BrainMap

Mr. Cristian Munteanu

Ph.D.

- INSTITUTUL DE BIOCHIMIE

Researcher | Teaching staff | Scientific reviewer | Manager

Currently I'm Senior Reseacher gr. III at the Institute of Biochemistry of the Romanian Academy and my main interest is related to the role of post-translational modifications in protein folding, sorting and degradation, with a particular emphasis regarding the activation of the immune system in cancer. My main background is centered around analytical biochemistry, data analytics and various mass spectrometry-based omics related fields.

Web of Science ResearcherID: I-9290-2016

Curriculum Vitae (07/04/2024)

Expertise & keywords

Usage of high speed robotics algorithms for in-sillico assisted experimental research of large biomolecular systems. Call name: P 4 - Proiecte de Cercetare Exploratorie, 2020
PN-III-P4-ID-PCE-2020-2444 2021 - 2023

Role in this project: Key expert

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: https://cyborg.biochim.ro

Abstract:

New biological entity development - protein engineering for medical or food security applications is extremely lengthy and costly and better in sillico assistance is paramount. For this purpose, our software - Robosample combines the speed of robot mechanics algorithms with Gibbs sampling to recover the correct free energy surfaces of biomolecules

This project is based on my work within the Illinois Institute of Technology as well as during the previous UEFISCDI TE2016 project. We propose a deeper merge between robotics and molecular simulation by introducing non-equilibrium sampling methods and new types of robotic joints never tried for molecules for which we have very promising preliminary data – for example we had a 6 times fold increase in folding time of extended deca-alanine into an α-helix.

We also aim to perform experimental work driven by our simulation analysis. Experimental work will involve novel antigenic peptide testing for melanoma immunotherapy using our Nano LC - MS System - Orbitrap Velos Pro System and HCV NS2-NS3 structure investigation through mutations. Assistance for experimental work will be provided for various partners in the following hot topics in molecular biosciences: plant-pathogen interaction.

The project also aims to make the software accessible to a wider scientific community. This will allow research groups focus more on analysis and less on implementation.

Molecular mechanisms of protein aggregation and unconventional secretion in the context of inflammation and neurodegenerative disorders Call name: P 1 - SP 1.1 - Proiecte de cercetare pentru stimularea tinerelor echipe independente
PN-III-P1-1.1-TE-2019-1705 2021 - 2023

Role in this project: Key expert

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: https://marichiritoiu4.wixsite.com/te156

Abstract:

Background: Inflammation is a hallmark of many pathologies such as autoimmune and neurodegenerative disorders, diabetes and atherosclerosis. Cytokines of the IL-1 family are primary mediators of inflammation. These are cytoplasmic proteins exported from macrophages and monocytes via the unconventional secretory pathway (UPS). I have previously shown that interleukin-1β (IL-1β) secretion form activated primary macrophages is regulated by the GRASP55-IRE1α axis and disrupting this pathway leads to intracellular aggregation of IL-1β, hampers its secretion and causes general proteome instability.

Hypothesis: Intracellular aggregation of cytoplasmic proteins (such IL-1β, α-synuclein and other) might be correlated with cargo availability for unconventional secretion, therefore modulating this process could provide potential methods to control pathological outcomes for inflammation and neurodegeneration.

Aim: Dissect the molecular mechanism and identify intracellular factors modulating aggregation and secretion of UPS cargoes. For this purpose we will use as model cargo IL-1β, produced by cells of the immune system and further corroborate the functional conservation of the identified factors for α-synuclein physiology in neurons and C. elegans model for Parkinson’s disease.

Expected results: This project should facilitate the understanding of signaling pathways and identify the intermediates transducing the information for the stress sensing machinery to induce cytoplasmic proteome instability. Also we estimate to indentify key proteins involved in UPS cargo aggregation, which could be used as targets to control the secretion of cytoplasmic proteins in the context of inflammation and neurodegeneration.

Role of TG2 in cancer tumor microenvironment for guiding metastasis prevention therapeutic approaches Call name: P 1 - SP 1.1 - Proiecte de cercetare pentru stimularea tinerelor echipe independente
PN-III-P1-1.1-TE-2019-0670 2020 - 2022

Role in this project: Key expert

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://www.biochim.ro/grant-29-tg2target/

Abstract:

