Amirata Saei Dibavar

Scopus Publications

Klebsiella pneumoniae LPS drives stromal-mediated repression of p53 and colorectal cancer chemoresistance
Konstantinos Fragkoulis, Barbara Łasut-Szyszka, Ákos Végvári, Diyoly Ayona, Amir Ata Saei, Marie-Stéphanie Aschtgen, Sylvain Peuget
Cell Death and Disease, 2026
The gut bacterial microbiota is increasingly recognized as a key modulator of colorectal cancer (CRC) initiation, progression and response to therapy. However, the mechanisms by which bacteria influence the response to anticancer drugs remain poorly understood. Here, we investigate the effects of microbiota-driven signaling on the tumor suppressor p53 and its impact on chemotherapy. We uncover a mechanism by which lipopolysaccharide (LPS) from Klebsiella pneumoniae and other Enterobacteria impairs p53 activity and promotes chemoresistance via paracrine signaling from the tumor microenvironment. While direct exposure to LPS did not alter the drug response of CRC cells, conditioned media from LPS-stimulated macrophages or fibroblasts suppressed p53 accumulation and attenuated the response to chemotherapeutic agents. Deep quantitative proteomics further revealed selective inhibition of a subset of p53 targets by inflammation. This same subset negatively correlated with inflammatory signature and immune infiltration in patients and was associated with improved survival following chemotherapy. Mechanistically, our data suggest that macrophage-derived extracellular vesicles contribute to p53 degradation in cancer cells. Overall, our findings reveal a microbiota-driven mechanism of p53 suppression via the microenvironment that contributes to chemoresistance, highlighting the impact of bacteria on tumor cell fate and therapeutic efficacy in CRC.
Solubility based mechanistic profiling of combinatorial drug therapy
Elham Gholizadeh, Ehsan Zangene, Uladzislau Vadadokhau, Danilo Ritz, Juho J. Miettinen, Rabah Soliymani, Marc Baumann, Mathias Wilhelm, Esko Kankuri, Paul A. Haynes, Caroline A. Heckman, Amir A. Saei, Mohieddin Jafari
Nature Communications, 2026
Acute myeloid leukemia (AML) remains challenging to treat due to extensive genetic heterogeneity, high relapse rates, and treatment-related toxicity. Although drug combinations offer therapeutic promise, their selection is often empirical. Here, we introduce Combinatorial Proteome Integral Solubility/Stability Alteration analysis (CoPISA), a high-throughput proteomics workflow that captures protein solubility/stability alterations uniquely induced by drug combinations. We applied CoPISA to two rationally designed AML drug pairs, LY3009120-sapanisertib (LS) and ruxolitinib-ulixertinib (RU), previously identified as the most effective and least toxic combinations among many candidates and validated in AML cell lines, patient-derived samples and zebrafish xenograft models. We uncovered an emergent mechanism termed "conjunctional targeting", in which combinatorial drug action induces combination-exclusive protein targets consistent with an AND-gate logic model. LS-specific converged on SUMOylation, chromatin condensation, and VEGF-linked adhesion, while RU-specific targets disrupted DNA-damage checkpoints, mitochondrial bioenergetics, and RNA-splicing. Post-translational modification analysis revealed combination-induced acetylation, methylation, and phosphorylation of key AML proteins, including NPM1. Network analysis demonstrated that a substantial fraction of AML-associated proteins targeted by CoPISA are unique to combinations, including DNMT3A, NPM1, and TP53. By uncovering a mechanistic layer beyond classical synergy, CoPISA provides a robust framework for the precision-guided design of combinatorial therapies in heterogeneous cancers.
