Article
Biochemistry & Molecular Biology
Max Luedemann, Daniela Stadler, Cho-Chin Cheng, Ulrike Protzer, Percy A. Knolle, Sainitin Donakonda
Summary: Drug-repurposing has identified a dual-purpose inhibitor, montelukast, that can inhibit SARS-CoV-2 infection and IL-6 production by immune cells. This study demonstrates that montelukast can disturb the RBD structure and inhibit SARS-CoV-2 infection, and it binds to a different site than the ACE2-binding site. The findings also suggest a potential allosteric mechanism for inhibiting SARS-CoV-2 infection.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Letter
Medicine, General & Internal
Xin Zhao, Rong Zhang, Shitong Qiao, Xiao Wang, Weibing Zhang, Wenjing Ruan, Lianpan Dai, Pengcheng Han, George F. Gao
Summary: This study found that neutralization against the SARS-CoV-2 omicron subvariants was reduced with both the inactivated and ZF2001 vaccines in China. However, heterologous boosting and a longer interval between doses resulted in higher neutralization levels.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Letter
Medicine, General & Internal
Xin Zhao, Rong Zhang, Shitong Qiao, Xiao Wang, Weibing Zhang, Wenjing Ruan, Lianpan Dai, Pengcheng Han, George F. Gao
Summary: This study indicates that neutralization against the SARS-CoV-2 omicron subvariants was reduced with both the inactivated and ZF2001 vaccines in China. However, heterologous boosting and a longer interval between doses resulted in higher neutralization levels.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Constantinos Kurt Wibmer, Frances Ayres, Tandile Hermanus, Mashudu Madzivhandila, Prudence Kgagudi, Brent Oosthuysen, Bronwen E. Lambson, Tulio de Oliveira, Marion Vermeulen, Karin van der Berg, Theresa Rossouw, Michael Boswell, Veronica Ueckermann, Susan Meiring, Anne von Gottberg, Cheryl Cohen, Lynn Morris, Jinal N. Bhiman, Penny L. Moore
Summary: The SARS-CoV-2 virus in the B.1.351 variant discovered in South Africa can evade neutralization by most antibodies when expressed, but does not affect binding by convalescent plasma. This suggests the potential for reinfection with antigenically distinct variants and predicts reduced efficacy of spike-based vaccines.
Article
Pharmacology & Pharmacy
Elena Campione, Caterina Lanna, Terenzio Cosio, Luigi Rosa, Maria Pia Conte, Federico Iacovelli, Alice Romeo, Mattia Falconi, Claudia Del Vecchio, Elisa Franchin, Maria Stella Lia, Marilena Minieri, Carlo Chiaramonte, Marco Ciotti, Marzia Nuccetelli, Alessandro Terrinoni, Ilaria Iannuzzi, Luca Coppeda, Andrea Magrini, Sergio Bernardini, Stefano Sabatini, Felice Rosapepe, Pier Luigi Bartoletti, Nicola Moricca, Andrea Di Lorenzo, Massimo Andreoni, Loredana Sarmati, Alessandro Miani, Prisco Piscitelli, Piera Valenti, Luca Bianchi
Summary: Lactoferrin exhibits antimicrobial and anti-inflammatory properties by chelating iron ions, interacting with bacteria and viruses to protect the host from infections. It has demonstrated direct antiviral activity against SARS-CoV-2 and may have a potential supplementary role in managing COVID-19 patients.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Multidisciplinary Sciences
Jianying Liu, Yang Liu, Hongjie Xia, Jing Zou, Scott C. Weaver, Kena A. Swanson, Hui Cai, Mark Cutler, David Cooper, Alexander Muik, Kathrin U. Jansen, Ugur Sahin, Xuping Xie, Philip R. Dormitzer, Pei-Yong Shi
Summary: Serum samples from individuals vaccinated with the BNT162b2 vaccine can neutralize various SARS-CoV-2 variants, indicating mass immunization as a central strategy to end the global COVID-19 pandemic.