Ovarian cancer (OC) is the leading cause of death among gynecological malignancies. Due to the insidious symptoms, it is diagnosed in late stages (III/IV) when the cancer cells have already disseminated. A major issue in the management of this disease is that OC tumors develops resistance to drugs used in front line treatment (platinum- and taxol-based compounds). Over the past decade, several studies have reported tissue transglutaminase (TG2) overexpression in cancer. Specifically, in OC, TG2 has been shown to promote all stages of tumor progression and has been linked to chemotherapeutic resistance. Our recent data suggest decreased tumor burden concurrently with increased infiltration, activation and effector functions of T cells, and loss of immunosuppressive signals in the tumor microenvironment (TME) resulting in development of an anti-tumorigenic phenotype in TG2 knock-out mice. Based on this evidence, TG2 therapeutic targeting shows a lot of promise for the management of metastatic ovarian cancer. In OC, it is already known that stromal and immune factors in the tumor microenvironment are modulating cancer cells/spheroids adhesion and invasion capacity We propose here fundamental research activities aimed to generate a better understanding of the role of TG2 in the context of TME using inhibitors as tools for deciphering cell communication pathways between different lineages in the tumor and also, to test combinations of TG2 inhibitors and drugs targeting the metastatic niche signaling to evaluate their potential in blocking OC dissemination.

Defining novel potential therapeutic targets in melanoma immunobiology using a combined proteome-immunopeptidome mass-spectrometry based analysis Call name: P 1 - SP 1.1 - Proiecte de cercetare Postdoctorală
PN-III-P1-1.1-PD-2019-1242 2020 - 2022

Role in this project: Project coordinator

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://oxprot.tk

Abstract:

The identification of numerous antigens of peptide origin on melanoma cells has placed immunotherapy as one of the most encouraging therapeutic alternative to the classical chemotherapies, which proved a low therapeutic response for metastatic melanoma. This has led the foundation of peptide-based immunotherapy, in which cancer vaccines containing one or several antigens are designed to boost the patient immune system for tumor recognition and rejection by clonal expansion of CD8+ cytotoxic T cells. As a result the search for new antigens with a superior immunological response for cancer treatment is one of the long-standing goals in translational research. One of the most encouraging antigens regarding clinical efficacy is tyrosinase, which undergoes unproductive folding in the endoplasmic reticulum (ER) of melanoma cells. This process leads to the selection of misfolded molecules for degradation and antigenic peptide production in the ubiquitin proteasome pathway. Our previous experiments have revealed that one of the most abundant tyrosinase epitopes presented on the cell surface of melanoma cells YMDGTMSQV (YMD peptide) can be oxidized to both of its Met residues and the oxidized forms results in improved CD8+ T cell activation. Moreover our preliminary results revealed that down regulating the expression level of one out of the four Methionine Sulfoxide Reductases (MSRs) responsible for oxidized Met reduction, results in a similar increased CD8+ T cell recognition suggesting a direct contribution of this enzyme in tumor recognition. Here we would like to address this aspect by analyzing the proteome and HLA-peptidome implications of each of the four intracellular MSRs enzymes (MSRA,MSRB1,MSRB2,MSRB3) using an innovative approach of SILAC (stable isotope labeling by amino acids in cell culture) based chemoproteomic technique. This would open the opportunity to discover novel modified antigens that could show superior immunological responses in immunotherapy.

Enhanced magnetic hyperthermia for malignant melanoma therapy Call name: P 2 - SP 2.1 - Proiect experimental - demonstrativ
PN-III-P2-2.1-PED-2019-3292 2020 - 2022

Role in this project: Key expert

Coordinating institution: INSTITUTUL NATIONAL DE CERCETARE DEZVOLTARE PENTRU FIZICA LASERILOR, PLASMEI SI RADIATIEI - INFLPR RA

Project partners: INSTITUTUL NATIONAL DE CERCETARE DEZVOLTARE PENTRU FIZICA LASERILOR, PLASMEI SI RADIATIEI - INFLPR RA (RO); INSTITUTUL DE BIOCHIMIE (RO); INSTITUTUL NATIONAL DE CERCETARE - DEZVOLTARE PENTRU FIZICA MATERIALELOR BUCURESTI RA (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://ema-hypermat.inflpr.ro

Abstract:

The main objective of the project “Enhanced magnetic hyperthermia for malignant melanoma therapy” (EMA-HYPERMAT) is to increase the level of TRL maturity of a technology for treatment of the malignant melanoma by means of magnetic hyperthermia, implying drug delivery nanosystems developed by us. Nanoparticles could be efficient cytostatic delivery systems, capable of tumor targeting; thereby, the use of such nanosystems decrease adverse effects, increase therapy effectiveness, and increase the survival of skin cancer patients. The combination of chemotherapeutics and hyperthermia can be adjusted, depending on the type and site of the tumor, also on the drug dose and temperature. We propose to combine the advantages of hyperthermia with the controlled delivery of the antitumoral loaded into magnetic particle systems. In this respect, the novelty of our proposal is related on the use of hyperthermia enhancers based on the combination of iron oxide/silica core-shell particles and superparamagnetic iron oxide nanoparticles (SPIONs) embedded into the thermoplastic polymeric nanospheres. Both particle systems bring specific advantages. For such formulations, smaller concentrations of the iron oxide nanoparticles are necessary in order to obtain similar performances in hyperthermia tests which results in lower toxicity, reduced immunogenicity and side effects while magnetic polymeric nanospheres will provide improved efficiency in the case of hyperthermia and a better drug release due to the higher loading capacity of the polymer matrix.