Preventing Proteomics Data Tombs Through Collective Responsibility and Community Engagement
Uladzislau Vadadokhau, Mai Soliman, Leticia Castillon, Paula Pastor Muñoz, Linda Id, Swethaa Natraj Gayathri, Ankita Srivastava, Tyko Runeberg, Tamara González-Armijos, Karina Šapovalovaitė, Milda Sakalauskaite, Sadiksha Adhikari, Oluwatosin Abe, Tiialotta Tohmola, Hao Li, Srividhya Sundaresan, Hanna Vesikukka, Jannica Roininen, Ehsan Zangene, Rabah Soliymani, Sami T. Tuomivaara, Veit Schwämmle, Amir A. Saei, Markku Varjosalo, Mohieddin Jafari
Scientific Data, 2026
Public proteomics repositories now host vast amounts of mass spectrometry data, yet much of it remains difficult to reuse, risking "data tombs" that are open access but not practically re-analyzable. In spring 2025, a graduate-level course at the University of Helsinki tasked six student teams with reanalyzing six projects from the Proteomics Identification Database (label-free quantification only) using a common R-based workflow (rpx, mzR, QFeatures, DEP/MSqRob2/limma/OmicsQ packages) that was shared across all teams. The teams reproduced identification, optional quantification, normalization, imputation, and differential expression analyses, and compared the outcomes to the original studies. As expected, systemic barriers recurred across cases: (i) no sample and data relationship format for proteomics metadata in any of the cases; (ii) missing details regarding decoy sets for false discovery rate assessment; (iii) proprietary-only outputs or software (e.g., Thermo.msf, Progenesis) that impeded open reanalysis in interoperable, community-standard formats; (iv) missing data-independent acquisition spectral libraries or protein sequences database files (FASTA); (v) absent or vague normalization/imputation/statistical parameters; (vi) inconsistent file naming; and (vii) insufficient biological/technical replication in at least one project. These shortcomings yielded large discrepancies in the analysis results (e.g., 13,068 vs. 4,923 proteins; 108 vs. 11 differentially expressed proteins), and, in one instance, a highlighted protein lacked robust support in the deposited identifications. We observed that reproducibility in mass spectrometry-based proteomics hinges less on instruments than on transparent metadata, open formats, and executable analysis provenance. We propose that data creators provide a minimum re-analysis package, including raw data and open formats, community standards, basic quality control summaries, data-independent acquisition spectral libraries, and complete parameter/code sets with pinned versions or containers. Moreover, we recommend repository-level nudges toward making such packages mandatory. This educational exercise simultaneously trains the students as well as stress-tests the community data practices to prevent proteomics "data tombs".
Small molecule inhibition of voltage dependent anion channel 1 reroutes mitochondrial metabolite flux
Seyed Majed Modaresi, Leilei Zhang, Amir Ata Saei, Morris Degen, Mohammad Khavani, Hassan Gharibi, Ákos Végvári, Zhiwei Ye, Jie Zhang, Evgeny Pavlov, Elizabeth A. Jonas, Kenneth D. Tew, Sebastian Hiller, Danyelle M. Townsend, Eduardo N. Maldonado
Molecules and Cells, 2026
Voltage dependent anion channels (VDACs 1, 2 and 3) in the outer mitochondrial membrane control the flux of anions and oxidizable substrates that sustain mitochondrial metabolism. Nicotinamide adenine dinucleotide (NADH) closes VDAC by binding to a pocket, conserved in all isoforms, located in the inner wall of the channel. Previously, we identified the small molecule SC18 that targets the NADH-binding pocket of VDAC1 employing computational analysis. Here, we explored the interaction between SC18 and VDAC1 using high-resolution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. Atomically resolved data precisely confirmed the computational results, showing that SC18 binds to a site on VDAC1 that partially overlaps with the NADH binding pocket. SC18, in the presence of NADH blocked the conductance of VDAC1 reconstituted in lipid bilayers. To determine the metabolic effect of SC18, we combined readouts of mitochondrial metabolism and glycolysis with functional metabolomics and proteomics. Short-term treatment with SC18 inhibited mitochondrial metabolism and adenosine triphosphate production. Treatment over 24 h and 48 h further reduced mitochondrial uptake of pyruvate and glutamine, utilization of tricarboxylic acid cycle intermediates, as well as lipid, DNA and amino acid synthesis. Concomitant with the inhibition of mitochondrial metabolism, cellular uptake of glucose and glutamine increased in parallel with augmented lactate release. These results indicate that compensatory enhanced glycolysis sustains adenosine triphosphate production after impaired mitochondrial function induced by SC18 blockage of VDAC1. Our work sets a mechanistic foundation for VDAC1 inhibition as a novel strategy to target and reprogram cancer metabolism through modulation of the biosynthetic ability of mitochondria.
