recent world pandemic disease that is caused by a newly discovered strain of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2). Patients with comorbidities are most vulnerable to this disease. ... ...

Abstract	Coronavirus disease-2019 (COVID-19) is a recent world pandemic disease that is caused by a newly discovered strain of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2). Patients with comorbidities are most vulnerable to this disease. Therefore, cancer patients are reported to be more susceptible to COVID-19 infection, particularly lung cancer patients. To evaluate the probable reasons behind the excessive susceptibility and fatality of lung cancer patients to COVID-19 infection, we targeted the two most crucial agents, Angiotensin-converting enzyme 2 (ACE2) and C-X-C motif 10 (CXCL10). ACE2 is a receptor protein that plays a vital role in the entry of SARS-CoV-2 into the host cell and CXCL10 is a cytokine mainly responsible for the lung cell damage involving in a cytokine storm. By using the UALCAN and GEPIA2 databases, we observed that ACE2 and CXCL10 are mostly overexpressed in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). We then identified the functional significance of ACE2 and CXCL10 in lung cancer development by determining the genetic alteration frequency in their amino acid sequences using the cBioPortal web portal. Lastly, we did the pathological assessment of targeted genes using the PANTHER database. Here, we found that ACE2 and CXCL10 along with their commonly co-expressed genes are involved respectively in the binding activity and immune responses in case of lung cancer and COVID-19 infection. Finally, based on this systemic analysis, we concluded that ACE2 and CXCL10 are two possible biomarkers responsible for the higher susceptibility and fatality of lung cancer patients towards the COVID-19.
Language	English
Publishing date	2021-02-09
Publishing country	Netherlands
Document type	Journal Article
ISSN	2666-5174
ISSN (online)	2666-5174
DOI	10.1016/j.crmicr.2021.100022
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Immunoinformatics aided-design of novel multi-epitope based peptide vaccine against Hendra henipavirus through proteome exploration

Mohammad Imran Hossan / Afrin Sultana Chowdhury / Mohammad Uzzal Hossain / Md Arif Khan / Tousif Bin Mahmood / Shagufta Mizan

Informatics in Medicine Unlocked, Vol 25, Iss , Pp 100678- (2021)

2021

Abstract: Hendra henipavirus (HeV) is an emerging zoonotic bat-borne paramyxovirus that is capable of causing severe public health complications in humans. It promotes both respiratory and neurological disorders in humans as well as in horses. Currently, there are ...

Abstract	Hendra henipavirus (HeV) is an emerging zoonotic bat-borne paramyxovirus that is capable of causing severe public health complications in humans. It promotes both respiratory and neurological disorders in humans as well as in horses. Currently, there are no therapeutics or vaccines available against the deadly HeV. We aimed to design a potent and novel prophylactic chimeric vaccine against HeV through an immunoinformatics approach. A proteome-wide screening was performed to identify the antigenic proteins followed by cytotoxic T-lymphocyte (CTL), linear B-lymphocyte (LBL), and helper T-lymphocyte (HTL) epitopes identification, conservancy analysis, population coverage, molecular docking and in silico simulation of both cellular and humoral immune response. A total of 17 T and B-cell epitopes (7 CTL, 5 HTL, and 5 LBL) were identified for vaccine design from the highest antigenic proteins, namely glycoprotein, fusion protein, and nucleoprotein. The proposed vaccine was found to be highly immunogenic, antigenic, non-toxic, non-allergenic, and stable, and could be efficient against HeV. Moreover, disulfide engineering and codon adaptation were employed to escalate stability and efficient expression in E. coli. Molecular docking and dynamics simulation analysis revealed the stability and strong affinity of the proposed vaccine towards the TL4 receptor. The immune simulation data confirmed elevated response of both B and T-cells against the vaccine subunit. The designed vaccine according to our in silico data is potent enough to elucidate substantial immune response and therefore can be considered as a potential immunogenic agent to control HeV infection. However, further experimental validation and clinical trials are required to confirm its efficacy and safety.
Keywords	Hendra henipavirus ; Multi-epitope vaccine ; Immunoinformatics ; Dynamics simulation ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	006
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 ; Online: A multi-omics approach to reveal the key evidence of GDF10 as a novel therapeutic biomarker for breast cancer

Ferdausur Rahman / Tousif Bin Mahmood / Al Amin / Rahat Alam / Jannatul Ferdous Jharna / Abdus Samad / Foysal Ahammad

Informatics in Medicine Unlocked, Vol 21, Iss , Pp 100463- (2020)

2020

Abstract: Breast cancer (BC) is the most common type of invasive cancer diagnosed in women. It is the second leading cause of death from cancer and the utmost important medical concern women face today. Growth differentiation factor 10 (GDF10) is a member of the ... ...

