Search

Your search keyword '"Shaden M. H. Mubarak"' showing total 11 results
Start Over Author "Shaden M. H. Mubarak"
11 results on '"Shaden M. H. Mubarak"'

1. Impact of SNPs, off-targets, and passive permeability on efficacy of BCL6 degrading drugs assigned by virtual screening and 3D-QSAR approach

Author

Solmaz Karimi, Farzaneh Shahabi, Shaden M. H. Mubarak, Hanie Arjmandi, Zahra Sadat Hashemi, Navid Pourzardosht, Alireza Zakeri, Mahdieh Mahboobi, Abolfazl Jahangiri, Mohammad Reza Rahbar, and Saeed Khalili

Subjects
Medicine, Science
Abstract

Abstract B-cell lymphoma 6 (BCL6) regulates various genes and is reported to be overexpressed in lymphomas and other malignancies. Thus, BCL6 inhibition or its tagging for degradation would be an amenable therapeutic approach. A library of 2500 approved drugs was employed to find BCL6 inhibitory molecules via virtual screening. Moreover, the 3D core structure of 170 BCL6 inhibitors was used to build a 3D QSAR model and predict the biological activity. The SNP database was analyzed to study the impact on the destabilization of BCL6/drug interactions. Structural similarity search and molecular docking analyses were used to assess the interaction between possible off-targets and BCL6 inhibitors. The tendency of drugs for passive membrane permeability was also analyzed. Lifitegrast (DB11611) had favorable binding properties and biological activity compared to the BI-3802. Missense SNPs were located at the essential interaction sites of the BCL6. Structural similarity search resulted in five BTB-domain containing off-target proteins. BI-3802 and Lifitegrast had similar chemical behavior and binding properties against off-target candidates. More interestingly, the binding affinity of BI-3802 (against off-targets) was higher than Lifitegrast. Energetically, Lifitegrast was less favorable for passive membrane permeability. The interaction between BCL6 and BI-3802 is more prone to SNP-derived variations. On the other hand, higher nonspecific binding of BI-3802 to off-target proteins could bring about higher undesirable properties. It should also be noted that energetically less desirable passive membrane translocation of Lifitegrast would demand drug delivery vehicles. However, further empirical evaluation of Lifitegrast would unveil its true potential.

Published
2022
Full Text
View/download PDF

2. A unique antigen against SARS-CoV-2, Acinetobacter baumannii, and Pseudomonas aeruginosa

Author

Mohammad Reza Rahbar, Shaden M. H. Mubarak, Anahita Hessami, Bahman Khalesi, Navid Pourzardosht, Saeed Khalili, Kobra Ahmadi Zanoos, and Abolfazl Jahangiri

Subjects
Medicine, Science
Abstract

Abstract The recent outbreak of COVID-19 has increased hospital admissions, which could elevate the risk of nosocomial infections, such as A. baumannii and P. aeruginosa infections. Although effective vaccines have been developed against SARS-CoV-2, no approved treatment option is still available against antimicrobial-resistant strains of A. baumannii and P. aeruginosa. In the current study, an all-in-one antigen was designed based on an innovative, state-of-the-art strategy. In this regard, experimentally validated linear epitopes of spike protein (SARS-CoV-2), OmpA (A. baumannii), and OprF (P. aeruginosa) were selected to be harbored by mature OmpA as a scaffold. The selected epitopes were used to replace the loops and turns of the barrel domain in OmpA; OprF311–341 replaced the most similar sequence within the OmpA, and three validated epitopes of OmpA were retained intact. The obtained antigen encompasses five antigenic peptides of spike protein, which are involved in SARS-CoV-2 pathogenicity. One of these epitopes, viz. QTQTNSPRRARSV could trigger antibodies preventing super-antigenic characteristics of spike and alleviating probable autoimmune responses. The designed antigen could raise antibodies neutralizing emerging variants of SARS-CoV-2 since at least two epitopes are consensus. In conclusion, the designed antigen is expected to raise protective antibodies against SARS-CoV-2, A. baumannii, and P. aeruginosa.