A ginsenoside metabolite and its derivative target PRELID3B against lung cancer cells
Jilin He, Chun-Nam Lok, Guanya Yang, Ying He, Yungen Liu, Amir Ata Saei, Yiwei Zhang, Chunlei Zhang, Yanting Zhu, Zhiwen Fu, Christian Michel Beusch, Pierre Sabatier, Roman A. Zubarev, Chi-Ming Che
Proceedings of the National Academy of Sciences of the United States of America, 2026
Ginseng is widely praised for its benefits on cancer patients, often attributed to its metabolite compound K ( CK ). Here, we synthesized a derivative ( CKD-4 ) that, compared with CK , exhibited enhanced cellular uptake, threefold greater cytotoxicity, and improved pharmacokinetics. CKD-4 induced significant growth inhibition on lung cancer patient-derived organoids, and on cell line-derived xenografts with minimal systemic toxicity. CKD-4 also suppressed orthotopic lung tumor growth in immunocompetent mice with enhanced antitumor immune infiltration. Using proteome integral solubility alteration and ProTargetMiner analyses, the mitochondrial phospholipid transfer protein PRELID3B was unbiasedly identified as a shared anticancer target of CK and CKD-4 . PRELID3B is a potential pancancer therapeutic target and prognostic biomarker supported by cancer genetics and transcriptomics evidence. Both CK and CKD-4 stabilize PRELID3B in cellular thermal shift assay and bind PRELID3B with K d of 23 µM and 5 µM, respectively, measured by biolayer interferometry. Multiomics analyses revealed that CK and CKD-4 share similar anticancer mechanisms, involving mitochondrial phospholipid depletion, integrated stress response activation, and immunomodulatory pathways induction associated with PRELID3B inhibition. This study provides the basis for the immunomodulatory and anticancer effects of ginseng metabolites through targeting PRELID3B, and illustrates the application of orthogonal proteomics in target identification of natural compounds.
Above-Filter Digestion Proteomics Reveals Drug Targets and Localizes Ligand Binding Site
Bohdana Sokolova, Hassan Gharibi, Maryam Jafari, Hezheng Lyu, Silvia Lovera, Massimiliano Gaetani, Amir Ata Saei, Roman A. Zubarev
Journal of Proteome Research, 2026
Identifying how drugs interact with proteins is fundamental to understanding their therapeutic effects and side effects. While numerous chemical proteomics methods exist for determining protein targets of drugs, each exhibits "blind spots," necessitating complementary approaches. We introduce Above-Filter Digestion Proteomics (AFDIP), which monitors trypsin digestion rates that decrease at ligand-binding sites, while potentially increasing elsewhere. Molecular dynamics simulations showed that these changes relate to backbone flexibility. Using AFDIP, we identified targets of various drugs and metabolites, allowing two-dimensional analysis with the drug concentration as the second dimension. The method identifies binding sites within ≤10 Å of crystallography-determined locations with improved resolution (≤5 Å) for larger proteins. Compared with existing proteolysis approaches, AFDIP offers simpler sample preparation, deeper proteome analysis, and broader sequence coverage. AFDIP addresses the blind spots of current techniques and provides structural insights, enhancing the chemical proteomics toolkit.
Mass spectrometry-based top-down proteomics for proteoform profiling of protein coronas
Seyed Amirhossein Sadeghi, Fei Fang, Reyhane Tabatabaeian Nimavard, Qianyi Wang, Guijie Zhu, Amir Ata Saei, Liangliang Sun, Morteza Mahmoudi
Nature Protocols, 2026
Toward a Species Search Engine: KISSE Offers a Rigorous Statistical Framework for Bone Collagen Tandem Mass Spectrometry Data
Hassan Gharibi, Amir Ata Saei, Alexey L. Chernobrovkin, Susanna L. Lundstrom, Hezheng Lyu, Zhaowei Meng, Akos Vegvari, Massimilliano Gaetani, Roman A. Zubarev
Advanced Science, 2025
DNA and bone collagen are two key sources of resilient molecular markers used to identify species from their remains. Collagen is more stable than DNA, and thus it is preferred for ancient and degraded samples. Current mass spectrometry‐based collagen sequencing approaches are empirical and lack a rigorous statistical framework. Based on the well‐developed approaches to protein identification in shotgun proteomics, a first approximation of the species search engine (SSE) is introduced. SSE named KISSE is based on a species‐specific library of collagenous peptides that uses both peptide sequences and their relative abundances. The developed statistical model can identify the species and the probability of correct identification, as well as determine the likelihood of the analyzed species not being in the library. The advantages and limitations of the proposed approach, and the possibility of extending it to other tissues is discussed.
A generative deep learning approach to de novo antibiotic design
Aarti Krishnan, Melis N. Anahtar, Jacqueline A. Valeri, Wengong Jin, Nina M. Donghia, Leif Sieben, Andreas Luttens, Yu Zhang, Seyed Majed Modaresi, Andrew Hennes, Jenna Fromer, Parijat Bandyopadhyay, Jonathan C. Chen, Danyal Rehman, Ronak Desai, Paige Edwards, Ryan S. Lach, Marie-Stéphanie Aschtgen, Margaux Gaborieau, Massimiliano Gaetani, Samantha G. Palace, Satotaka Omori, Lutete Khonde, Yurii S. Moroz, Bruce Blough, Chunyang Jin, Edmund Loh, Yonatan H. Grad, Amir Ata Saei, Connor W. Coley, Felix Wong, James J. Collins
Cell, 2025
Beyond the known cuts: trypsin specificity in native proteins
Marcelo Gaspar, Bohdana Sokolova, Amir Ata Saei, José C. Marques, Roman A. Zubarev
Chemical Communications, 2025
Peptides from trypsin digestion of native proteomes reveal that size, charge and local sequence motifs influence cleavage speed.