Abstract	Breast cancer (BC) is the most common type of invasive cancer diagnosed in women. It is the second leading cause of death from cancer and the utmost important medical concern women face today. Growth differentiation factor 10 (GDF10) is a member of the transforming growth factor β (TGF-β) superfamily and has been found to play a central role during the growth and differentiation of developing tissues. Recent studies have demonstrated the linkage between GDF10 and different types of cancer. But the relation of GDF10 expression in developing BC has not been established with concrete evidence. Therefore, we performed a multi-omics analysis to evaluate the potentiality of GDF10 as a therapeutic biomarker for human BC. We analyzed the mRNA expression patterns of GDF10 in BC subtypes using Oncomine, GEPIA2, immunohistochemistry, and UALCAN databases. Resultant data obtained from the analysis has provided clear evidence to the downregulation of GDF10 expression in BC subtypes. Additionally, three subsequent missense mutations were identified with a frequency of 0.62%–2.95% copy number alterations in the GDF10 protein sequence by analyzing 16 BCE studies from the cBioPortal database. Furthermore, the Kaplan-Meier plots revealed a positive correlation between the downregulation of GDF10 and the lower survival rate of the BC patients. The co-expressed genes profile of GDF10 was also associated with BC development. ABCA8 has been identified as the most positively co-expressed gene, which was confirmed by correlation analysis using bc-GenExMiner and UCSC Xena server. We also determined different cancer progression pathways mediated by GDF10 and its co-expressed genes by utilizing the Enrichr database. Cumulatively, the outcome data conclude that the down expression of GDF10 is associated with BC progression and patient's survival, which may serve as a therapeutic biomarker for treating BC.
Keywords	GDF10 ; Breast cancer ; Therapeutic target ; Mutation in GDF10 ; Prognostic rate ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	616
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: Assessment of ACE2, CXCL10 and Their co-expressed Genes: An In-silico Approach to Evaluate the Susceptibility and Fatality of Lung Cancer Patients towards COVID-19 Infection

Mahmood, Tousif Bin / Chowdhury, Afrin Sultana / Hasan, Mehedee / Aakil, Md. Mezbah-Ul-Islam / Hossan, Mohammad Imran

bioRxiv

Abstract: Background: COVID-19 is a recent pandemic that started to spread out worldwide from Wuhan, China. This disease is caused by a newly discovered strain of the coronavirus, namely SARS CoV-2. Lung cancer patients are reported to be more susceptible to COVID- ...

Abstract	Background: COVID-19 is a recent pandemic that started to spread out worldwide from Wuhan, China. This disease is caused by a newly discovered strain of the coronavirus, namely SARS CoV-2. Lung cancer patients are reported to be more susceptible to COVID-19 infection. To evaluate the probable reasons behind the excessive susceptibility and fatality of lung cancer patients to COVID-19 infection, we targeted two most crucial biomarkers of COVID-19, ACE2 and CXCL10. ACE2 plays a vital role in the SARS CoV-2 entry into the host cell while CXCL10 is a cytokine mainly responsible for the lung cell damage involving in a cytokine storm. Methods: Firstly, we used the TIMER, UALCAN and GEPIA2 databases to analyze the expression and correlation of ACE2 and CXCL10 in LUAD and LUSC. After that, using the cBioPortal database, we performed an analytical study to determine the genetic changes in ACE2 and CXCL10 protein sequences that are responsible for lung cancer development. Finally, we analyzed different functional approaches of ACE2, CXCL10 and their co-expressed genes associated with lung cancer and COVID-19 development by using the PANTHER database. Results: Initially, we observed that ACE2 and CXCL10 are mostly overexpressed in LUAD and LUSC. We also found the functional significance of ACE2 and CXCL10 in lung cancer development by determining the genetic alteration frequency in their amino acid sequences. Lastly, by doing the functional assessment of the targeted genes, we identified that ACE2 and CXCL10 along with their commonly co-expressed genes are respectively involved in the binding activity and immune responses in case of lung cancer and COVID-19 infection. Conclusions: Finally, on the basis of this systemic analysis, we came to the conclusion that ACE2 and CXCL10 are possible biomarkers responsible for the higher susceptibility and fatality of lung cancer patients towards the COVID-19.
Keywords	covid19
Language	English
Publishing date	2020-05-27
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.05.27.119610
Database	COVID19

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Article ; Online: Assessment of ACE2, CXCL10 and Their co-expressed Genes: An In-silico Approach to Evaluate the Susceptibility and Fatality of Lung Cancer Patients towards COVID-19 Infection

Mahmood, Tousif Bin / Chowdhury, Afrin Sultana / Hasan, Mehedee / Aakil, Md. Mezbah-Ul-Islam / Hossan, Mohammad Imran

bioRxiv

Abstract: Background COVID-19 is a recent pandemic that started to spread out worldwide from Wuhan, China. This disease is caused by a newly discovered strain of the coronavirus, namely SARS CoV-2. Lung cancer patients are reported to be more susceptible to COVID- ... ...