Validation of Iba1 protein as a new therapeutic target in human microglia Call name: P 2 - SP 2.1 - Proiect experimental - demonstrativ
PN-III-P2-2.1-PED-2019-3103 2020 - 2022

Role in this project: Key expert

Coordinating institution: UNIVERSITATEA BUCURESTI

Project partners: UNIVERSITATEA BUCURESTI (RO); INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://neurobiologie.ro/ro/47-romana/contracte-nationale/209-validarea-proteinei-iba1-ca-o-noua-tinta-terapeutica-in-microgliile-umane

Abstract:

Microglia are the resident immune cells of the central nervous system (CNS). In the healthy CNS microglia are not dormant, but survey the environment by extending and retracting their ramified processes without overall cell displacement. After an injury to the CNS or peripheral nervous system, microglia rapidly activates: the cell body increases in size, proximal processes become thicker, distal branches are less ramified, specific membrane ruffles develop and the cells move to the damaged site where they show increased phagocytic activity and release of pro-inflammatory mediators aimed to restore CNS homeostasis. Iba1 is a cytoskeleton protein specifically located only in microglia and macrophages where it acts as an actin-cross linking protein. In a previous study we showed that by silencing Iba1 expression in BV2 microglia cell line using specific anti-Iba1 siRNA, the migration, proliferation and cell adhesion were significantly reduced, while other activities that involve cytoskeleton and potentially Iba1, like phagocytosis and the functioning of P2x7 receptors, were significantly increased. In the present study we aim to investigate if our custom-made anti-Iba1 siRNA is equally efficient in silencing Iba1 protein in human microglia. All the human microglia experiments will be performed on the HMC3 human microglia cell line and will be doubled by similar experiments on rat microglia primary cultures which will serve as a reference. Silencing Iba1 in human microglia might be relevant for CNS diseases associated with increased microglia activation.

Context-dependent therapeutic targeting of ovarian cancer metastasis using TG2 small molecule inhibitors Call name: P 2 - SP 2.1 - Proiect experimental - demonstrativ
PN-III-P2-2.1-PED-2019-1543 2020 - 2022

Role in this project:

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://www.biochim.ro/grant-30-tg2therapy/

Abstract:

Ovarian cancer (OC) is the leading cause of death among gynecological malignancies. Due to the insidious symptoms, it is diagnosed in late stages when the cancer cells have already disseminated. A major issue in the management of this disease is that OC tumors develops resistance to drugs used in front line treatment. Over the past decade, several studies have reported tissue transglutaminase (TG2) overexpression in cancer. Specifically, in OC, TG2 has been shown to promote all stages of tumor progression. TG2 was found to be highly expressed in ovarian cancer stem cells and linked to chemotherapy resistance. Our recent data suggest decreased tumor burden concurrently with increased infiltration, activation and effector functions of T cells, and loss of immunosuppressive signals in the tumor microenvironment resulting in development of an anti-tumorigenic phenotype in TG2 knock-out mice. The physiological roles of TG2 are regulated by cellular context and localization. At the plasma membrane, TG2 binds to the gelatin-binding domain of fibronectin (FN) with high affinity and this complex provides a binding site for beta 1 and beta 3 integrins thus increasing cells capacity to attach and migrate onto the metastatic niche. In this project we aim at developing new inhibitors targeting the TG2-FN interaction. We propose new drug development activities for testing second generation compounds with improved pharmacokinetics features and to assess TG2 inhibitors’ potential to be used as anti-metastatic drugs in combination with other chemo- and immune-therapeutic agents.