Protein corona composition modulates uptake of polymeric micelles by colorectal cancer cells
Munira Sirazum, Ahmed Abdelfattah, Prashant Pandey, Aliakbar Ashkarran, Soheyl Tadjiki, Shahriar Sharifi, Hassan Gharibi, Amir Ata Saei, Morteza Mahmoudi, Afsaneh Lavasanifar
Nanoscale Advances, 2025
Beyond Correlation: Establishing Causality in Protein Corona Formation for Nanomedicine
Arshia Rafieioskouei, Kenneth Rogale, Amir Ata Saei, Morteza Mahmoudi, Borzoo Bonakdarpour
Molecular Pharmaceutics, 2025
Monitoring Functional Posttranslational Modifications Using a Data-Driven Proteome Informatic Pipeline
Payman Nickchi, Uladzislau Vadadokhau, Mehdi Mirzaie, Marc Baumann, Amir A. Saei, Mohieddin Jafari
Proteomics, 2025
AI-driven prediction of cardio-oncology biomarkers through protein corona analysis
Avirup Guha, Seyed Amirhossein Sadeghi, Harikrishnan Hyma Kunhiraman, Fei Fang, Qianyi Wang, Arshia Rafieioskouei, Shaun Grumelot, Hassan Gharibi, Amir Ata Saei, Maryam Sayadi, Neal L. Weintraub, Sachi Horibata, Phillip Chung-Ming Yang, Borzoo Bonakdarpour, Mohammad Ghassemi, Liangliang Sun, Morteza Mahmoudi
Chemical Engineering Journal, 2025
The role of protein corona in advancing plasma proteomics
Amir Ata Saei, Liangliang Sun, Morteza Mahmoudi
Proteomics, 2025
One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug-Target Identification
Zhaowei Meng, Amir Ata Saei, Hezheng Lyu, Massimiliano Gaetani, Roman A. Zubarev
Analytical Chemistry, 2024
A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities
Hassan Gharibi, Ali Akbar Ashkarran, Maryam Jafari, Elizabeth Voke, Markita P. Landry, Amir Ata Saei, Morteza Mahmoudi
Nature Communications, 2024
Small molecule modulation of protein corona for deep plasma proteome profiling
Ali Akbar Ashkarran, Hassan Gharibi, Seyed Amirhossein Sadeghi, Seyed Majed Modaresi, Qianyi Wang, Teng-Jui Lin, Ghafar Yerima, Ali Tamadon, Maryam Sayadi, Maryam Jafari, Zijin Lin, Danilo Ritz, David Kakhniashvili, Avirup Guha, Mohammad R. K. Mofrad, Liangliang Sun, Markita P. Landry, Amir Ata Saei, Morteza Mahmoudi
Nature Communications, 2024
Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification
Amir A. Saei, Albin Lundin, Hezheng Lyu, Hassan Gharibi, Huqiao Luo, Jaakko Teppo, Xuepei Zhang, Massimiliano Gaetani, Ákos Végvári, Rikard Holmdahl, Steven P. Gygi, Roman A. Zubarev
Advanced Science, 2024
Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates
Zhaowei Meng, Amir Ata Saei, Hassan Gharibi, Xuepei Zhang, Hezheng Lyu, Susanna L. Lundström, Ákos Végvári, Massimiliano Gaetani, Roman A. Zubarev
Analytical Chemistry, 2024
Standardizing Protein Corona Characterization in Nanomedicine: A Multicenter Study to Enhance Reproducibility and Data Homogeneity
Ali Akbar Ashkarran, Hassan Gharibi, Seyed Majed Modaresi, Amir Ata Saei, Morteza Mahmoudi
Nano Letters, 2024
Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak
Yaroslav Lyutvinskiy, Konstantin O. Nagornov, Anton N. Kozhinov, Natalia Gasilova, Laure Menin, Zhaowei Meng, Xuepei Zhang, Amir Ata Saei, Tingting Fu, Julia Chamot-Rooke, Yury O. Tsybin, Alexander Makarov, Roman A. Zubarev
Journal of the American Society for Mass Spectrometry, 2024
Chemical Proteomics Reveals that the Anticancer Drug Everolimus Affects the Ubiquitin-Proteasome System
Anna A. Lobas, Amir Ata Saei, Hezheng Lyu, Roman A. Zubarev, Mikhail V. Gorshkov
ACS Pharmacology and Translational Science, 2024
Ultralight Ultrafast Enzymes**
Xuepei Zhang, Zhaowei Meng, Christian M. Beusch, Hassan Gharibi, Qing Cheng, Hezheng Lyu, Luciano Di Stefano, Jijing Wang, Amir A. Saei, Ákos Végvári, Massimiliano Gaetani, Roman A. Zubarev