Abstract	Background COVID-19 is a recent pandemic that started to spread out worldwide from Wuhan, China. This disease is caused by a newly discovered strain of the coronavirus, namely SARS CoV-2. Lung cancer patients are reported to be more susceptible to COVID-19 infection. To evaluate the probable reasons behind the excessive susceptibility and fatality of lung cancer patients to COVID-19 infection, we targeted two most crucial biomarkers of COVID-19, ACE2 and CXCL10. ACE2 plays a vital role in the SARS CoV-2 entry into the host cell while CXCL10 is a cytokine mainly responsible for the lung cell damage involving in a cytokine storm. Methods Firstly, we used the TIMER, UALCAN and GEPIA2 databases to analyze the expression and correlation of ACE2 and CXCL10 in LUAD and LUSC. After that, using the cBioPortal database, we performed an analytical study to determine the genetic changes in ACE2 and CXCL10 protein sequences that are responsible for lung cancer development. Finally, we analyzed different functional approaches of ACE2, CXCL10 and their co-expressed genes associated with lung cancer and COVID-19 development by using the PANTHER database. Results Initially, we observed that ACE2 and CXCL10 are mostly overexpressed in LUAD and LUSC. We also found the functional significance of ACE2 and CXCL10 in lung cancer development by determining the genetic alteration frequency in their amino acid sequences. Lastly, by doing the functional assessment of the targeted genes, we identified that ACE2 and CXCL10 along with their commonly co-expressed genes are respectively involved in the binding activity and immune responses in case of lung cancer and COVID-19 infection. Conclusions Finally, on the basis of this systemic analysis, we came to the conclusion that ACE2 and CXCL10 are possible biomarkers responsible for the higher susceptibility and fatality of lung cancer patients towards the COVID-19.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.05.27.119610
Database	COVID19

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Article ; Online: Identification of pyrrolizidine alkaloids and flavonoid glycosides through HR-LCMS/MS analysis, biological screening, DFT and molecular docking studies on Heliotropium dasycarpum Ledeb.

Mahreen Mukhtar / Muhammad Saleem / Mamona Nazir / Naheed Riaz / Nusrat Shafiq / Hammad Saleem / Saba Tauseef / Saima Khan / Muhammad Ehsan Mazhar / Rasool Bakhsh Tareen / Mian Habib ur Rahman Mahmood / Muhammad Imran Tousif / Suvash Chandra Ojha

Arabian Journal of Chemistry, Vol 16, Iss 5, Pp 104655- (2023)

2023

Abstract: The current study was carried out to reveal the chemical profile and biological screening of Heliotropium dasycarpum Ledeb, as well as the feasibility of its industrial application. Therefore, the methanolic extract (HdM) of H. dasycarpum was divided ... ...

Abstract	The current study was carried out to reveal the chemical profile and biological screening of Heliotropium dasycarpum Ledeb, as well as the feasibility of its industrial application. Therefore, the methanolic extract (HdM) of H. dasycarpum was divided into n-hexane (HdH), ethyl acetate (HdE) and water (HdW) soluble fractions. All the fractions were inactive against acetylcholinesterase (AChE) enzyme, 3T3 and HeLa cell lines, but showed immunomodulatory effect up to 37 %. HdE fraction further displayed significant anti-urease activity with IC50 value of 74.072 ± 0.002, while HdM was found moderate inhibitor (63 %). Thus HdE was subjected to HR-LCMS/MS analysis in positive and negative ionization modes, and a qualitative analytical method with a data mining strategy was utilized. The secondary metabolites were identified by dereplication strategy using molecular networking as a bioinformatics tool, which disclosed the presence of 08 known alkaloids of heliotrine-type (1, 3, 5–10), and 05 (12–16) known flavonoids and flavonoid glycosides along with 03 new (2, 4 and 11) putative pyrrolizidine analogues. DFT simulations of identified compounds were performed using multiple quantum chemical and geometrical descriptors in order to determine their quantitative structure activity relationship. These secondary metabolites were docked against the enzyme urease which substantiated the inhibitory action of pyrrolizidine alkaloids and flavonoid glycosides. Furthermore, ADME analysis provided the base for the use of these compounds for further studies as drug leads and to unveil industrial application of H. dasycarpum in formulating products against gastritis, peptic ulcer and gastric cancer.
Keywords	Heliotropium dasycarpum ; HR-LCMS/MS ; DFT calculations ; Biological screening ; Molecular docking studies ; ADME studies ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Missense mutations in spike protein of SARS-CoV-2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor.

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Article ; Online: A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia.

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Article ; Online: Evaluation of the susceptibility and fatality of lung cancer patients towards the COVID-19 infection: A systemic approach through analyzing the ACE2, CXCL10 and their co-expressed genes.

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Article ; Online: Immunoinformatics aided-design of novel multi-epitope based peptide vaccine against Hendra henipavirus through proteome exploration

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Article ; Online: A multi-omics approach to reveal the key evidence of GDF10 as a novel therapeutic biomarker for breast cancer

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Article ; Online: Assessment of ACE2, CXCL10 and Their co-expressed Genes: An In-silico Approach to Evaluate the Susceptibility and Fatality of Lung Cancer Patients towards COVID-19 Infection

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Article ; Online: Assessment of ACE2, CXCL10 and Their co-expressed Genes: An In-silico Approach to Evaluate the Susceptibility and Fatality of Lung Cancer Patients towards COVID-19 Infection

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Article ; Online: Identification of pyrrolizidine alkaloids and flavonoid glycosides through HR-LCMS/MS analysis, biological screening, DFT and molecular docking studies on Heliotropium dasycarpum Ledeb.

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