Article
Biophysics
Olga I. Guliy, Stella S. Evstigneeva, Lev A. Dykman
Summary: Antibody phage display is a useful technique for producing antibodies to specific antigens, replacing the traditional hybrid-oma technology. It simplifies the process by manipulating DNA and bacteria, shortening the time and reducing the cost of antibody production. Antibodies prepared through phage display can be used as selective receptors in biosensors.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Biochemistry & Molecular Biology
Tulika Tulika, Rasmus W. Pedersen, Charlotte Rimbault, Shirin Ahmadi, Esperanza Rivera-de-Torre, Monica L. Fernandez-Quintero, Johannes R. Loeffler, Markus-Frederik Bohn, Anne Ljungars, Line Ledsgaard, Bjorn G. Voldborg, Fulgencio Ruso-Julve, Jan Terje Andersen, Andreas H. Laustsen
Summary: In this study, a new method was proposed to discover antibodies that bind alpha-cobratoxin from the venom of Naja kaouthia in a pH-dependent manner using a naive antibody phage display library. The discovered antibody showed pH-dependent binding without histidine residues and exhibited higher off-rate at pH 5.5 compared to pH 7.4. Molecular dynamics simulations suggested that different protonation states of titratable residues might contribute to the pH-dependent binding properties of the antibody. This method can be used to discover recycling antibodies against different targets without the need for histidine doping.
Review
Immunology
Kristian Daniel Ralph Roth, Esther Veronika Wenzel, Maximilian Ruschig, Stephan Steinke, Nora Langreder, Philip Alexander Heine, Kai-Thomas Schneider, Rico Ballmann, Viola Fuehner, Philipp Kuhn, Thomas Schirrmann, Andre Frenzel, Stefan Duebel, Maren Schubert, Gustavo Marcal Schmidt Garcia Moreira, Federico Bertoglio, Giulio Russo, Michael Hust
Summary: Antibodies are crucial for the diagnosis and treatment of diseases caused by pathogens. Their importance has been highlighted during the COVID-19 pandemic, and new technologies like antibody phage display have advanced the discovery of human monoclonal antibodies for therapeutic purposes. These technologies have expanded the possibilities for generating antibodies against a wide range of pathogens and toxins.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Immunology
Chao-Yang Huang, Ying-Yung Lok, Chia-Hui Lin, Szu-Liang Lai, Yen-Yu Wu, Chih-Yung Hu, Chu-Bin Liao, Chen-Hsuan Ho, Yu-Ping Chou, Yi-Hsuan Hsu, Yu-Hsun Lo, Edward Chern
Summary: In this study, a large and highly diverse synthetic human scFv antibody library was constructed, and novel TIM-3-neutralizing antibodies with immunomodulatory functions were identified. These findings demonstrate the potential of this library for biomedical research and the therapeutic potential of the three fully human TIM-3-neutralizing antibodies.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Junxia Wang, Liang Li, Yingkun Zhang, Kaifeng Zhao, Xiaofeng Chen, Haicong Shen, Yuanqiang Chen, Jia Song, Yuqiang Ma, Chaoyong Yang, Hongming Ding, Zhi Zhu
Summary: Efficient molecular selection is crucial for various biomedical applications. By utilizing deterministic lateral-displacement microfluidics, the equilibrium of dissociation can be greatly shifted, leading to improved selection efficiency and better discrimination of ligand affinity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Adel M. Zakri, Abdullah A. Al-Doss, Ahmed A. Ali, Emad M. Samara, Basem S. Ahmed, Mohammed A. Al-Saleh, Ali M. Idris, Omar A. Abdalla, Markus Sack
Summary: This study isolated two camel-derived nanobodies against Tomato leaf curl Sudan virus (ToLCSDV) using phage display technology. The nanobodies also cross-reacted with Tomato yellow leaf curl virus and showed significant enzyme-linked immunosorbent assay reactivity with plants infected with typical begomovirus symptoms. These results pave the way for developing diagnostics for begomovirus detection, design of novel nanomaterials based on virus-like particles, and nanobody-mediated begomovirus resistance in economically important crops.