Angewandte Chemie International Edition, 2024
Multi-omics exploration of biomolecular corona in nanomedicine therapeutics and diagnostics
Amir Ata Saei, Morteza Mahmoudi
Nanomedicine, 2024
Massive Solubility Changes in Neuronal Proteins upon Simulated Traumatic Brain Injury Reveal the Role of Shockwaves in Irreversible Damage
Amir Ata Saei, Hassan Gharibi, Hezheng Lyu, Brady Nilsson, Maryam Jafari, Hans Von Holst, Roman A. Zubarev
Molecules, 2023
Sex-Specific Silica Nanoparticle Protein Corona Compositions Exposed to Male and Female BALB/c Mice Plasmas
Ali Akbar Ashkarran, Hassan Gharibi, Jason W. Grunberger, Amir Ata Saei, Nitish Khurana, Raziye Mohammadpour, Hamidreza Ghandehari, Morteza Mahmoudi
ACS Bio and Med Chem Au, 2023
Multi-omics analysis of magnetically levitated plasma biomolecules
Ali Akbar Ashkarran, Hassan Gharibi, Dalia Abou Zeki, Irina Radu, Farnaz Khalighinejad, Kiandokht Keyhanian, Christoffer K. Abrahamsson, Carolina Ionete, Amir Ata Saei, Morteza Mahmoudi
Biosensors and Bioelectronics, 2023
NCF1-dependent production of ROS protects against lupus by regulating plasmacytoid dendritic cell development and functions
Huqiao Luo, Vilma Urbonaviciute, Amir Ata Saei, Hezheng Lyu, Massimiliano Gaetani, Ákos Végvári, Yanpeng Li, Roman A. Zubarev, Rikard Holmdahl
Jci Insight, 2023
Measurements of heterogeneity in proteomics analysis of the nanoparticle protein corona across core facilities
Ali Akbar Ashkarran, Hassan Gharibi, Elizabeth Voke, Markita P. Landry, Amir Ata Saei, Morteza Mahmoudi
Nature Communications, 2022
Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides
Hassan Gharibi, Alexey L. Chernobrovkin, Amir Ata Saei, Xuepei Zhang, Massimiliano Gaetani, Alexander A. Makarov, Roman A. Zubarev
Analytical Chemistry, 2022
First Experimental Evidence for Reversibility of Ammonia Loss from Asparagine
Jijing Wang, Sergey Rodin, Amir Ata Saei, Xuepei Zhang, Roman A. Zubarev
International Journal of Molecular Sciences, 2022
Mass Spectrometry, Structural Analysis, and Anti-Inflammatory Properties of Photo-Cross-Linked Human Albumin Hydrogels
Shahriar Sharifi, Amir Ata Saei, Hassan Gharibi, Nouf N. Mahmoud, Shannon Harkins, Naruphorn Dararatana, Erika M. Lisabeth, Vahid Serpooshan, Ákos Végvári, Anna Moore, Morteza Mahmoudi
ACS Applied Bio Materials, 2022
Redox regulation of PTPN22 affects the severity of T-cell-dependent autoimmune inflammation
Jaime James, Yifei Chen, Clara M Hernandez, Florian Forster, Markus Dagnell, Qing Cheng, Amir A Saei, Hassan Gharibi, Gonzalo Fernandez Lahore, Annika Åstrand, Rajneesh Malhotra, Bernard Malissen, Roman A Zubarev, Elias SJ Arnér, Rikard Holmdahl
Elife, 2022
Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass
Hassan Gharibi, Alexey L. Chernobrovkin, Gunilla Eriksson, Amir Ata Saei, Zena Timmons, Andrew C. Kitchener, Daniela C. Kalthoff, Kerstin Lidén, Alexander A. Makarov, Roman A. Zubarev
Journal of the American Chemical Society, 2022
Breathomics: Review of Sample Collection and Analysis, Data Modeling and Clinical Applications
Maryam Khoubnasabjafari, Mohamad Reza Afshar Mogaddam, Elaheh Rahimpour, Jafar Soleymani, Amir Ata Saei, Abolghasem Jouyban
Critical Reviews in Analytical Chemistry, 2022
System-wide identification and prioritization of enzyme substrates by thermal analysis