Published
2022
Full Text
View/download PDF

3. Recent Advances in Understanding the Pathogenesis of Rheumatoid Arthritis: New Treatment Strategies

Author

Anna-Lena Mueller, Zahra Payandeh, Niloufar Mohammadkhani, Shaden M. H. Mubarak, Alireza Zakeri, Armina Alagheband Bahrami, Aranka Brockmueller, and Mehdi Shakibaei

Subjects
rheumatoid arthritis, inflammation, auto-antibodies, autophagy, epigenetic, citrullination, Cytology, QH573-671
Abstract

Rheumatoid arthritis (RA) is considered a chronic systemic, multi-factorial, inflammatory, and progressive autoimmune disease affecting many people worldwide. While patients show very individual courses of disease, with RA focusing on the musculoskeletal system, joints are often severely affected, leading to local inflammation, cartilage destruction, and bone erosion. To prevent joint damage and physical disability as one of many symptoms of RA, early diagnosis is critical. Auto-antibodies play a pivotal clinical role in patients with systemic RA. As biomarkers, they could help to make a more efficient diagnosis, prognosis, and treatment decision. Besides auto-antibodies, several other factors are involved in the progression of RA, such as epigenetic alterations, post-translational modifications, glycosylation, autophagy, and T-cells. Understanding the interplay between these factors would contribute to a deeper insight into the causes, mechanisms, progression, and treatment of the disease. In this review, the latest RA research findings are discussed to better understand the pathogenesis, and finally, treatment strategies for RA therapy are presented, including both conventional approaches and new methods that have been developed in recent years or are currently under investigation.

Published
2021
Full Text
View/download PDF

4. Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences

Author

Zahra Sadat Hashemi, Mahboubeh Zarei, Shaden M. H. Mubarak, Anahita Hessami, Maysam Mard-Soltani, Bahman Khalesi, Alireza Zakeri, Mohammad Reza Rahbar, Abolfazl Jahangiri, Navid Pourzardosht, and Saeed Khalili

Subjects
SARS-CoV-2, Structural analyses, Drug Discovery, Mutation, Molecular Medicine, Bioengineering, Spike protein, Biochemistry, hormones, hormone substitutes, and hormone antagonists, Article, Analytical Chemistry, Lineage B.1.1.7
Abstract

The structural consequences of ongoing mutations on the SARS-CoV-2 spike-protein remains to be fully elucidated. These mutations could change the binding affinity between the virus and its target cell. Moreover, obtaining new mutations would also change the therapeutic efficacy of the designed drug candidates. To evaluate these consequences, 3D structure of a mutant spike protein was predicted and checked for stability, cavity sites, and residue depth. The docking analyses were performed between the 3D model of the mutated spike protein and the ACE2 protein and an engineered therapeutic ACE2 against COVID-19. The obtained results revealed that the N501Y substitution has altered the interaction orientation, augmented the number of interface bonds, and increased the affinity against the ACE2. On the other hand, the P681H mutation contributed to the increased cavity size and relatively higher residue depth. The binding affinity between the engineered therapeutic ACE2 and the mutant spike was significantly higher with a distinguished binding orientation. It could be concluded that the mutant spike protein increased the affinity, preserved the location, changed the orientation, and altered the interface amino acids of its interaction with both the ACE2 and its therapeutic engineered version. The obtained results corroborate the more aggressive nature of mutated SARS-CoV-2 due to their higher binding affinity. Moreover, designed ACe2-baased therapeutics would be still highly effective against covid-19, which could be the result of conserved nature of cellular ACE2. Supplementary Information The online version contains supplementary material available at 10.1007/s10989-021-10346-1.