Integrated development project for advanced medical treatment technologies Call name: P 1 - SP 1.2 - Proiecte complexe realizate in consorții CDI
PN-III-P1-1.2-PCCDI-2017-0728 2018 - 2021

Role in this project: Key expert

Coordinating institution: INSTITUTUL NATIONAL DE CERCETARE DEZVOLTARE PENTRU FIZICA LASERILOR, PLASMEI SI RADIATIEI - INFLPR RA

Project partners: INSTITUTUL NATIONAL DE CERCETARE DEZVOLTARE PENTRU FIZICA LASERILOR, PLASMEI SI RADIATIEI - INFLPR RA (RO); INSTITUTUL NATIONAL DE CERCETARE-DEZVOLTARE MEDICO-MILITARA „CANTACUZINO” (RO); INSTITUTUL DE BIOCHIMIE (RO); UNIVERSITATEA BUCURESTI (RO); UNIVERSITATEA PITESTI (RO)

Affiliation: UNIVERSITATEA BUCURESTI (RO)

Project website: http://teramed.inflpr.ro/

Abstract:

In order to increase community’s quality of life, the aim of the project proposal entitled “Integrated development project for advanced medical treatment technologies” (TERAMED) is to develop novel technologies with respect to the treatment of osseous and cutaneous conditions and oncological disorders. Given our experience in healthcare research and the current requirements of multidisciplinary and interinstitutional collaboration towards the personalized treatment purpose, the TERAMED project aims genuine synthesis and processing of biomaterials, but also functional and therapeutic evaluation relevant for clinical trials. The main objectives of the “Medical devices functionalized by laser technologies and alternatives for enhanced osseous integration and regeneration” subproject are to design and produce inorganic, composite or hybrid coatings for superior osteoconductive and osteoinductive performances of titanium-based implants. Smart wound patches and polymeric gels functionalized with antimicrobial and wound healing biomolecules incorporated within micro- and nanoparticles constitute the purpose of the “Medical devices (patches and gels) based on composite biomaterials obtained by laser, plasma and radiation technologies and alternatives for enhanced healing of cutaneous injuries” subproject. The “Technologies based on magnetic triggered nanostructures for oncological therapy: early diagnosis and targeted treatment” subproject aims the development of multifunctional medical devices for specific and selective diagnosis and treatment of breast cancer and melanoma. The general impact of the TERAMED project ensues from the beneficial conjunction of the clinical potential of the proposed medical devices, the feasible technological transfer and the economic advantages of interinstitutional collaboration.

From the classical nutrition to precise nutrition in animal production, scientific basis for the nutrition security of the population Call name: P 1 - SP 1.2 - Proiecte complexe realizate in consorții CDI
PN-III-P1-1.2-PCCDI-2017-0473 2018 - 2021

Role in this project: Key expert

Coordinating institution: INSTITUTUL NATIONAL DE CERCETARE-DEZVOLTARE PENTRU BIOLOGIE SI NUTRITIE ANIMALA - IBNA BALOTESTI

Project partners: INSTITUTUL NATIONAL DE CERCETARE-DEZVOLTARE PENTRU BIOLOGIE SI NUTRITIE ANIMALA - IBNA BALOTESTI (RO); UNIVERSITATEA BUCURESTI (RO); UNIVERSITATEA BABES BOLYAI (RO); INSTITUTUL DE BIOCHIMIE (RO); UNIVERSITATEA "ŞTEFAN CEL MARE" DIN SUCEAVA (RO); UNIVERSITATEA DE STIINTE AGRICOLE SI MEDICINA VETERINARA CLUJ-NAPOCA (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://www.ibna.ro/proiecte-de-cercetare/item/110-pn-iii-p1-1-2-pccdi-2017-0473

Abstract:

The overall objective of the project is to strengthen the institutional capacity of IBNA by developing new research directions based on „omics” technologies – nutrigenomics, toxicogenomics, proteomics, metabolomics – and to relaunch the Laboratory of Biotechnology. This will generate a set of innovative outcomes in animal nutrition. The innovative aspects of the project include: use of agro-food wastes as adsorption and detoxifying agents for feed contaminants; testing the effect of phytoadditives (plants or plant extracts not yet used for such purposes) as antibiotic replacers (willow bark extracts) on the interaction between the intestinal tract physiology and the intestinal microflora; investigation of several less characterized and used protein-oleaginous sources (cowpea, Jerusalem artichoke, etc.); in vitro experimental models to evaluate the decontaminating potential of wastes under conditions of concurrent fungal, viral and microbial contamination; development of new feeding products which ensure a more efficient use of the protein in ruminants.

The project covers three regions of development and the partners are prestigious institutions, with complementary infrastructure and expertise, with converging scientific interests. The consolidation of new directions will enhance, both for IBNA (the relaunched institution), and for its partners, their capacity of applying for/running research projects, allowing studies with a high level of complexity, which generate practical results, relevant for the development of the animal production sector.

The project will impact on the human resources, the budget allowing the employment of 14 researchers (of which 10 by IBNA), whose specialisation is already ensured; it will also support the enhancement of the scientific expertise of the senior researchers by using vouchers. The training periods will enrich the portfolio of methods and techniques that can be applied for the directions in which IBNA aims to develop/relaunch.