Amir Ata Saei, Christian M. Beusch, Pierre Sabatier, Juan Astorga Wells, Hassan Gharibi, Zhaowei Meng, Alexey Chernobrovkin, Sergey Rodin, Katja Näreoja, Ann-Gerd Thorsell, Tobias Karlberg, Qing Cheng, Susanna L. Lundström, Massimiliano Gaetani, Ákos Végvári, Elias S. J. Arnér, Herwig Schüler, Roman A. Zubarev
Nature Communications, 2021
An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation
Pierre Sabatier, Christian M. Beusch, Amir A. Saei, Mike Aoun, Noah Moruzzi, Ana Coelho, Niels Leijten, Magnus Nordenskjöld, Patrick Micke, Diana Maltseva, Alexander G. Tonevitsky, Vincent Millischer, J. Carlos Villaescusa, Sandeep Kadekar, Massimiliano Gaetani, Kamilya Altynbekova, Alexander Kel, Per-Olof Berggren, Oscar Simonson, Karl-Henrik Grinnemo, Rikard Holmdahl, Sergey Rodin, Roman A. Zubarev
Nature Communications, 2021
Nanotechnology for Targeted Detection and Removal of Bacteria: Opportunities and Challenges
Mohammad J. Hajipour, Amir Ata Saei, Edward D. Walker, Brian Conley, Yadollah Omidi, Ki‐Bum Lee, Morteza Mahmoudi
Advanced Science, 2021
Predictive biomarker panel in proliferative lupus nephritis, two-dimensional shotgun proteomics
Iranian Journal of Kidney Diseases, 2021
Can the biomolecular corona induce an allergic reaction? - A proof-of-concept study
Anne Muehe, Hossein Nejadnik, Henrik Muehe, Jarrett Rosenberg, Hassan Gharibi, Amir Ata Saei, Shu-Chen Lyu, Kari C. Nadeau, Morteza Mahmoudi, Heike E. Daldrup-Link
Biointerphases, 2021
Immunotargeting and therapy of cancer by advanced multivalence antibody scaffolds
Vala Kafil, Amir Ata Saei, Mohammad Reza Tohidkia, Jaleh Barar, Yadollah Omidi
Journal of Drug Targeting, 2020
COVID-19: Nanomedicine Uncovers Blood-Clot Mystery
Amir Ata Saei, Shahriar Sharifi, Morteza Mahmoudi
Journal of Proteome Research, 2020
Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin
Amir Ata Saei, Hjalmar Gullberg, Pierre Sabatier, Christian M. Beusch, Katarina Johansson, Bo Lundgren, Per I. Arvidsson, Elias S.J. Arnér, Roman A. Zubarev
Redox Biology, 2020
Thermal proteome profiling identifies oxidative-dependent inhibition of the transcription of major oncogenes as a new therapeutic mechanism for select anticancer compounds
Sylvain Peuget, Jiawei Zhu, Gema Sanz, Madhurendra Singh, Massimiliano Gaetani, Xinsong Chen, Yao Shi, Amir Ata Saei, Torkild Visnes, Mikael S. Lindström, Ali Rihani, Lidia Moyano-Galceran, Joseph W. Carlson, Elisabet Hjerpe, Ulrika Joneborg, Kaisa Lehti, Johan Hartman, Thomas Helleday, Roman Zubarev, Galina Selivanova
Cancer Research, 2020
ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery
Amir Ata Saei, Christian Michel Beusch, Alexey Chernobrovkin, Pierre Sabatier, Bo Zhang, Ülkü Güler Tokat, Eleni Stergiou, Massimiliano Gaetani, Ákos Végvári, Roman A. Zubarev
Nature Communications, 2019
Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution
Massimiliano Gaetani, Pierre Sabatier, Amir A. Saei, Christian M. Beusch, Zhe Yang, Susanna L. Lundström, Roman A. Zubarev
Journal of Proteome Research, 2019
Crosstalk between P53 and DNA damage response in ageing
Amir Mohammadzadeh, Mohammad Mirza-Aghazadeh-Attari, Shahin Hallaj, Amir Ata Saei, Mohammad Reza Alivand, Amir Valizadeh, Bahman Yousefi, Maryam Majidinia
DNA Repair, 2019
DNA damage response and repair in ovarian cancer: Potential targets for therapeutic strategies
Mohammad Mirza-Aghazadeh-Attari, Caspian Ostadian, Amir Ata Saei, Ainaz Mihanfar, Saber Ghazizadeh Darband, Shirin Sadighparvar, Mojtaba Kaviani, Hossein Samadi Kafil, Bahman Yousefi, Maryam Majidinia
DNA Repair, 2019
Repurposing of auranofin: Thioredoxin reductase remains a primary target of the drug