Article
Allergy
Gilles Augusto, Mona O. Mohsen, Simon Zinkhan, Xuelan Liu, Monique Vogel, Martin F. Bachmann
Summary: The study found that newly emerged SARS-CoV-2 variants have higher affinity for the ACE2 receptor and are able to partially bypass immunity generated against the wild-type virus, resulting in increased transmissibility.
Letter
Medicine, General & Internal
Jingyou Yu, Ai-ris Y. Collier, Marjorie Rowe, Fatima Mardas, John D. Ventura, Huahua Wan, Jessica Miller, Olivia Powers, Benjamin Chung, Mazuba Siamatu, Nicole P. Hachmann, Nehalee Surve, Felix Nampanya, Abishek Chandrashekar, Dan H. Barouch
Summary: Although immunity from two doses of BNT162b2 vaccine diminishes over time, a booster dose significantly enhances the neutralizing antibodies against both the BA.1 and BA.2 variants.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Laura A. VanBlargan, John M. Errico, Peter J. Halfmann, Seth J. Zost, James E. Crowe, Lisa A. Purcell, Yoshihiro Kawaoka, Davide Corti, Daved H. Fremont, Michael S. Diamond
Summary: The emergence of the B.1.1.529 Omicron variant raises concerns about the efficacy of antibody countermeasures. This study shows that some of the antibodies currently in clinical use may lose their ability to neutralize the Omicron variant.
Article
Cell Biology
Prerna Arora, Amy Kempf, Inga Nehlmeier, Luise Graichen, Martin S. Winkler, Martin Lier, Sebastian Schulz, Hans-Martin Jaeck, Anne Cossmann, Metodi Stankov, Georg M. N. Behrens, Stefan Poehlmann, Markus Hoffmann
Summary: The SARS-CoV-2 variants C.1.2 and B.1.621 show increased entry into certain cell lines but do not exhibit increased ACE2 binding. These variants are resistant to bamlanivimab neutralization but remain sensitive to antibody cocktails used for COVID-19 therapy. Furthermore, C.1.2 and B.1.621 partially escape neutralization by antibodies induced upon infection and vaccination.
Article
Cell Biology
Takuya Tada, Hao Zhou, Belinda M. Dcosta, Marie Samanovic, Amber Cornelius, Ramin S. Herati, Mark J. Mulligan, Nathaniel R. Landau
Summary: The recently identified SARS-CoV-2 variants Mu and C.1.2 have spike proteins with mutations that may resist natural and vaccine-induced antibodies. Neutralizing antibody titers in the serum of vaccinated individuals without previous infection and convalescent individuals show partial resistance against these viruses. In contrast, individuals with previous SARS-CoV-2 infection who were subsequently vaccinated have higher neutralizing titers against these variants, suggesting the importance of vaccination for individuals with previous infection. The heavily mutated C.1.2 spike protein is the most resistant to antibody neutralization to date, but it has low affinity for angiotensin-converting enzyme 2 (ACE2), which implies it may cause milder disease or be less transmissible.
Article
Biochemistry & Molecular Biology
Zhen Cui, Wenxin Luo, Ruihong Chen, Yalun Li, Zhoufeng Wang, Yong Liu, Shuo Liu, LeiLei Feng, Zijing Jia, Ruixin Cheng, Jun Tang, Weijin Huang, Yanjun Zhang, Huawen Liu, Xiangxi Wang, Weimin Li
Summary: The emergence of adapted variants of the SARS-CoV-2 virus has led to an increase in breakthrough infections worldwide. Analysis of immune responses in vaccinated individuals reveals limited resistance to Omicron in those with no prior infection but significant immunity in those previously infected. T-cell responses remain largely unaffected, indicating the importance of T-cell-mediated cellular immunity. Administration of a third vaccine dose enhances neutralizing antibodies and memory B cells, improving protection against emerging variants.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)
Review
Biochemistry & Molecular Biology
Manojit Bhattacharya, Srijan Chatterjee, Sang-Soo Lee, Chiranjib Chakraborty
Summary: This review discusses single-domain antibodies (sdAbs), also known as nanobodies, their structure, and their effectiveness against the deadly SARS-CoV-2 virus and other viral infections. Compared to conventional therapeutics, such as mAbs, convalescent plasma therapy, and vaccines, nanobodies have a stable structure and suitable mechanism of action, making them more resistant to evolving variants with numerous mutations. Nanobodies developed for SARS-CoV-2 and its mutant variants show greater neutralization potential. Engineering these specialized antibodies using modern biotechnological approaches will be beneficial in treating the COVID-19 pandemic and other viral infections.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Letter
Medicine, General & Internal