Development of advanced platforms for the analysis and modeling of complex biological systems Call name: P 1 - SP 1.2 - Proiecte complexe realizate in consorții CDI
PN-III-P1-1.2-PCCDI-2017-0046 2018 - 2021

Role in this project: Key expert

Coordinating institution: INSTITUTUL NATIONAL DE CERCETARE-DEZVOLTARE PENTRU ELECTROCHIMIE SI MATERIE CONDENSATA - INCEMC TIMISOARA

Project partners: INSTITUTUL NATIONAL DE CERCETARE-DEZVOLTARE PENTRU ELECTROCHIMIE SI MATERIE CONDENSATA - INCEMC TIMISOARA (RO); INSTITUTUL DE BIOCHIMIE (RO); UNIVERSITATEA DE STIINTE AGRICOLE SI MEDICINA VETERINARA CLUJ-NAPOCA (RO); INSTITUTUL NATIONAL DE CERCETARE - DEZVOLTARE CHIMICO - FARMACEUTICA - I.C.C.F. BUCURESTI (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: https://www.incemc.ro/index.php?page=AZ/PN-III-P1-1.2-PCCDI-2017-0046.html

Abstract:

The complex project 'Development of advanced platforms for the analysis and modeling of complex biological systems' (TEHNOBIOSIST) coordinated by INCEMC Timisoara, in collaboration with IBAR Bucuresti, USAMV Cluj-Napoca and ICCF Bucuresti consists of 3 projects with the following objectives: 1. designing and functionalization of a bioanalytical platform in multiplex system for microfluidics-mass spectrometry coupling and its applications in modern glycoproteomics; 2. development of proteomic methods employing microfluidic and bioinformatic technologies for pharmacological assays; 3. implementation of these advanced systems for authenticity and quality assessment of Romanian vegetal oils.

The platforms designed within TEHNOBIOSIST will provide a major technical-economical and bioeconomical input derived from: i) complete automatization; ii) reducing the working time, sample consumption and analysis costs; iii) increase in the reproducibility, sensitivity of the experiment and accuracy of generated data; iv) development and updating of the existing databases with the newly identified biomarkers.

By the foreseen results, TEHNOBIOSIST has a marked bioeconomical impact: innovation in the analytical field which will enhance a thorough study of complex biological systems; hiring of young researchers; reorganization of R&D national system on modern and high performance bases; innovation, development and upgrading of the research infrastructure existing at the institutions involved in the project and last, but not least, providing (after patenting/publication) the pharmaceutical companies, the analytical system producers, bioclinical laboratories and the economical agents in charge with the control of food product quality with new and efficient techniques, optimized for a broad range of analyses and of new scientific results based on which they can focus their activity, their own research and production in the sense of improving the quality of life and products in Romania.

Mass spectrometry based investigation of the oxidative stress as a potential key-player in the immunobiology of melanoma Call name: P 1 - SP 1.1 - Proiecte de cercetare Postdoctorală
PN-III-P1-1.1-PD-2016-1528 2018 - 2020

Role in this project: Project coordinator

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://imunopep.tk

Abstract:

A promising approach of the therapeutic strategy in melanoma is based on cancer cells potential to trigger an immune response by expressing at the cell surface of antigenic peptides derived from proteins such as Melan-A, Gp100, MAGEs, Tyrosinase. This has led to therapies based on cancer vaccines in which an antigenic peptide or a cocktail of antigens are used to boost the immune system of the patient for tumor cell recognition and rejection. This strategy offers the advantages of an increased specificity and a lower toxicity compared with the traditional interventions. One of the most promising melanoma antigens is tyrosinase, which was frequently found as overexpressed in melanomas. It wash shown that this protein undergoes unproductive folding in the endoplasmic reticulum (ER) leading to the selection of the incorrectly folded molecules for degradation via the ubiquitin proteasome system. In this pathway peptides are generated, which can form stable complexes with HLA molecules in ER and be presented to the tumor cell surface for CD8+ T cell recognition and melanoma cell destruction. Our preliminary experiments suggest that the tyrosinase-derived peptide YMDGTMSQV (YMD) presented in complex with HLA-A*0201 can be oxidized to both of the Met residues from its sequence. We have found from immunological CTL assays that a hydrogen peroxide (H2O2) oxidized YMD peptide triggers an increased immune response, in comparison with the native peptide. We aim here to characterize the oxidation forms induced by the H2O2 treatment of the peptide, develop a preparative or semi-preparative method for obtaining these forms, analyze their CD8+ T cell response and study the possibility of intracellular oxidation and presentation of these forms in cells isolated from melanoma patients. This will provide the opportunity to study the tumor immunobiology, whilst obtaining antigens with increased immunogenicity for subsequent use in the immunotherapy of melanoma.