Xiaonan Zhang, Karthik Selvaraju, Amir Ata Saei, Padraig D'Arcy, Roman A. Zubarev, Elias SJ. Arnér, Stig Linder
Biochimie, 2019
Proteasome inhibitor b-AP15 induces enhanced proteotoxicity by inhibiting cytoprotective aggresome formation
Ellin-Kristina Hillert, Slavica Brnjic, Xiaonan Zhang, Magdalena Mazurkiewicz, Amir Ata Saei, Arjan Mofers, Karthik Selvaraju, Roman Zubarev, Stig Linder, Padraig D'Arcy
Cancer Letters, 2019
Oxidative stress induced by the deubiquitinase inhibitor b-ap15 is associated with mitochondrial impairment
Xiaonan Zhang, Belén Espinosa, Amir Ata Saei, Padraig D'Arcy, Roman A. Zubarev, Stig Linder
Oxidative Medicine and Cellular Longevity, 2019
Dynamic Proteomics Reveals High Plasticity of Cellular Proteome: Growth-Related and Drug-Induced Changes in Cancer Cells are Comparable
Pierre Sabatier, Amir Ata Saei, Shiyu Wang, Roman A. Zubarev
Proteomics, 2018
Bare surface of gold nanoparticle induces inflammation through unfolding of plasma fibrinogen
Bahar Kharazian, Samuel E. Lohse, Forough Ghasemi, Mohamad Raoufi, Amir Ata Saei, Fatemeh Hashemi, Fakhrossadat Farvadi, Reza Alimohamadi, Seyed Amir Jalali, Mohammad A. Shokrgozar, Nasser L. Hadipour, Mohammad Reza Ejtehadi, Morteza Mahmoudi
Scientific Reports, 2018
The deubiquitinase inhibitor b-AP15 induces strong proteotoxic stress and mitochondrial damage
Xiaonan Zhang, Paola Pellegrini, Amir Ata Saei, Ellin-Kristina Hillert, Magdalena Mazurkiewicz, Maria Hägg Olofsson, Roman A. Zubarev, Pádraig D'Arcy, Stig Linder
Biochemical Pharmacology, 2018
Formulation, characterization and cytotoxicity evaluation of ketotifen-loaded nanostructured lipid carriers
Jafar Ezzati Nazhad Dolatabadi, Aida Azami, Ali Mohammadi, Hamed Hamishehkar, Vahid Panahi-Azar, Yalda Rahbar Saadat, Amir Ata Saei
Journal of Drug Delivery Science and Technology, 2018
Comparative Proteomics of Dying and Surviving Cancer Cells Improves the Identification of Drug Targets and Sheds Light on Cell Life/Death Decisions
Amir Ata Saei, Pierre Sabatier, Ülkü Güler Tokat, Alexey Chernobrovkin, Mohammad Pirmoradian, Roman A. Zubarev
Molecular and Cellular Proteomics, 2018
Nanoparticle Surface Functionality Dictates Cellular and Systemic Toxicity
Amir Ata Saei, Mahdieh Yazdani, Samuel E. Lohse, Zahra Bakhtiary, Vahid Serpooshan, Mahdi Ghavami, Mahtab Asadian, Samaneh Mashaghi, Erik C. Dreaden, Alireza Mashaghi, Morteza Mahmoudi
Chemistry of Materials, 2017
Microparticles containing erlotinib-loaded solid lipid nanoparticles for treatment of non-small cell lung cancer
Zahra Bakhtiary, Jaleh Barar, Ayuob Aghanejad, Amir Ata Saei, Elhameh Nemati, Jafar Ezzati Nazhad Dolatabadi, Yadollah Omidi
Drug Development and Industrial Pharmacy, 2017
Theranostic MUC-1 aptamer targeted gold coated superparamagnetic iron oxide nanoparticles for magnetic resonance imaging and photothermal therapy of colon cancer
Morteza Azhdarzadeh, Fatemeh Atyabi, Amir Ata Saei, Behrang Shiri Varnamkhasti, Yadollah Omidi, Mohsen Fateh, Mahdi Ghavami, Saeed Shanehsazzadeh, Rassoul Dinarvand
Colloids and Surfaces B Biointerfaces, 2016
Targeted superparamagnetic iron oxide nanoparticles for early detection of cancer: Possibilities and challenges
Zahra Bakhtiary, Amir Ata Saei, Mohammad J. Hajipour, Mohammad Raoufi, Ophir Vermesh, Morteza Mahmoudi
Nanomedicine Nanotechnology Biology and Medicine, 2016
Possibilities in Germ Cell Research: An Engineering Insight
Fereshteh Esfandiari, Omid Mashinchian, Mohammad Kazemi Ashtiani, Mohammad Hossein Ghanian, Katsuhiko Hayashi, Amir Ata Saei, Morteza Mahmoudi, Hossein Baharvand