Article
Biochemistry & Molecular Biology
Tulika Tulika, Rasmus W. Pedersen, Charlotte Rimbault, Shirin Ahmadi, Esperanza Rivera-de-Torre, Monica L. Fernandez-Quintero, Johannes R. Loeffler, Markus-Frederik Bohn, Anne Ljungars, Line Ledsgaard, Bjorn G. Voldborg, Fulgencio Ruso-Julve, Jan Terje Andersen, Andreas H. Laustsen
Summary: Recycling IgG antibodies can bind to antigens at physiological pH and release them at lower pH, achieving comparable therapeutic effect at lower doses. The pH-dependent antigen-antibody binding may not always be driven by histidine residues. The study presents a methodology using a natural antibody phage display library to discover recycling antibodies without the need for histidine doping.
Article
Chemistry, Multidisciplinary
David N. Philpott, Surath Gomis, Hansen Wang, Randy Atwal, Abdellali Kelil, Tanja Sack, Brandon Morningstar, Chris Burnie, Edward H. Sargent, Stephane Angers, Sachdev Sidhu, Shana O. Kelley
Summary: The rapid on-cell phage display platform presented in this study accelerates the development of high-performance human antibodies by mimicking the complex in vivo binding environment, improving screening efficiency and accuracy.
ACS CENTRAL SCIENCE
(2022)
Review
Microbiology
Ana S. S. Andre, Isa Moutinho, Joana N. R. Dias, Frederico Aires-da-Silva
Summary: The discovery of hybridoma technology and the development of phage display technology have opened a new era in antibody research and clinical development. Over the past thirty years, display selection technologies such as phage display have been widely promoted as ideal alternatives to traditional methods, with significant advancements in design, construction, and selection of antibody libraries. With the emergence of new therapeutic antibodies, phage display is expected to continue playing a central role, especially in challenging cases. In vivo phage display methods offer an advantage over conventional in vitro procedures for generating therapeutic antibodies against difficult targets and unmet medical needs.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Medicine, Research & Experimental
Yang Zhang
Summary: Antibody phage display technology is an important method for discovering monoclonal antibodies and has been widely used in the discovery of fully human antibodies. The technology has proven to be valuable with the approval of several top-selling antibody drugs.
Review
Chemistry, Multidisciplinary
Michael A. Firer, Galia Luboshits
Summary: The development and clinical efficacy of ADCs have attracted significant interest in academia and industry, with ten ADCs having received FDA approval. These drugs specifically deliver cytotoxic agents to target cells, showing promise in providing long-term clinical benefits for patients with hematological malignancies.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Multidisciplinary Sciences
Justina Rutkauskaite, Simon Berger, Stavros Stavrakis, Oliver Dressler, John Heyman, Xavier Casadevall i Solvas, Andrew deMello, Linas Mazutis
Summary: In this study, a droplet microfluidic approach was developed for high-throughput screening and sorting of antibody-secreting cells. The method utilizes Forster resonance electron transfer (FRET) signal to mediate the binding of antibodies and probes, enabling functional characterization of individual cells. The system efficiently screens antigen-specific cells and provides important data on antibody secretion rate and membrane-bound fraction.
Article
Biochemical Research Methods
Charlotte Rimbault, Pelle D. Knudsen, Anna Damsbo, Kim Boddum, Hanif Ali, Celeste M. Hackney, Lars Ellgaard, Markus -Frederik Bohn, Andreas H. Laustsen
Summary: Phage display technology is a powerful tool for selecting monoclonal antibodies against a diverse set of antigens. However, generating monoclonal antibodies against animal toxins is challenging due to difficulties in obtaining them from venom. This study successfully expressed alpha-cobratoxin in E. coli and used it as an antigen in a phage display selection campaign, resulting in the isolation of a scFv with similar binding affinity to a control scFv against the native toxin. The selected scFv inhibits the interaction between the acetylcholine receptor and the native toxin in vitro, representing the first entirely in vitro antibody selection strategy for generating neutralizing monoclonal antibodies against a snake toxin.
