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Article ; Online: Evaluation of MERS-CoV Neutralizing Antibodies in Sera Using Live Virus Microneutralization Assay.

Algaissi, Abdullah / Hashem, Anwar M

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2099, Page(s) 107–116

Abstract: The microneutralization (MN) assay is a standard and important technique in virology, immunology, and epidemiology. It is a highly specific and sensitive assay for evaluating virus-specific neutralizing antibodies (nAbs) in human and animal sera. It ... ...

Abstract	The microneutralization (MN) assay is a standard and important technique in virology, immunology, and epidemiology. It is a highly specific and sensitive assay for evaluating virus-specific neutralizing antibodies (nAbs) in human and animal sera. It provides the most precise answer to whether or not an individual or animal has antibodies that can neutralize or inhibit the infectivity of a specific virus strain. However, using live virus-based MN assay might require working under high containment facilities especially when dealing with high-risk pathogens such as the Middle East respiratory syndrome-coronavirus (MERS-CoV). In this chapter, we describe the isolation, amplification, and titration of MERS-CoV, as well as detailed MN assay to measure nAb levels in sera from different mammalian species.
MeSH term(s)	Animals ; Antibodies, Neutralizing/blood ; Chlorocebus aethiops ; Coronavirus Infections/virology ; Cytopathogenic Effect, Viral ; Humans ; Mammals ; Middle East Respiratory Syndrome Coronavirus/immunology ; Neutralization Tests ; Vero Cells
Chemical Substances	Antibodies, Neutralizing
Keywords	covid19
Language	English
Publishing date	2020-01-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0211-9_9
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Article ; Online: HDAC inhibition by

Algaissi, Abdullah / Tabassum, Heena / Khan, Elhan / Dwivedi, Sonam / Lohani, Mohtashim / Khamjan, Nizar A / Farasani, Abdullah / Ahmad, Iffat Zareen

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–19

Abstract: A wide variety of natural products have been widely used in chemoprevention therapy because they have antioxidant, anti-inflammatory, and anticancer activity. In the present study, we shed light on the 5th day germinated sprouts ... ...

Abstract	A wide variety of natural products have been widely used in chemoprevention therapy because they have antioxidant, anti-inflammatory, and anticancer activity. In the present study, we shed light on the 5th day germinated sprouts of
Language	English
Publishing date	2023-11-10
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2279283
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Article ; Online: Exploration of comprehensive marine natural products database against dengue viral non-structural protein 1 using high-throughput computational studies.

Bhat, Basharat Ahmad / Algaissi, Abdullah / Khamjan, Nizar A / Dar, Tanvir Ul Hassan / Dar, Sajad Ahmad / Varadharajan, Venkatramanan / Qasir, Naif A / Lohani, Mohtashim

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–10

Abstract: Dengue virus (DENV) non-structural protein 1 (NS1) is a versatile quasi-protein essential for the multiplication of the virus. This study applied high-throughput virtual screening (HTVS) and molecular dynamics (MD) simulation to detect the potential ... ...

Abstract	Dengue virus (DENV) non-structural protein 1 (NS1) is a versatile quasi-protein essential for the multiplication of the virus. This study applied high-throughput virtual screening (HTVS) and molecular dynamics (MD) simulation to detect the potential marine natural compounds against the NS1 of DENV. The structure of the NS1 protein was retrieved from Protein Data Bank with (PDB ID: 4O6B). Missing residues were added using modeler software. Molecular operating environment (MOE) programme was used to prepare the protein before docking. Virtual screening was performed on PyRx software to identify natural compounds retrieved from Comprehensive Marine Natural Products Database (CMNPD) against the NS1 protein, and best-docked compounds were examined by molecular docking and molecular dynamic (MD) simulation. Out of 31,561 marine compounds, the top 10 compounds showed docking scores lesser than -8.0 kcal/mol. One of the best hit compounds, CMNPD6802, was further analyzed using MD simulation study at 100 nanoseconds and Molecular Mechanics with Generalized Born and Surface Area Solvation (MM/GBSA). Based on its total binding energy, determined using the MM/GBSA approach, CMNPD6802 was ranked first. Its pharmacokinetic properties concerning the target protein NS1 were also evaluated. The results of the MD simulation showed that CMNPD6802 remained in close contact with the protein throughout the activation period, mapped using principal component analysis. These findings suggest that CMNPD6802 could serve as an NS1 inhibitor and may be a potential candidate for treating DENV infections.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2297006
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Article ; Online: COVID-19 and malaria co-infection: a systematic review of clinical outcomes in endemic areas.