Nicole P. Hachmann, Jessica Miller, Ai-ris Y. Collier, John D. Ventura, Jingyou Yu, Marjorie Rowe, Esther A. Bondzie, Olivia Powers, Nehalee Surve, Kevin Hall, Dan H. Barouch
Summary: A small study found that omicron subvariants BA.2.12.1, BA.4, and BA.5 of SARS-CoV-2 were more likely to evade neutralizing antibodies induced by both vaccination and previous infection compared to the prior omicron subvariants BA.1 and BA.2.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Letter
Medicine, General & Internal
Nicole P. Hachmann, Jessica Miller, Ai-ris Y. Collier, Dan H. Barouch
Summary: Neutralization titers against omicron subvariant BA.4.6 were lower compared to subvariants BA.4 and BA.5 induced by infection or vaccination against SARS-CoV-2.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Ismail Erol, Seyfullah Enes Kotil, Ozkan Fidan, Ahmet E. Yetiman, Serdar Durdagi, Fatih Ortakci
Summary: The COVID-19 pandemic caused by the novel coronavirus (SARS-CoV-2) is a serious health concern, and specific biotherapeutics are needed. This study investigates the binding energies between bacteriocins and spike protein receptor-binding domain (RBD) to prevent virus spread. The results suggest that pediocin PA-1, salivaricin P, and salivaricin B have potential as inhibitors against SARS-CoV-2 variants.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Review
Endocrinology & Metabolism
Esra Ayan, Hasan DeMirci
Summary: Insulin is crucial for regulating glucose metabolism and other signaling pathways in mammals. Its absence can lead to various diseases, but recombinant insulin is commonly used for diabetes treatment. Understanding insulin, biosimilars, and biobetters holistically can aid in designing pharmacologically user-friendly molecules and personalized medicine-oriented therapeutic strategies. This atlas aims to review insulin from a biotechnological, basic science, and clinical perspective, explaining insulin-related disorders and their molecular mechanisms, exploring production strategies for insulin/analogs, and highlighting their structural mechanism of action. Computational analysis also provides insights into the structural dynamics of insulin.
CURRENT DIABETES REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Baris Cakilkaya, Ibrahim Halil Kavakli, Hasan DeMirci
Summary: Researchers identified a (6-4) PL protein from Vibrio cholerae that repairs UV-induced DNA damage and determined its crystal structure, revealing interactions with two chromophore cofactors. The study also found a potential DNA-binding region and conformational changes that facilitate DNA repair. This research provides valuable insights into the DNA repair process.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Yakup Kolcuoglu, Olcay Bekircan, Hilal Fazli, Emine Sahin, Asli Ture, Atilla Akdemir, Senay Hamarat Sanlier
Summary: EGFR mediates signaling cascade in various biological processes and its dysregulation can lead to malignancy. EGFR is a prominent macromolecule in targeted cancer chemotherapy. Novel molecules with a specific structure were suggested and synthesized. Compound 8g showed the closest IC50 value to Gefitinib, a well-known EGFR inhibitor, with noncompetitive inhibition.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Muhammed Trawally, Kubra Demir-Yazici, Serap Ipek Dingis-Birgul, Kerem Kaya, Atilla Akdemir, Ozlen Guzel-Akdemir
Summary: Tuberculosis is a curable disease with a high mortality rate of 1.5 million lives per year. The prevalence of multi-drug resistant strains makes its eradication challenging. In this study, a series of dithiocarbamate/dithiocarbonate-nitrosaccharin hybrids were synthesized and evaluated for their antimycobacterial activity. Some compounds showed promising activity against M. tuberculosis strain H37Rv. In-silico studies identified enoyl ACP-reductase (InhA) and polyketide synthase 13 (Pks13) as potential targets for the most potent compound 6g. (c) 2022 Elsevier B.V. All rights reserved.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Food Science & Technology
Hivda Ulbegi Polat, Muge Serhatli, Arzu Tas Ekiz, Irem Abaci, Ozge Aksoy, Gamze Cakirca, Saban Tekin, Abdulmajeed Aziz Hamoud Al-Zendani, Mohammed Abdulmajeed Aziz Al-Zendani, Omer Korkmaz, Celalettin Peru
Summary: This study investigates the antiviral activity of a plant extract derived from the roots of Saussurea lappa against SARS-CoV-2 infection. Vero E6 cells are used to test the neutralizing effect of the extract, and a challenge experiment in mice is conducted. The results demonstrate that the extract protects mice against SARS-CoV-2 in 90% of the cases.