Published
2021

6. Dear Colleagues! YOUR COMMENTS AND THOUGHTS ARE VERY VALUABLE

Author

Zghair, Fadhil Sami, Zakaria, Saif Khalid, Smaisim, Ghassan Fadhil, D, Shiva Kumar H, Chetverikov, Alexander P., Lusciano, Francesco, Bulcsu Szekely, Merizgui Tahar, Shih-Wen Huang, Behrendt, Cezary, Tran, Tan, Wedad M. El-Kholy, PAVAN KUMAR, Al-Najjar, Hussein M. Taqi, Dnyaneshwar Namdev Jagtap, Mrad, Sonia, Hasanaj, Petrit, Zamani, Mohammad Reza, Trisna, Beni Adi, Nnarayan Billava, Dar, Basharat A. M., Al-Siyabi, Sultan, Ahmed, Firas, Edbey, Khaled, Amjed Lateef Jabbar, Parthapratim De, Beemnet Mengesha Kassahun, Nandkishor Meshram, Pundir, Ashok, K. Sinha, Apichit Maneengam, Adeeb, Eman R., Kalhoro, Abdul Naeem, Sulaiman, Mohammed, Faraci, Rocco, Al-Dulamey, Qusay, Hongduo Cao, Lashkari, Hassan, Nibras Husein Mhawesh, Sumana Gop, M. Senapathy, Abdelgadir, Ehsan Mohammed, Aldalimi, Wafaa, Gala, Francisco Javier, Niharika Keot, Ketchakmadze, Ivane, Munaf D. F. Al-Aseebee, Ishak Saat, Al-Rawi, Muna Sameer, Gulrux Zakirova, Noraldeen, Farooq, Khudhir, Zina Saab, Michał Ruszkowski, Refugio, Craig, Al-Qadi, Naim S., Mohammed, Hussain, Jaafer Hmood Eidi, Kadhum, Naser Jawad, P. Contreras, Masrour, Mohammed, Nishanbaev, Sabir, Al-Khresheh, Mohammad Hamad, Wassan M.Hussen, Yehya A. Salih, Hatem, Abeer Dakhil, Waggas Galib Atshan, Vaseashta, Ashok, Usmonova, Malika, Omayma A. Eldahshan, Fariborz Parandin, Sahli Youcef, Enas Hussein Ali, Cortés, Farid B., Thiago Santos, El-Shazly, Mohamed, Alwardi, Anwar, Sofián El-Astal, Huse Fatkić, Sheykhangafshe, Farzin Bagheri, Paweł Przybyłowicz, Nazaruddin Sinaga, Mustafa, Firas Mahmood, Doğan, Mustafa, Bresam, Sabah, Hooshang Rostamnejad Takleh, Deneva, Vera, Olutosin Ademola Otekunrin, Evens Emmanuel, Lordkipanidze, Revaz, Sihag, Parveen, Shaden M H Mubarak, Dafchahi, Fatemeh Hoodneh, Chebbi, Sabrine, Abdelhalim Zekry, Ramzan Ahmed, Dheyaa Falih Bannay, LEÓN-DUARTE, Gustavo Adolfo, Boukhari, Sofiane, Ma'moun M. Abu-Ayyad, Shadrack Katuu, Hasan, Mohammed Faez, Abhijit Mitra, Chinaza Godswill Awuchi, Hussein, Emad Kamil, Weiss, Michael Noah, Mkhelif, Adnan Z., Gafsi, Yosra, Avargani, Mina Karimi, Charos Toshtemirova, Mehdizadeh, Mohammad, Hassen, Jasim, Zaidan, Majeed Rashid, Wa'Il A. Godaymi Al-Tumah, Fazliddin Sodiqovich Jalilov, Kversøy, Kjartan Skogly, Espejo, Mariano Ruiz, Kittichai Jookjantra, Murawski, Krzysztof, Harito, Christian, Ramírez, Víctor Hugo San Martín, Zerrouki, Toufik, Rasouli, Hassan, Vega-Baudrit, José Roberto, Trindade, Carlos Alberto Matos, Azzad Bader, Almalikee, Hussein, Al-Khashman, Omar Ali, Sözbir, Bayram, Khan, Mohammad Jobair, Morell, Christophe, Ashkan Shekaari, González, Francisco Martínez, Portalone, Gustavo, Ziapour, Arash, Ketchakmadze, Dimitri, Yu-Da Lin, Ayala, Alejandro Pedro, Yañez, Osvaldo Andres, Iliyasu Musa Omoyine, Lazzarotto, Marcelo, Muhammad, Haroon, Shyi-Long Lee, Dr Umang Patel, Housaindokht, Mohammad Reza, Diaz-Sobac, Rafael, Izadyar, Mohammad, Geethu, Radhika, Gunajyoti Das, Antarip Halder, Semikov, Rostyslav, Gehan A Hegazy, Costa, João G., Arslan, Taner, Md Zahidul Islam, Pathak, Govind, Silva, Gabrielle, Torun, Gökhan, Nguyen, Thi Tran, Junnan Lu, Vinnarasi Saravanan, Nihar R Jena, Evangelisti, Luca, Vilanova-Costa, Cesar Augusto Sam Tiago, Martínez-Araya, Jorge Ignacio, Bozorgmehr, Mohammad Reza, Joaquin Barroso-Flores, Silva, Gabriel Da, Miandehy, Mohsen, Fahimi, Peyman, Miorelli, Jonathan, Whiteside, Alexander, Junhwan Kim, Nguyen Tien Trung, and Ol'ha O Brovarets