Mohamed, Amal H / Eltyeb, Ebtihal / Said, Badria / Eltayeb, Raga / Algaissi, Abdullah / Hober, Didier / Alhazmi, Abdulaziz H

PeerJ

2024 Volume 12, Page(s) e17160

Abstract: Background: COVID-19 and malaria cause significant morbidity and mortality globally. Co-infection of these diseases can worsen their impact on public health. This review aims to synthesize literature on the clinical outcomes of COVID-19 and malaria co- ... ...

Abstract	Background: COVID-19 and malaria cause significant morbidity and mortality globally. Co-infection of these diseases can worsen their impact on public health. This review aims to synthesize literature on the clinical outcomes of COVID-19 and malaria co-infection to develop effective prevention and treatment strategies. Methods: A comprehensive literature search was conducted using MeSH terms and keywords from the start of the COVID-19 pandemic to January 2023. The review included original articles on COVID-19 and malaria co-infection, evaluating their methodological quality and certainty of evidence. It was registered in PROSPERO (CRD42023393562). Results: Out of 1,596 screened articles, 19 met the inclusion criteria. These studies involved 2,810 patients, 618 of whom had COVID-19 and malaria co-infection. Plasmodium falciparum and vivax were identified as causative organisms in six studies. Hospital admission ranged from three to 18 days. Nine studies associated co-infection with severe disease, ICU admission, assisted ventilation, and related complications. One study reported 6% ICU admission, and mortality rates of 3%, 9.4%, and 40.4% were observed in four studies. Estimated crude mortality rates were 10.71 and 5.87 per 1,000 person-days for patients with and without concurrent malaria, respectively. Common co-morbidities included Diabetes mellitus, hypertension, cardiovascular diseases, and respiratory disorders. Conclusion: Most patients with COVID-19 and malaria co-infection experienced short-term hospitalization and mild to moderate disease severity. However, at presentation, co-morbidities and severe malaria were significantly associated with higher mortality or worse clinical outcomes. These findings emphasize the importance of early detection, prompt treatment, and close monitoring of patients with COVID-19 and malaria co-infection.
MeSH term(s)	Humans ; COVID-19/epidemiology ; COVID-19/complications ; COVID-19/mortality ; Coinfection/epidemiology ; Malaria/epidemiology ; SARS-CoV-2 ; Hospitalization/statistics & numerical data ; Comorbidity ; Malaria, Falciparum/epidemiology ; Malaria, Falciparum/complications
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Systematic Review ; Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359 ; 2167-8359
ISSN (online)	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.17160
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Article: Immunoinformatics Strategy to Develop a Novel Universal Multiple Epitope-Based COVID-19 Vaccine.

Khamjan, Nizar A / Lohani, Mohtashim / Khan, Mohammad Faheem / Khan, Saif / Algaissi, Abdullah

Vaccines

2023 Volume 11, Issue 6

Abstract: Currently available COVID vaccines are effective in reducing mortality and severity but do not prevent transmission of the virus or reinfection by the emerging SARS-CoV-2 variants. There is an obvious need for better and longer-lasting effective vaccines ...

Abstract	Currently available COVID vaccines are effective in reducing mortality and severity but do not prevent transmission of the virus or reinfection by the emerging SARS-CoV-2 variants. There is an obvious need for better and longer-lasting effective vaccines for various prevailing strains and the evolving SARS-CoV-2 virus, necessitating the development of a broad-spectrum vaccine that can be used to prevent infection by reducing both the transmission rate and re-infection. During the initial phases of SARS-CoV-2 infection, the nucleocapsid (N) protein is one of the most abundantly expressed proteins. Additionally, it has been identified as the most immunogenic protein of SARS-CoV-2. In this study, state-of-the-art bioinformatics techniques have been exploited to design novel multiple epitope vaccines using conserved regions of N proteins from prevalent strains of SARS-CoV-2 for the prediction of B- and T-cell epitopes. These epitopes were sorted based on their immunogenicity, antigenicity score, and toxicity. The most effective multi-epitope construct with possible immunogenic properties was created using epitope combinations. EAAAK, AAY, and GPGPG were used as linkers to connect epitopes. The developed vaccines have shown positive results in terms of overall population coverage and stimulation of the immune response. Potential expression of the chimeric protein construct was detected after it was cloned into the Pet28a/Cas9-cys vector for expression screening in
Language	English
Publishing date	2023-06-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines11061090
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Article ; Online: Immunoinformatics Strategy to Develop a Novel Universal Multiple Epitope-Based COVID-19 Vaccine