Trends in Biotechnology, 2015
Superparamagnetic iron oxide nanoparticles for in vivo molecular and cellular imaging
Shahriar Sharifi, Hajar Seyednejad, Sophie Laurent, Fatemeh Atyabi, Amir Ata Saei, Morteza Mahmoudi
Contrast Media and Molecular Imaging, 2015
Nanotoxicology: Advances and pitfalls in research methodology
Morteza Azhdarzadeh, Amir Ata Saei, Shahriar Sharifi, Mohammad J Hajipour, Alaaldin M Alkilany, Mohammad Sharifzadeh, Fatemeh Ramazani, Sophie Laurent, Alireza Mashaghi, Morteza Mahmoudi
Nanomedicine, 2015
Toxicity of nanoparticles
Nanoparticles for Biotherapeutic Delivery, 2015
Biomedical applications of superparamagnetic nanoparticles in molecular scale
Masoud Rahman, Amir A. Saei, Houshang Amiri, Morteza Mahmoudi
Current Organic Chemistry, 2015
Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks
Abolfazl Barzegari, Nazli Saeedi, Amir Ata Saei
Future Microbiology, 2014
Superparamagnetic iron oxide nanoparticles for delivery of therapeutic agents: Opportunities and challenges
Sophie Laurent, Amir Ata Saei, Shahed Behzadi, Arash Panahifar, Morteza Mahmoudi
Expert Opinion on Drug Delivery, 2014
Fe3O4 nanoparticles engineered for plasmid DNA delivery to Escherichia coli
Amir Ata Saei, Abolfazl Barzegari, Mostafa Heidari Majd, Davoud Asgari, Yadollah Omidi
Journal of Nanoparticle Research, 2014
Inhibition of survivin restores the sensitivity of breast cancer cells to docetaxel and vinblastine
Parisa Ghanbari, Mahsa Mohseni, Maryam Tabasinezhad, Bahman Yousefi, Amir Ata Saei, Simin Sharifi, Mohammad Reza Rashidi, Nasser Samadi
Applied Biochemistry and Biotechnology, 2014
Vibration and glycerol-mediated plasmid DNA transformation for Escherichia coli
Dariush Shanehbandi, Amir A. Saei, Habib Zarredar, Abolfazl Barzegari
FEMS Microbiology Letters, 2013
Soy protein, genistein, and daidzein improve serum paraoxonase activity and lipid profiles in rheumatoid arthritis in rats
Majid Mohammadshahi, Fatemeh Haidari, Amir Ata Saei, Bahman Rashidi, Soltanali Mahboob, Mohammad-Reza Rashidi
Journal of Medicinal Food, 2013
Electrochemical biosensors for glucose based on metal nanoparticles
Amir Ata Saei, Jafar Ezzati Nazhad Dolatabadi, Parvaneh Najafi-Marandi, Alireza Abhari, Miguel de la Guardia
Trac Trends in Analytical Chemistry, 2013
Haematococcus as a promising cell factory to produce recombinant pharmaceutical proteins
Amir Ata Saei, Parisa Ghanbari, Abolfazl Barzegari
Molecular Biology Reports, 2012
The microbiome: The forgotten organ of the astronauts body - Probiotics beyond terrestrial limits
Amir Ata Saei, Abolfazl Barzegari
Future Microbiology, 2012
Aldehyde and xanthine oxidase activities in tissues of streptozotocin- induced diabetic rats: Effects of vitamin e and selenium supplementation
Tayyebeh Ghaffari, Mohammad Nouri, Amir Ata Saei, Mohammad-Reza Rashidi
Biological Trace Element Research, 2012
Designing probiotics with respect to the native microbiome
Abolfazl Barzegari, Amir Ata Saei
Future Microbiology, 2012
Cellular toxicity of nanogenomedicine in MCF-7 cell line: MTT assay
Somaieh Ahmadian, Jaleh Barar, Amir Ata Saei, Mohammad Amin Abolghassemi Fakhree, Yadollah Omidi
Journal of Visualized Experiments, 2009
Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model - Effect of solute structure
Pharmazie, 2008
Solubility of sodium diclofenac in binary water + alcohol solvent mixtures at 25°C
A.A. Saei, F. Jabbaribar, M.A.A. Fakhree, W.E. Acree, A. Jouyban
Journal of Drug Delivery Science and Technology, 2008

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