Article
Biochemistry & Molecular Biology
Frederik Peissert, Louis Pluss, Anna Maria Giudice, Tiziano Ongaro, Alessandra Villa, Abdullah Elsayed, Lisa Nadal, Sheila Dakhel Plaza, Luigi Scietti, Emanuele Puca, Roberto De Luca, Federico Forneris, Dario Neri
Summary: Programmed cell death protein 1 (PD-1) is an immunoregulatory target that can be targeted by different monoclonal antibodies for cancer therapy. In this study, researchers identified a new anti-PD-1 antibody with unique binding specificity and demonstrated its ability to block the interaction between PD-1 and PD-L1.
Article
Biology
Taishi Kondo, Kazuhiro Matsuoka, Shun Umemoto, Tomoshige Fujino, Gosuke Hayashi, Yasumasa Iwatani, Hiroshi Murakami
Summary: In this study, affinity maturation of monobodies against SARS-CoV-2 spike protein and their neutralizing activity against several variants were reported. One monobody showed extremely high affinity and efficiently neutralized multiple variants. These monobodies could be useful for neutralizing current and future SARS-CoV-2 variants.
LIFE SCIENCE ALLIANCE
(2022)
Article
Pharmacology & Pharmacy
Bahram Yavari, Seyyed Shamsadin Athari, Yadollah Omidi, Akram Jalali, Rezvan Najafi
Summary: EpCAM aptamer-activated nanoparticles were synthesized to enhance treatment efficiency in colorectal cancer. The nanoparticles showed superior cytotoxicity in vitro and effectively inhibited tumor growth in vivo without causing significant side effects.
JOURNAL OF DRUG TARGETING
(2023)
Article
Chemistry, Analytical
Sattar Akbari Nakhjavani, Balal Khalilzadeh, Hadi Afsharan, Nashmin Hosseini, Mohammad Hossein Ghahremani, Sandro Carrara, Savas Tasoglu, Yadollah Omidi
Summary: Recently, there has been increased interest in electrochemiluminescent (ECL) immunosensors for biomarker detection. A highly enhanced ECL immunosensing platform was designed for ultrasensitive detection of carcinoembryonic antigen (CEA) using functional nanostructures. By entrapping CEA biomolecules using a sandwich approach and incorporating luminol/silver nanoparticles as the signaling probe, the immunosensor exhibited excellent sensitivity and selectivity for CEA detection. It also demonstrated good repeatability and stability in real human serum, making it a potential candidate for clinical CEA detection and monitoring.
Article
Biochemistry & Molecular Biology
Mitra Torabi, Ayuob Aghanejad, Pouria Savadi, Abolfazl Barzegari, Yadollah Omidi, Jaleh Barar
Summary: Magnetic mesoporous silica nanoparticles (MMSNPs) have been developed as multifunctional drug delivery systems for targeted therapy. Magnetic cores were synthesized using the thermal decomposition method, and mesoporous silica was coated onto the cores to enhance biocompatibility. Sunitinib (SUN) was loaded into the MMSNPs and MUC-1 aptamers were attached to the particles. Characterization studies showed that the engineered MMSNPs had a smooth surface, spherical shape, and an average size of 97.6 nm. Biological analysis demonstrated that the targeted MMSNPs had the greatest impact on MUC-1 overexpressing cells compared to MUC-1 negative cells. In conclusion, the synthesized MMSNP-SUN-MUC-1 nanosystem is a unique multifunctional targeted delivery system for ovarian cancer cells that overexpress MUC-1.