MOLECULAR NUTRITION & FOOD RESEARCH
(2023)
Article
Food Science & Technology
Oznur Karaoglu, Muge Serhatli, Ebru Pelvan, Bulent Karadeniz, Ilknur Demirtas, Gamze Cakirca, Hande Sipahi, Yagmur Ozhan, Gozdem Karapinar, Mohammad Charehsaz, Ahmet Aydin, Erdem Yesilada, Cesarettin Alasalvar
Summary: This study aimed to design a chewable tablet formulation with propolis and herbal extracts for the prevention of SARS-CoV-2 virus variants and other viral infections. The combination of herbal extracts with propolis showed synergistic antiviral activity, and the chewable tablet exhibited high efficacy against both Wuhan and Omicron variants. The findings suggest that this combination could be used as a food supplement for oral cavity prevention of SARS-CoV-2.
JOURNAL OF FUNCTIONAL FOODS
(2023)
Article
Chemistry, Physical
Eyyup Murat Karakurt, Yuksel Cetin, Alper Incesu, Huseyin Demirtas, Mehmet Kaya, Yasemin Yildizhan, Merve Tosun, Yan Huang
Summary: This study investigated the microstructures, mechanical performances, corrosion resistances, and in vitro studies of porous Ti-xNb-10Zr (x: 10 and 20; at. %) alloys. The alloys exhibited a dual-phase microstructure, good mechanical properties, and biocompatibility.
Article
Multidisciplinary Sciences
Mehmet Gul, Esra Ayan, Ebru Destan, J. Austin Johnson, Alaleh Shafiei, Abdullah Kepceoglu, Merve Yilmaz, Fatma Betuel Ertem, Ilkin Yapici, Bilge Tosun, Niluefer Baldir, Nurettin Tokay, Zelis Nergiz, Gozde Karakadioglu, Seyide Seda Paydos, Cahine Kulakman, Cengiz Kaan Ferah, Omur Guven, Necati Atalay, Enver Kamil Akcan, Haluk Cetinok, Nazli Eylul Arslan, Kardelen Sabanoglu, Bengisu Asci, Serra Tavli, Helin Gumusboga, Sevde Altuntas, Masami Otsuka, Mikako Fujita, Saban Tekin, Halilibrahim Ciftci, Serdar Durdagi, Ezgi Karaca, Burcu Kaplan Turkoz, Burak Veli Kabasakal, Ahmet Kati, Hasan DeMirci
Summary: High-resolution biomacromolecular structure determination is crucial for understanding protein function and dynamics. Serial crystallography has limitations in terms of sample volume requirements and access to X-ray beamtime. To overcome these limitations, a plate-reader module adapted for a 72-well Terasaki plate is introduced for biomacromolecule structure determination using a home X-ray source. The first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight) provides valuable information about the structural dynamics of the lysozyme. Turkish DeLight offers robust and rapid ambient temperature biomacromolecular structure determination with minimal radiation damage.
