Sunday, December 21, 2014

Personalized genetic screen analysis by novel advanced approaches

Personalized genetic screen analysis by novel advanced approaches

We bring to the ordinary people advanced information obtained by high-end technology. Based on a DNA test, we can provide:

-  significant information about how an identified mutation alters protein structure and functions;
-  answer at a highly sufficient level the question whether it is a disease-causing mutation or not;
-  inform you whether existing drugs, if any, can influence your particular case (mutation);
-  propose experimental treatment and even natural products that might help physicians in case no approved drugs exist;
 - propose an individual project for each client;

This has implications for many bioinformatics prediction tools such as SIFT and PolyPhen, as these tools largely rely on residue conservation (i.e. whether one mutation is common to many species or not), limiting the use of conservation-based tools.

Thus, the current efforts of many scientific groups are focused on the development of new tools adding structural information to traditional bioinformatics predictions. However, these techniques are limited to simple descriptors which can save computational time. Instead, we suggest projects which are more time-consuming but tailored to each person,without any compromise of the accuracy.

Our approach combines all available methodologies and provides the best possible information about a certain mutation discovered in an individual.





At Micar21 Ltd, we are helping usher in the new era of personalized medicine by enabling a fundamental change in healthcare with customized treatments and data-driven insights tailored to the individual.

At the heart of personalized medicine, DNA sequencing technology is advancing at an even more rapid pace than the cell phone revolution. By decreasing cost and increasing speed for the analysis of whole genome sequence (WGS) data, our technology platform makes it easier to discover links between DNA sequence variations and human diseases.

In particular, we bring to ordinary people advanced information obtained by high-end technology. Based on a DNA test, we can provide significant information – at a high level of confidence – about how an identified mutation alters protein structure and functions, whether it is disease-causing and whether existing drugs, if any, can influence a certain mutation.

All this information can be highly helpful for any physician in choosing an accurate corresponding treatment. Even more, if no approved treatment exists, we can propose an experimental one to physicians.

Each our client will receive a personal project.

Molecular Basis of Inactive B-RAFWT and B-RAFV600E Ligand Inhibition, Selectivity and Conformational Stability: An in Silico Study

Molecular Basis of Inactive B-RAFWT and B-RAFV600E Ligand Inhibition, Selectivity and Conformational Stability: An in Silico Study

Filip Fratev *†, Svava Ósk Jónsdóttir †, Elina Mihaylova ‡ and Ilza Pajeva §

Center for Biological Sequence Analysis, Department of Systems Biology, 
Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Kongens Lyngby, Denmark, 
Micar Ltd., 39 Asparuh Str., 1000 Sofia, Bulgaria, and 
Centre of Biochemical Engineering “Ivan Daskalov”, Bl. 105 Acad G. Bontchev Str., 1113 Sofia, Bulgaria

Mol. Pharmaceutics, 2009, 6 (1), pp 144–157
DOI: 10.1021/mp8001107
Publication Date (Web): December 2, 2008
Copyright © 2008 American Chemical Society



The B-RAF kinase plays an important role both in tumor induction and maintenance in several cancers. The molecular basis of the inactive B-RAFWT and B-RAFV600E inhibition and selectivity of a series of inhibitors was examined with a combination of molecular dynamics (MD), free energy MM-PBSA and local-binding energy (LBE) approaches. The conformational stability of the unbounded kinases and in particular the processes of the B-RAFV600E mutant activation were analyzed. A unique salt bridge network formed mainly by the catalytic residues was identified in the unbounded B-RAFs. The reorganization of this network and the restriction of the active segment flexibility upon ligand binding inhibit both B-RAFWT and B-RAFV600E, thus appearing as an important factor for ligand selectivity. A significant correlation between the binding energies of the compounds in B-RAFWT and their inhibition effects on B-RAFV600E was revealed, which can explain the low mutant selectivity observed for numerous inhibitors. Our results suggest that the interactions between the activation segment and the αC-helix, as well as between the residues in the salt bridge network, are the major mechanism of the B-RAFV600E activation. Overall data revealed the important role of Lys601 for ligand activity, selectivity and protein stabilization, proposing an explanation of the observed strong kinase activation in the K601E mutated form.
© Micar21 All rights reserved.

Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow

Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow

Irene Kouskoumvekaki *†, Rasmus K. Petersen ‡§, Filip Fratev †∥, Olivier Taboureau †⊥, Thomas E. Nielsen # ∇, Tudor I. Oprea †○, Si B. Sonne §, Esben N. Flindt ‡§, Svava Ósk Jónsdóttir †◆, and Karsten Kristiansen *§

† Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
‡ BioLigands, Science Park, 5230, Odense, Denmark
§ Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen, Denmark
∥ Micar 21 Ltd., 34B Persenk Str., 1407, Sofia, Bulgaria
⊥ UMR-S973, MTi, University Paris Diderot, F-75013 Paris, France
# Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
∇ Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
○ Translational Informatics Division, Department of Internal Medicine, MSC09 5025, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131, United States
◆ Department of Toxicology and Risk Assessment, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860 Søborg, Denmark

J. Chem. Inf. Model., 2013, 53 (4), pp 923–937
DOI: 10.1021/ci3006148
Publication Date (Web): February 24, 2013
Copyright © 2013 American Chemical Society



Full agonists to the peroxisome proliferator-activated receptor (PPAR)γ, such as Rosiglitazone, have been associated with a series of undesired side effects, such as weight gain, fluid retention, cardiac hypertrophy, and hepatotoxicity. Nevertheless, PPARγ is involved in the expression of genes that control glucose and lipid metabolism and is an important target for drugs against type 2 diabetes, dyslipidemia, atherosclerosis, and cardiovascular disease. In an effort to identify novel PPARγ ligands with an improved pharmacological profile, emphasis has shifted to selective ligands with partial agonist binding properties. Toward this end we applied an integrated in silico/in vitro workflow, based on pharmacophore- and structure-based virtual screening of the ZINC library, coupled with competitive binding and transactivation assays, and adipocyte differentiation and gene expression studies. Hit compound 9 was identified as the most potent ligand (IC50 = 0.3 μM) and a relatively poor inducer of adipocyte differentiation. The binding mode of compound 9 was confirmed by molecular dynamics simulation, and the calculated free energy of binding was −8.4 kcal/mol. A novel functional group, the carbonitrile group, was identified to be a key substituent in the ligand–protein interactions. Further studies on the transcriptional regulation properties of compound 9 revealed a gene regulatory profile that was to a large extent unique, however functionally closer to that of a partial agonist.
© Micar21 All rights reserved.

Structural insight into the UNC-45–myosin complex

Structural insight into the UNC-45–myosin complex

Filip Fratev1,*, Svava Ósk Jónsdóttir2 and Ilza Pajeva3

Article first published online: 10 APR 2013
DOI: 10.1002/prot.24270


UNC-45;myosin;molecular dynamics;docking;HCM

The UNC-45 chaperone protein interacts with and affects the folding, stability, and the ATPase activity of myosins. It plays a critical role in the cardiomyopathy development and in the breast cancer tumor growth. Here we propose the first structural model of the UNC-45–myosin complex using various in silico methods. Initially, the human UNC-45B binding epitope was identified and the protein was docked to the cardiac myosin (MYH7) motor domain. The final UNC45B–MYH7 structure was obtained by performing of total 630 ns molecular dynamics simulations. The results indicate a complex formation, which is mainly stabilized by electrostatic interactions. Remarkably, the contact surface area is similar to that of the myosin-actin complex. A significant interspecies difference in the myosin binding epitope is observed. Our results reveal the structural basis of MYH7 exons 15–16 hypertrophic cardiomyopathy mutations and provide directions for drug targeting. 
Proteins 2013; 81:1212–1221. © 2013 Wiley Periodicals, Inc.

Combination of Genetic Screening and Molecular Dynamics as a Useful Tool for Identification of Disease-Related Mutations: ZASP PDZ Domain G54S Mutation Case

Filip Fratev *†‡, Elina Mihaylova ‡, and Ilza Pajeva †

† Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Block 105, 1113 Sofia, Bulgaria
‡ Micar21 Ltd., Persenk Str. 34B, 1407 Sofia, Bulgaria

J. Chem. Inf. Model., 2014, 54 (5), pp 1524–1536
DOI: 10.1021/ci5001136
Publication Date (Web): April 14, 2014
Copyright © 2014 American Chemical Society


Cypher/ZASP (LDB3 gene) is known to interact with a network of proteins. It binds to α-actinin and the calcium voltage channels (LTCC) via its PDZ domain. Here we report the identification of a highly conserved ZASP G54S mutation classified as a variant of unknown significance in a sample of an adult with hypertrophic cardiomyopathy (HCM). The initial bioinformatics calculations strongly evaluated G54S as damaging. Furthermore, we employed accelerated and classical molecular dynamics and free energy calculations to study the structural impact of this mutation on the ZASP apo form and to address the question of whether it can be linked to HCM. Seventeen independent MD runs and simulations of 2.5 μs total were performed and showed that G54S perturbs the α2 helix position via destabilization of the adjacent loop linked to the β5 sheet. This also leads to the formation of a strong H-bond between peptide target residues Leu17 and Gln66, thus restricting both the α-actinin2 and LTCC C-terminal peptides to access their natural binding site and reducing in this way their binding capacity. On the basis of these observations and the adult’s clinical data, we propose that ZASPG54S and presumably other ZASP PDZ domain mutations can cause HCM. To the best of our knowledge, this is the first reported ZASP PDZ domain mutation that might be linked to HCM. The integrated workflow used in this study can be applied for the identification and description of other mutations that might be related to particular diseases.