Published
2020
Full Text
View/download PDF

7. Research Topic 'Proton Transfer Processes in Biological Reactions: A Computational Approach' Frontiers in Chemistry journal

Author

Ol'ha O Brovarets, Hovorun, Dmytro Mykolayovych, Matta, Cherif F., Pérez-Sánchez, Horacio, Srivastava, Ruby, Ramírez, Víctor Hugo San Martín, Dr. Mohamed Mohamed Tolba Said, S. Tolosa Arroyo, Ashqer, Issam, Hidalgo, Antonio, Saade Abdalkareem Jasim, Saadoun Salimi, Sandipan Chakraborty, Sergienko, Ruslan, Bresam, Sabah, S. Feroz, S. Thamotharan, Meteab, Waleed Younus, Nishanbaev, Sabir, Chalanchi, Saber Mohammadi, S. M. Gorbatyuk, Sabnam S. Ullah, Sonne, Christian, Chebbi, Sabrine, Sadiq Kadhem Abidali, Saeid Ebrahimi, S. Askarian, S. Karimi, Sahli Youcef, Sahnawaz Alam, Zakaria, Saif Khalid, Banihani, Saleem Ali, Salifu Osman, Saiu, Salvatore, Almufti, Saman M., Sanat Ghosh, Sandor G Vari, Wategaonkar, Sanjay, Sarabjeet Kaur, Saranya Vasudevan, Santhosh George, Saravanan Kandasamy, Mamilov, Serge, Seada Hussen, Khomyak, Semen, Gaouar, Semir Bechir Suheil, Senapathy Marisennayya, Balci, Serdar, Kulikov, Sergey B., Leble, Sergey, Marchenko, Sergey, Ivanov, Sergey P, Burian, Sergii, Pustovit, Sergii, Vernygorodskyi, Sergii, Durand, Sergio, Sousa, Sérgio F., Okovytyy, Sergiy I, Senchurov, Sergiy, Dubovyk, Serhii, Holota, Serhii, Vasylevskyi, Serhii I., Blavatskyy, Serhiy, Vakal, Serhii, Shaden Khalifa, Shaaban Saad Elnesr, Shaden M H Mubarak, Rampino, Sergio, Shadrack Katuu, Stepanian, Stepan G., Rohman, Shahnaz, Portukhay, Sofiya, Evangelisti, Luca, Zand, Mohammad Reza Ahmadi, Wensheng Bian, De-Melo, Adriane Alexandre Machado, Hongduo Cao, González, Francisco Martínez, Oliynyk, Timothy, Tiwari, Ekta, Tiezza, Marco Dalla, Nguyen Tien Trung, To, Takahiro, Martínez-Araya, Jorge Ignacio, Vilanova-Costa, Cesar Augusto Sam Tiago, Martínez-Calderon, Miguel, Ortigosa, Pilar Martínez, Zerrouki, Toufik, Małgorzata Kiełczykowska, Lozovaya, Natalia, Zhyganiuk, Igor Viktorovich, Kouzari, Katerina, Małgorzata Gniewosz, Hudz, Nataliia, Moghani, Maryam Zeraati, Battino, Maurizio, Batista, Patrick Rodrigues, Ivashkiv, Iryna, Mashhour, Omar Farouk Al, Waggas Galib Atshan, Slman, Wafaa Jasim, Changwei Wang, Guendouzi Abdelkrim, G.E. Marin, Demo, Gabriel, Silva, Gabriel Da, Silva, Gabrielle, Zaychenko, Ganna, Gabrielis Kundrotas, Merino, Gabriel, Sobczyk, Garret Eugene, Gehan A Hegazy, Boyd, Georgina, Smaisim, Ghassan Fadhil, Mol, Gilbert Pushpam Sheeja, Ribaudo, Giovanni, Lorenzo, Giuseppe De, Skorobagatko, Gleb A., Baryshnikov, Gleb, Gokhan Torun, and Torun, Gökhan