SCIENTIFIC REPORTS
(2023)
Article
Cell Biology
Zehra Degirmenci, Sena Unver, Turker Kilic, Timucin Avsar
Summary: The effect of MEG3 on glioma cells and the potential use of chemotherapeutics in glioma by modulating MEG3 expression were evaluated. Silencing of MEG3 inhibited cell proliferation and migration, while overexpression of MEG3 promoted proliferation in glioma cells. Moreover, MEG3 inhibition improved the chemosensitivity of glioma cells to 5-fluorouracil.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2023)
Article
Biochemical Research Methods
Zeyad Tareq Jasim Alabdulraheem, Serdar Durdagi
Summary: The complex nature of Alzheimer's disease makes it difficult to understand the exact molecular processes leading to neuron death. However, two molecular factors - amyloid-beta plaques and tau tangles - are believed to be linked to the disease. In this study, the researchers identified a genetic marker for brain atrophy and investigated its interaction with amyloid beta, potentially leading to increased aggregation. They also constructed 3D models of the protein encoded by the genetic marker and used virtual screening to identify potential drug targets.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Biochemistry & Molecular Biology
Esra Ayan, Hasan Demirci, Muhittin Abdulkadir Serdar, Francesca Palermo, Ahmet Tarik Baykal
Summary: This study aims to reveal the role of gut microbiota in the pathogenesis of Alzheimer's Disease (AD), particularly regarding changes in the proteome and molecular pathways. The data indicates that the microbiota, proteome, and molecular changes exist long before the manifestation of disease symptoms. Moreover, disparities exist between the normal-aged flora and the gut microbiota of late-stage AD mice, emphasizing the potential value of identified phyla, proteins, and pathways as markers for the early and late stages of AD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Necati Atalay, Enver Kamil Akcan, Mehmet Gul, Esra Ayan, Ebru Destan, Fatma Betuel Ertem, Nurettin Tokay, Baris Cakilkaya, Zelis Nergiz, Gozde Karakadioglu, Abdullah Kepceoglu, Ilkin Yapici, Bilge Tosun, Nilufer Baldir, Gunseli Yildirim, J. Austin Johnson, Omur Guven, Alaleh Shafiei, Nazli Eylul Arslan, Merve Yilmaz, Cahine Kulakman, Seyide Seda Paydos, Zeynep Sena Cinal, Kardelen Sabanoglu, Aysegul Pazarceviren, Aysenur Yilmaz, Basak Canbay, Bengisu Asci, Esra Kartal, Serra Tavli, Mehmet Caliseki, Gunce Goc, Arif Mermer, Gamze Yesilay, Sevde Altuntas, Hiroshi Tateishi, Masami Otsuka, Mikako Fujita, Saban Tekin, Halilibrahim Ciftci, Serdar Durdagi, Gizem Dinler Doganay, Ezgi Karaca, Burcu Kaplan Turkoz, Burak Veli Kabasakal, Ahmet Kati, Hasan Demirci
Summary: X-ray crystallography is a powerful technique for determining high-resolution atomic structures of biomacromolecules. The establishment of an X-ray diffraction facility in Istanbul, Turkiye will enable scientists to easily analyze the structure of biomacromolecules from single crystals. This article describes the technical details of a state-of-the-art X-ray and provides a practical guide for sample preparation and data analysis.
TURKISH JOURNAL OF BIOLOGY
(2023)
Article
Chemistry, Medicinal
Omur Guven, Belgin Sever, Faika Basoglu-Unal, Abdulilah Ece, Hiroshi Tateishi, Ryoko Koga, Mohamed O. Radwan, Nefise Demir, Mustafa Can, Mutlu Dilsiz Aytemir, Jun-ichiro Inoue, Masami Otsuka, Mikako Fujita, Halilibrahim Ciftci, Hasan Demirci
Summary: TRAF6 is a protein with important biological functions, and its structural studies play a crucial role in the development of new therapeutic drugs. By analyzing the structure and mechanism of TRAF6, we have identified new compounds that interact with its key regions and demonstrated their favorable pharmacokinetic properties, making them potential TRAF6 inhibitors in the future.
Article
Orthopedics
Bilge Kagan Yilmaz, Mehmet Nuri Konya, Sinan Ince, Hasan Huseyin Demirel, Yuksel Cetin, Aysen Gungor
Summary: This study aimed to determine the bioefficacy of epidermal growth factor (EGF), boric acid (BA), and their combination on cartilage injury in rats. The results showed that EGF and low-dose BA application had a positive effect on cartilage healing in rats.
JOINT DISEASES AND RELATED SURGERY
(2023)