Nizar A. Khamjan / Mohtashim Lohani / Mohammad Faheem Khan / Saif Khan / Abdullah Algaissi

Vaccines, Vol 11, Iss 1090, p

2023 Volume 1090

Abstract	Currently available COVID vaccines are effective in reducing mortality and severity but do not prevent transmission of the virus or reinfection by the emerging SARS-CoV-2 variants. There is an obvious need for better and longer-lasting effective vaccines for various prevailing strains and the evolving SARS-CoV-2 virus, necessitating the development of a broad-spectrum vaccine that can be used to prevent infection by reducing both the transmission rate and re-infection. During the initial phases of SARS-CoV-2 infection, the nucleocapsid (N) protein is one of the most abundantly expressed proteins. Additionally, it has been identified as the most immunogenic protein of SARS-CoV-2. In this study, state-of-the-art bioinformatics techniques have been exploited to design novel multiple epitope vaccines using conserved regions of N proteins from prevalent strains of SARS-CoV-2 for the prediction of B- and T-cell epitopes. These epitopes were sorted based on their immunogenicity, antigenicity score, and toxicity. The most effective multi-epitope construct with possible immunogenic properties was created using epitope combinations. EAAAK, AAY, and GPGPG were used as linkers to connect epitopes. The developed vaccines have shown positive results in terms of overall population coverage and stimulation of the immune response. Potential expression of the chimeric protein construct was detected after it was cloned into the Pet28a/Cas9-cys vector for expression screening in Escherichia coli. The developed vaccine performed well in computer-based immune response simulation and covered a diverse allelic population worldwide. These computational findings are very encouraging for the further testing of our candidate vaccine, which could eventually aid in the control and prevention of SARS-CoV-2 infections globally.
Keywords	SARS-CoV-2 ; vaccine design ; nucleocapsid ; B cell ; T cell ; Medicine ; R
Subject code	570
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Evaluation of MERS-CoV Neutralizing Antibodies in Sera Using Live Virus Microneutralization Assay

Algaissi, Abdullah / Hashem, Anwar M

Methods Mol Biol

Abstract	The microneutralization (MN) assay is a standard and important technique in virology, immunology, and epidemiology. It is a highly specific and sensitive assay for evaluating virus-specific neutralizing antibodies (nAbs) in human and animal sera. It provides the most precise answer to whether or not an individual or animal has antibodies that can neutralize or inhibit the infectivity of a specific virus strain. However, using live virus-based MN assay might require working under high containment facilities especially when dealing with high-risk pathogens such as the Middle East respiratory syndrome-coronavirus (MERS-CoV). In this chapter, we describe the isolation, amplification, and titration of MERS-CoV, as well as detailed MN assay to measure nAb levels in sera from different mammalian species.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #710717
Database	COVID19

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Article ; Online: Campesterol and dithymoquinone as a potent inhibitors of SARS cov-2 main proteases-promising drug candidates for targeting its novel variants.

Algaissi, Abdullah / Khan, Elhan / Tabassum, Heena / Samreen, Sadiyah / Khamjan, Nizar A / Lohani, Mohtashim / Khan, Saif / Kameli, Nader / Madkhali, Faisal / Ahmad, Iffat Zareen

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–15

Abstract: The sudden outbreak of the COVID-19 pandemic has currently taken approximately 2.4 million lives, with no specific medication and fast-tracked tested vaccines for prevention. These vaccines have their own adverse effects, which have severely affected the ...

Abstract	The sudden outbreak of the COVID-19 pandemic has currently taken approximately 2.4 million lives, with no specific medication and fast-tracked tested vaccines for prevention. These vaccines have their own adverse effects, which have severely affected the global healthcare system. The discovery of the main protease structure of coronavirus (Mpro/Clpro) has resulted in the identification of compounds having antiviral potential, especially from the herbal system. In this study, the computer-associated drug design tools were utilised to analyze the reported phytoconstituents of
Language	English
Publishing date	2024-01-30
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2301684
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Article ; Online: Natural and synthetic drugs and formulations for intravaginal HPV clearance.