Review
Polymer Science
Niloofar Babanejad, Kwadwo Mfoafo, Anusha Thumma, Yadollah Omidi, Hossein Omidian
Summary: Macroporous-interconnected cryostructures are prepared through a cryo-process, where polymerization and internal crosslinking occur at sub-freezing temperatures. These structures have been extensively studied for their potential applications in tissue engineering, cancer research, drug delivery, and sensors/biosensors. With their unique properties, such as assisting cell trafficking and providing a favorable environment for cell attachment during transplantation, cryostructures are ideal for the preparation of 3D systems for drug delivery, cell culture, tissue engineering, and macromolecule purification. In addition, cryostructures have been investigated to improve the properties of controlled-release pharmaceutical dosage forms. This review provides comprehensive insights into the preparation, characterization, and various biomedical and pharmaceutical applications of 3D cryostructures.
Article
Biochemical Research Methods
Negar Hossein-Nezhad Daneshvar, Yosef Masoudi-Sobhanzadeh, Yadollah Omidi
Summary: In this study, a machine learning framework was introduced, which selected features through an optimization algorithm and proposed a voting mechanism for accurate classification of biological/clinical data. The results showed that this method improved prior studies by approximately 10% in terms of accuracy, precision, recall, specificity, and F-measure on large-scale datasets. In conclusion, the proper configuration of efficient algorithms and methods can enhance the prediction power of machine learning approaches, aiding in the design of practical diagnosis healthcare systems and effective treatment plans.
BMC BIOINFORMATICS
(2023)
Article
Biology
Yosef Masoudi-Sobhanzadeh, Mohammad M. Pourseif, Ava Khalili-Sani, Behzad Jafari, Aysan Salemi, Yadollah Omidi
Summary: In this study, an optimization algorithm (Trader) was used to align amino acid sequences associated with antimicrobial peptides (AMPs) of Staphylococcus aureus and Arthrospira platensis. Similar sequences were identified, and candidate peptides were generated and filtered based on biochemical and biophysical properties. The 3D structures of the peptides were simulated using homology modeling techniques. Molecular docking approaches were then used to investigate the interactions between the generated peptides and S. aureus proteins. Results showed that four peptides had better molecular interactions, suggesting that the antimicrobial property of A. platensis may be attributed to its ability to disrupt the membrane and functions of pathogens.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Pharmacology & Pharmacy
Hossein Omidian, Jafar Razmara, Sepideh Parvizpour, Hamed Tabrizchi, Yosef Masoudi-Sobhanzadeh, Yadollah Omidi
Summary: The life cycle of a drug starts from its discovery and ends when it is disposed. Various entities such as drug discovery companies, manufacturers, regulatory agencies, suppliers, pharmacies, patients, and healthcare providers are involved in this process. Transparency, traceability, automation, and data security play crucial roles in ensuring effective and safe transactions among all parties. However, challenges like scalability, energy consumption, regulations, standards, and complexity hinder the adoption of new technology that can fulfill these requirements. This article highlights how blockchain technology can track, accelerate, and enhance the efficiency of complex operations like pharmaceutical development.
DRUG DISCOVERY TODAY
(2023)
Article
Pharmacology & Pharmacy
Kwadwo Mfoafo, Yadollah Omidi, Hossein Omidian
Summary: Thermoresponsive polymers have been widely used for the development of stimuli-responsive drug formulations in various routes of administration. However, their use has been limited by obstacles such as high polymer concentration, wide gelation temperature, low gel strength, poor mucoadhesiveness, and short retention. In-situ thermoresponsive mucoadhesive hydrogel blends or hybrids have been suggested as a solution to improve drug bioavailability and efficacy. This article highlights the development and assessment of such hydrogels in different administration routes.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2023)
Article
Multidisciplinary Sciences
Anna Torkamannia, Yadollah Omidi, Reza Ferdousi
Summary: This study presented a novel computational approach using a deep neural network-based binary classification model to predict synergistic drug combinations. Various physicochemical, genomic, protein-protein interaction, and protein-metabolite interaction information were used to predict the synergy effects of different drug combinations. The proposed deep neural network model demonstrated high accuracy in predicting synergistic drug combinations with a prediction accuracy of 92.21% and an AUC of 97.32% in tenfold cross-validation.