Free energy prediction of biomolecular processes using high speed robotics algorithms and its use in in-silico driven experimental research. Call name: P 1 - SP 1.1 - Proiecte de cercetare pentru stimularea tinerelor echipe independente
PN-III-P1-1.1-TE-2016-1852 2018 - 2020

Role in this project: Key expert

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://old.biochim.ro/ib/projects/robofep/robofep.php

Abstract:

Critical quantities in experimental biomolecular research such as affinity constants, IC50s or rate constants are a direct reflection of the free energy in their associated processes. Therefore, in silico prediction of free energy can greatly enhance research effectiveness both in terms of costs and system detailed understanding. However, to predict in silico the free energy of a bio-molecular process is at the time being overwhelmingly difficult, especially when large biomolecules such as proteins or nucleic acids are involved - as a huge number of their configurations needs to be drawn from their practically infinite statistical thermodynamic ensemble.

To address these difficulties, we aim in this project to improve, adapt and use high speed robotics algorithms for molecular sampling that can easily escape the spatial and temporal scales in which classical methods are usually trapped. This project builds further upon a Hamiltonian Monte Carlo algorithm that we have recently developed to reproduce the Boltzmann distribution necessary for correct free energy predictions. Herein we plan to develop two new multiscaling methods, namely Generalized Adaptive Mixing (GAM) and Dynamic Adaptive Constraing (DAC), that can hike between scales without losing any level of force field detail or statistical mechanics rigor. These new methods can be a major leap in molecular simulation strategies.

We also aim by this project to implement these in the already existing Application Programming Interfaces (APIs) Simbody and Molmodel – for which we collaborate with groups from Stanford and Upsalla universities.

Last but not least we aim herein to use our methods to assist experimental work performed either by members of our team or in cooperation with various partners in the following hot topics in molecular biosciences: plant-pathogen interaction, HIV and HCV drug design and immunotherapy.

Structure assisted investigation of critical protein families involved in plant immunity Call name: P 4 - Proiecte de Cercetare Exploratorie
PN-III-P4-ID-PCE-2016-0650 2017 - 2019

Role in this project: Key expert

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://www.biochim.ro/grant-7-strassist/

Abstract:

We aim by this proposal to build up upon our previous experience in tackling new aspects related to the molecular structure, interactions and functioning of two major protein classes of plant immune system: the R-gene products and the constitutive tandems formed as a first layer of plant immunity in tomato by cell surface receptor-like kinases (RLKs) and receptor like proteins (RLPs), in an attempt to understanding their functioning.

Related to R-proteins we intend to further build upon results obtained on the structure of CC-, NB- and LRR- domains and their interactions, by addressing new problems, such as: (1) The quantification of LRR domain structural diversity of 130 R proteins we have recently identified in the potato genome in collaboration with Aska Goverse from Wageningen University, member of the Potato Genome Consortium. (2) The investigation of the structural basis of CC domain interactions in RGA4 and RGA5 R-protein families from rice by combining molecular modeling and simulation with crystallography, NMR and yeast-two hybrid, in collaboration with the group of Thomas Kroj form INRA Montpellier. (3) And finally the investigation of interactions taking place in the complexes formed by Arabidopsis ZAR1, ZED1 with the AVR HopZ1a by combining bioinformatics, molecular modelling and laboratory experiments, in collaboration with the group of Jennifer Lewis from Berkeley University.

Related to RLK-RPS, the first layer of plant immunity - we intend to combine our experience in glycobiology and biocomputing in aiming to investigate the glycosylation of tomato Cf4/9 and model its constitutive interactions with SOBIR1, the suppressor of BIR1 RLK, in collaboration with Matthieu Joosten from the Laboratory of Phytopathology from Wageningen.