Khamjan, Nizar A / Beigh, Saba / Algaissi, Abdullah / Megha, Kanu / Lohani, Mohtashim / Darraj, Majid / Kamli, Nader / Madkhali, Faisal / Dar, Sajad Ahmad

Journal of infection and public health

2023 Volume 16, Issue 9, Page(s) 1471–1480

Abstract: Background: Except for a few preventative Human Papillomavirus (HPV) vaccines, there is currently no cure for HPV infection. There are a number of cutting-edge strategies and potent medications or herbal formulations that can be applied topically for ... ...

Abstract	Background: Except for a few preventative Human Papillomavirus (HPV) vaccines, there is currently no cure for HPV infection. There are a number of cutting-edge strategies and potent medications or herbal formulations that can be applied topically for early clearance of HPV infection before HPV DNA gets integrated into host cell genome. This is facilitated due to cervical cancer having distinct and well-recognized long precancerous stages. Objectives: This review aims to outline every possible medication and formulation, both natural and synthetic, that can be applied topically as intravaginal application to help remove HPV infection at an early precancerous stage. Results: Several anti-HPV/HPV clearance compounds and formulations for high-grade lesions are undergoing clinical trials. However, the majority of compounds are still in the early stages of development and require additional research to become viable HPV clearance candidates. Synthetic drugs may be more promising because they may have a more targeted effect; however, they may also have significant adverse effects. On the other hand, natural medications are safer to use. They are less specific, but have minimal to no adverse effects. Conclusions: This article may serve as a valuable resource of information for managing and preventing precancerous carcinogenic HPV infections. Research could be directed toward developing candidate drugs to make evidence-based decisions about advancing them to clinical trials and, eventually, to the market for potential use in the prevention and control of cervical cancer, which is almost always preventable or even curable if detected early.
MeSH term(s)	Female ; Humans ; Uterine Cervical Neoplasms/drug therapy ; Uterine Cervical Neoplasms/prevention & control ; Uterine Cervical Neoplasms/pathology ; Papillomavirus Infections/drug therapy ; Papillomavirus Infections/prevention & control ; Synthetic Drugs ; Papillomavirus Vaccines/therapeutic use ; Precancerous Conditions ; Papillomaviridae
Chemical Substances	Synthetic Drugs ; Papillomavirus Vaccines
Language	English
Publishing date	2023-06-26
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2467587-8
ISSN	1876-035X ; 1876-0341
ISSN (online)	1876-035X
ISSN	1876-0341
DOI	10.1016/j.jiph.2023.06.016
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Article ; Online: Preparedness and response to COVID-19 in Saudi Arabia: Building on MERS experience.

Algaissi, Abdullah A / Alharbi, Naif Khalaf / Hassanain, Mazen / Hashem, Anwar M

Journal of infection and public health

2020 Volume 13, Issue 6, Page(s) 834–838

Abstract: Nearly four months have passed since the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which caused the rapidly spreading Coronavirus Disease 2019 (COVID-19) pandemic. To date, there have been more than 2.3 million ... ...

Abstract	Nearly four months have passed since the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which caused the rapidly spreading Coronavirus Disease 2019 (COVID-19) pandemic. To date, there have been more than 2.3 million confirmed cases and more than 160,000 deaths globally caused by COVID-19. Chinese health authorities, where the virus emerged, have taken prompt strict public health measures to control and prevent the spread of the outbreak. In Saudi Arabia, unprecedented precautionary strict measures were applied to prevent virus entry to the country or to mitigate its impact when it arrives. Here, we review the response of Saudi Arabia to COVID-19 pandemic and how did the experience learned from the Middle East respiratory syndrome coronavirus (MERS-CoV) epidemic since 2012 has helped the country to be better prepared for the current COVID-19 pandemic. We also discuss the country readiness, improvement in research and development, and the unprecedented rapid precautionary measures that have been taken by the Saudi government thus far.
MeSH term(s)	Animals ; Betacoronavirus ; COVID-19 ; Camelus/virology ; Communicable Disease Control/methods ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Disease Transmission, Infectious/prevention & control ; Humans ; Middle East Respiratory Syndrome Coronavirus ; Pandemics/prevention & control ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; SARS-CoV-2 ; Saudi Arabia/epidemiology ; Travel ; Zoonoses/epidemiology ; Zoonoses/virology
Keywords	covid19
Language	English
Publishing date	2020-05-11
Publishing country	England
Document type	Journal Article ; Review
ISSN	1876-035X
ISSN (online)	1876-035X
DOI	10.1016/j.jiph.2020.04.016
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