Published
2020
Full Text
View/download PDF

8. The Role of Probiotics in Parkinson’s Disease: A Review Study.

Author

Shaden, M. H. Mubarak, Mohammad, Ekrahi, El-Saber, Bathiha Gaber, Mojtaba, Memariani, Hamed, Memariani, and Abdolmajid, Ghasemian

Subjects
*PARKINSON'S disease, *PROBIOTICS, *NEURODEGENERATION
Abstract

An upward trend in the incidence of Parkinson’s disease (PD), known as one of the most prominent neurodegenerative maladies, has evoked great concerns among medical community over the past decades. Recently, studies have suggested the initiation of PD in the gastrointestinal tract decades before the advent of manifestations. Accumulating evidence suggests that intracellular deposition of α-synuclein (α-syn) in patients with PD is associated with systemic inflammation leading to the neuroinflammation and neuropsychiatric disorders. The α-syn protein accumulation can be initiated from GI cells and distribute into CNS cells through trans-synaptic cell to cell transmission. Without doubt, gut microbiota affects the enteric nervous system (ENS) known as the “second brain”. Patients with PD have a different balance of bacteria in their intestines, as compared to healthy population. Metabolites from gut microbiota affect the enteric wall such as neurodegeneration. Probiotics have a substantial role in the neutralization or inhibition of reactive oxygen species (ROS) and free radicals and thus improve the PD symptoms. The anti-inflammatory role of probiotics also inhibits the neurodegeneration and PD development. Hence, probiotics contribute to the improvement of PD through several mechanisms which need more in-depth verification. [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
View/download PDF

9. Point mutation detection by economic HRM protocol primer design

Author

Dhafer A F, Al-Koofee, Jawad Mohammed, Ismael, and Shaden M H, Mubarak

Abstract

Globally more than 100 million SNPs in populations. These variations approximately 4-5 million SNPs in a people genome, occur almost every 1000 nucleotides on average and present either unique or in many in individuals. They can act as genetic signs, associated with illness and respond to chemicals and drugs. SNPs occurrence within or near a gene play important role in disease throughout affecting gene task. Frequently many protocols have been used to study single nucleotide polymorphism (SNP) among human variants genome. Restriction fragment length polymorphism (RFLP), Amplification refractory mutation system PCR(ARMS-PCR), sequencing and SNaPshot assays considered familial methods. The potential risk of contamination after PCR is common due to further other steps. In this direction, a high resolution melting (HRM) real-time PCR method is an alternative, reducing the post-PCR transferring steps. uVariants is clarified as appropriate website for designing primers used for SNP recognition by easy and inexpensive protocol called HRM. The researchers can focus on the interest of reference SNP ID number, or "rs" ID to avoid loss time. In this article description how to uses uVariants website for primer design used in HRM technique.To describe uVariants and uDesign software, application and usefulness of HRM technique primer design in the genotyping SNPs among people and public health.uVariants and uDesign are freely accessible at: https://www.dna.utah.edu/variants/;https://www.dna.utah.edu/udesign/app.php respectively.The network server supports the browsers: Chrome, Firefox, Torch, CoolNovo, 360 Browser, Internet Explorer, Opera, and Safari.

Published
2019

Catalog

Books, media, physical & digital resources
See catalog results