Miniaturized bio-platform for simultaneous melanoma combination therapy and tumorigenicity screening Call name: P 2 - SP 2.1 - Proiect experimental - demonstrativ
PN-III-P2-2.1-PED-2016-1628 2017 - 2018

Role in this project: Key expert

Coordinating institution: INSTITUTUL NATIONAL DE CERCETARE DEZVOLTARE PENTRU FIZICA LASERILOR, PLASMEI SI RADIATIEI - INFLPR RA

Project partners: INSTITUTUL NATIONAL DE CERCETARE DEZVOLTARE PENTRU FIZICA LASERILOR, PLASMEI SI RADIATIEI - INFLPR RA (RO); INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://lspi.inflpr.ro/2017/PED/PED131/Home.html

Abstract:

Cancer is among the major causes of mortality nowadays, estimations provided by the World Health Organization revealing that its incidence is expected to increase by about 70%, up to 22 million cases, during the next two decades. Melanoma is the most aggressive skin cancer due to its high multi-drug resistance, frequent relapse and decreased survival rate. All major therapies, including chemo-, immuno-, and radio-therapies have failed to increase patients survival rates significantly due to a complex interplay of genetic, host, and environmental factors. It was recently evidenced that tumour cells may exhibit ‘plasticity’ in response to microenvironmental cues. The geometric features of cell-matter interface may influence a population of cells that can guide cancer cells towards a stem-cell-like state. The goal of this project proposal is to design, fabricate and test the performances of a miniaturized bioplatform that will simultaneously address two objectives: i) the synergistic co-targeting of melanoma cells by a precise mixture of signaling path inhibitors and epigenetic modulators; and ii) the evaluation of cells tumorigenicity guided by the geometric features of the patterns assembled on substrates. One pot laser technique Combinatorial Matrix Assisted Pulsed Laser Evaporation will be applied through specific designed masks to develop bioplatforms with innovative configurations. Several in vitro assays will be performed to evaluate biochips performances against different melanoma cell lines, while melanocytes and dermal fibroblasts will be used as controls. Moreover, in order to reproduce the in vivo environment and interactions, we will grow spheroids (mini-tumors) on the laser-fabricated patterns. Such mini-bio-labs that combine smart materials and cell-instructive interfaces could push forward advances in combination cancer therapy, new drugs formulations and hopefully personalized therapeutic strategies.

Indentification of first in class chemical scaffolds against Hepatitis C Virus NS2 cysteine protease Call name: P 3 - SP 3.2 - Proiecte ERA.NET - COFUND
ERA.NET.RUS PLUS-HCVCYSPROT 2016 - 2018

Role in this project: Key expert

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO); INSTITUTUL DE CHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://www.hcvcysprot.com

Abstract:

Hepatitis C Virus (HCV) infects 120-130 million people worldwide. Most of cases evolve to chronicity inflicting liver disease ranging from fibrosis to cirrhosis and hepatocellular carcinoma. The standard therapy consisting of interferon alpha and ribavirin has been recently complemented by direct acting antivirals (DAA) which

target NS3 protease, NS5A protein and NS5B polymerase. The FDA approved DAAs and the others in advanced clinical trials increase significantly the sustained virological response and moreover there is proof of concept for an interferon free therapy. However, the new DAAs do not provide full genotype coverage and there are still significant side-effects. Thus, there is an unmet need for new antiviral strategies. The majority of the present antiviral therapies have focused on three major targets: NS3 protease, NS5B polymerase and NS5A protein. A very attractive target is represented by the second viral protease, NS2 cysteine autoprotease. NS2 protease is crucial for polypeptide processing and viral replication. Up to date, the identification of NS2 protease inhibitors was hampered by the scarce of robust enzymatic assays which might be automated for highthroughput screening campaigns. The aim of the project is to identify first in

class chemical scaffolds with inhibitory activity for HCV NS2 protease. To accomplish that, we will take

advantage of a unique cell based NS2 enzymatic assay to perform the primary screening. The resulted hits will be confirmed by secondary screenings in Hepatitis C Virus cell culture system. The mode of action will be confirmed by drug resistant mutations identification in HCVcc and in “in vitro”biochemical assays for NS2 protease activity. The validated scaffolds will be derivatized for structure –activity relationship (SAR) studies.

Validation of the combined use of RNAi and mass spectrometry for the identification of microglial therapeutic targets important for neuropathic pain and Alzheimer disease Call name: Joint Applied Research Projects - PCCA 2013 - call
PN-II-PT-PCCA-2013-4-0294 2014 - 2017

Role in this project: Key expert

Coordinating institution: UNIVERSITATEA BUCURESTI

Project partners: UNIVERSITATEA BUCURESTI (RO); INSTITUTUL DE BIOCHIMIE (RO); PHARMA SERV INTERNATIONAL SRL (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://neurobiologie.ro/Contracte-nationale/validarea-folosirii-combinate-a-tehnicii-de-rnai-si-spectrometrie-de-masa-pentru-identificarea-unor-tinte-terapeutice-din-microglii-importante-pentru-durerea-neuropatica-si-maladia.html

Abstract:

Neuropathic pain is prevalent among older patients, mainly because many diseases that cause neuropathic pain increase in incidence with age. Furthermore, older patients frequently suffer of neurodegenerative diseases like Alzheimer, which complicates drug regimens and increase the burden in economic and therapeutic terms. Therefore, is very important to better understand the pathologic mechanism of these two ailments, in order to find a better treatment with less side effects and drug-drug interactions. Iba-1, a specific marker for microglia, is an actin-cross linking protein involved in membrane ruffling and phagocytosis in microglia and macrophages which seems to be crucial for their survival and pro-inflammatory activity. Its silencing could represent a new therapeutic target for neuropathic pain and potentially for Alzheimer disease, given its strong up-regulation in microglia activated in these two conditions. In this project we want to show that by using specially designed siRNA molecules we can silence the Iba-1 gene which can have consequences on microglia activation, cytokinesis and phagocytosis potentially through P2X7 inactivation. The end-product of this project will be an intellectual property (IP) patent for the discovery of a new drug targeting a specific protein in microglia/macrophages and new mass spectrometry protocols to measure the silencing efficiency. We firmly believe that the outcome of this project will lead to a better understanding of the Iba-1 role in microglia, of the P2X7 functioning at cellular and molecular level and will open future clinical development pathways for other treatments for neuropathic pain, and potentially Alzheimer disease.

Selection of protein degradative pathways in the pathogenesis of human diseases Call name: Exploratory Research Projects - PCE-2012 call
PN-II-ID-PCE-2012-4-0350 2013 - 2016

Role in this project: Key expert

Coordinating institution: INSTITUTUL DE BIOCHIMIE

Project partners: INSTITUTUL DE BIOCHIMIE (RO)

Affiliation: INSTITUTUL DE BIOCHIMIE (RO)

Project website: http://www.biochim.ro/ib/projects/prodegrad/prodegrad.php

Abstract:

A considerable fraction of all newly synthesized secretory polypeptides fail to attain their native conformation due to mutations, transcriptional and translational errors, folding defects or endoplasmic reticulum (ER) stress conditions. Besides the lack of function, the accumulation of aggregated proteins jeopardize the ER homeostasis and the cell functioning. Terminally misfolded polypeptides are retained and eventually removed by the ER associated degradation pathway(ERAD).We have recently found that besides the mannosidase-like domain, EDEM1 protein, one of the important players of the ERAD has an intrinsically disordered domain with high prediction for favoring protein-protein interactions. Indeed, we showed that this domain is responsible for the interaction with a misfolded tyrosinase mutant. In sum, we suggest that the ER associated degradation of glycoproteins depends less on the glycan recognition signals while rather relying on the direct recognition of the misfolded region of the polypeptide. The aim of this project is to validate this working hypothesis using ERAD substrates involved in tumor antigen degradation/peptide presentation and viral disassembly. Finally, we will use transgenic C.elegans as models for Huntington, Alzheimer and Parkinson diseases, to decipher the pathology and toxicity of protein aggregation. Overall, our approach will reveal new insights into the mechanistic details of the ERAD pathway and help identify new therapeutic targets.

Modeling molecular complexes and assemblies with experimental and bioinformatic constraints Call name: Exploratory Research Projects - PCE-2011 call
PN-II-ID-PCE-2011-3-0342 2011 - 2016

Role in this project: Key expert

Coordinating institution: Institutul de Biochimie al Academiei Romane

Project partners: Institutul de Biochimie al Academiei Romane (RO)

Affiliation:

Project website: http://www.biochim.ro/ib/projects/molint/molint_e.php

Abstract:

Protein-protein and protein-DNA assembiles in three types of systems will be investigated by constrained molecular modeling and simulation, aiming to assist and drive experimental research within the particular fields explored. The first field relates to the domain architecture of resistance gene products in plants and their interaction with effector proteins, an interaction that is instrumental in plant pathogen defense mechanisms. The second explores the structural basis of the differential functioning of human topoisomerases and the effects of some point mutations proven to induce differential malignant effects in topo II alpha and beta. Finally the third line of research tackles the structural biology of RAG-DNA synaptic complexes, involved in the assembly of the gene segments coding for the variable portions of lymphocyte antigen receptors. The three directions reflect the diversity of macromolecular assemblage in biological systems but also unveil common roots residing in the molecular geometry, interactions and dynamics at atomic level, and hence they can be tackled by common approach in which we intend to bring some contributions. On this line we intend to continue the endeavor started in a previous PN2-ID project to develop and implement in-silico techniques and use them as a motive force in molecular life sciences, when intertwined with the experimental approach.

FILE DESCRIPTION	DOCUMENT
List of research grants as project coordinator or partner team leader
Significant R&D projects for enterprises, as project manager
R&D activities in enterprises
Peer-review activity for international programs/projects