SCIENTIFIC REPORTS
(2023)
Review
Multidisciplinary Sciences
Sajini D. Hettiarachchi, Young M. Kwon, Yadollah Omidi, Robert C. Speth
Summary: The renin-angiotensin system (RAS) plays a role in several disorders and drugs that target this system are limited in their efficacy. Nanoparticle-mediated drug delivery systems offer a potential solution to overcome these limitations.
Review
Polymer Science
Nazanin Amiryaghoubi, Marziyeh Fathi, Jaleh Barar, Hossein Omidian, Yadollah Omidi
Summary: The function and success of organ/tissue engineering depend on the integrity and function of blood vessels and microvascular system. In vitro and in vivo strategies have been used to regenerate autologous vascular grafts. Advanced nanobiomaterials and technologies have revolutionized the engineering and regeneration of vessels and microvessels. Various natural and synthetic polymers have been utilized as scaffolds for vascular tissue engineering, including polyglycolic acid, poly-l-lactic acid, and polyurethane. Hybrid scaffolds with advanced bio-materials and nanostructures, such as graphene, have also been used. This review aims to discuss the applications of polymer-grafted graphene-based hybrid scaffolds in microvascular tissue engineering and regeneration.
EUROPEAN POLYMER JOURNAL
(2023)
Article
Pharmacology & Pharmacy
Azam Safary, Mostafa Akbarzadeh-Khiavi, Jaleh Barar, Yadollah Omidi
Summary: Induced autoimmunity or autoinflammatory-like conditions have been reported as rare adverse events following COVID-19 vaccination, but there is insufficient evidence to confirm their occurrence. Further research and monitoring are needed to understand the immunological mechanisms triggered by the vaccines.
Article
Pharmacology & Pharmacy
Ali Pourali, Yadollah Omidi
Summary: Cardiac troponin (cTn) is a complex protein attached to tropomyosin on the actin filament, serving as a vital biomolecule for calcium-mediated regulation of contractile apparatus and indicating cardiomyocyte dysfunction and ischemic phenomena in the heart tissue. Rapid and accurate analysis of cTn using electrochemical biosensors and microfluidics devices can greatly assist in the diagnosis and management of acute myocardial infarction (AMI). This editorial highlights the significance of cTn as a crucial biomarker in AMI diagnosis.
Article
Pharmacology & Pharmacy
Mitra Torabi, Ayuob Aghanejad, Pouria Savadi, Abolfazl Barzegari, Yadollah Omidi, Jaleh Barar
Summary: Mesoporous silica nanoparticles (MSNPs) were fabricated using the sol-gel method and modified with polyethylene glycol-600 (PEG600). Sunitinib (SUN) was loaded into the MSNPs, and MSNPs-PEG and MSNPs-PEG/SUN were grafted with mucin 16 (MUC16) aptamers. The biological impacts of the MSNPs on ovarian cancer cells were evaluated, and the results showed higher toxicity and apoptosis induction in MUC16 overexpressing OVCAR-3 cells.
Article
Pharmacology & Pharmacy
Mohammad Samiei, Elaheh Dalir Abdollahinia, Nazanin Amiryaghoubi, Marziyeh Fathi, Jaleh Barar, Yadollah Omidi
Summary: In this study, an injectable thermosensitive hydrogel was synthesized for promoting osteogenic differentiation of human dental pulp stem cells. The results showed that the hydrogel exhibited high biocompatibility and biodegradability, and had potential applications in dental tissue engineering.
