Publications

2022

41. 4- phenylbutyric acid—Identity crisis; can it act as a translation inhibitor? D. Stein, Z. Slobodnik, B. Tam, M. Einav, B. Akabayov, S. Berstein, D. Toiber (2022). Aging Cell. 2022;00:e13738.

40. MolOptimizer: a molecular optimization toolkit for fragment-based screening. S-J. Viswas, D. Vilenchik, B. Akabayov (2022). Submitted.

39. Machine learning approaches to optimize small-molecule inhibitors for RNA targeting. H. Grimberg , V.S. Tiwari, B. Tam, L. Gur-Arie, D. Gingold, L. Polachek, B. Akabayov (2022). Journal of Cheminformatics, 14 (4).

2021

38. Inferring primase-DNA specific recognition by using a data-driven approach. A. Soffer*, S.A. Eisdorfer*, M. Ifrach, S. Ilic, A. Afek, H. Schussheim, D. Vilenchik, B. Akabayov, (2021). Nucleic Acids Research, 49(20), 11447–11458.

37. Cell-penetrating peptide conjugates of indole-3-acetic acid-based DNA primase/Gyrase inhibitors as potent antitubercular agents against planktonic and biofilm culture of Mycobacterium smegmatis. R.P. Dewangan, M. Singh, S. Ilic, B. Tam, B. Akabayov, (2021). Chemical Biology & Drug Design, 98(5), 722-732.

36. Molecular Dynamics Simulations of Duplexation of Acyclic Analogs of Nucleic Acids for Antisense Inhibition. R. Galindo-Murillo, J. S. Cohen, B. Akabayov (2021). Molecular Therapy – Nucleic Acids, 23, P527-535.

2020

35. In vivo biogenesis of a de novo designed iron-sulfur protein. B. Jagilinki, S. Ilic, C. Trncik, A. Tyryshkin, D. Pike, W. Lubitz, E. Bill, B. Akabayov, O. Einsle, J. Birrell, D. Noy, V. Nanda (2020). ACS Synthetic Biology,  9(12), 3400–3407.

34. Engineering Stem Cell Factor Ligands with Different c-Kit Agonistic Potencies. T. Tilayov, T. Hingaly, Y. Greenshpan, S. Cohen, B. Akabayov, R. Gazit, N. Papo, (2020). Molecules, 25(20):4850.

33. Dual acting small-Molecule inhibitors targeting Mycobacterial DNA replication. M. Singh*, S. Ilic*, B. Tam*, Y. Ben-Ishay, D. Sherf, D. Pappo, B. Akabayov, (2020). Chemistry – A European Journal, 26 (47), 10849-10860.

32. Nanobodies Targeting Prostate-specific Membrane Antigen for the Imaging and Therapy of Prostate Cancer. L. Rosenfeld, A. Sananes, Y. Zur, S. Cohen, K. Dhara, S. Gelkop, E. Ben Zeev, A. Shahar, L. Lobel, B. Akabayov, E. Arbely, N. Papo, (2020). Journal of Medicinal Chemistry. 63(14):7601-7615.

31. The Amuvatinib Derivative, N-(2H-1,3-Benzodioxol-5-yl)-4-{thieno[3,2-d]pyrimidin-4-yl}piperazine-1-carboxamide, Inhibits Mitochondria and Kills Tumor Cells under Glucose Starvation. R. Marciano, H. Ben-David, B. Akabayov, B. Rotblat, (2020). International Journal of Molecular Sciences, 21(3), 1041.

2019

29. Discovery of small-molecule inhibitors targeting the ribosomal peptidyl transferase  center (PTC) of M. tuberculosis. B. Tam, D. Sherf, S. Cohen, S. Adi Eisdorfer, M. Peretz, A. Soffer, D. Vilenchik, S.R. Akabayov, G. Wagner, B. Akabayov, (2019). Chemical Science, 2019, 10, 8764-8767. [Cover: c9sc90211b]

28. DNA sequence recognition by DNA-primase using high-throughput primase profiling (HTPP). S. Ilic, S. Cohen, A. Afek, R. Gordan, D.B. Lukatsky, B. Akabayov, (2019). JoVE, (152), e59737.

27. Specific and label-free immunosensing of protein-protein interactions with silicon-based immunoFETs. I-M. Bhattacharyya*, S. Cohen*, A. Shalabny,  M. Bashouti, B. Akavayov, G. Shalev, (2019). Biosensors and Bioelectronics, 132:143-161.

2018

26. DnaG primase- a target for the development of novel antibacterial agents. S. Ilic, S. Cohen, M. Singh, B. Tam,  B. Akabayov, (2018). Special issue in Antibiotics (Basel): Bacterial DNA replication and replication inhibitors. 13;7(3). pii: E72.

25. DNA sequence context controls the binding and processivity of the T7 DNA primase. A. Afek*, S. Ilic*, J. Horton, D. Lukatsky*, R. Gordan*, B. Akabayov*, (2018). iScience, 2(141-147). 

24. NMR-fragment based virtual screening: a brief overview. M. Singh, B. Tam, and B. Akabayov, (2018). Molecules (Special issue: Recent Advances in Biomolecular NMR Spectroscopy), 23(2). pii: E233.

2017

23. Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase. S. Iilic, S.R. Akabayov, R. Froimovici, R. Meiry, D. Vilenchik, A. Hernandes, H. Arthanari, B. Akabayov, (2017). Scientific Reports, 7(1):5797.

22. Engineering a monomeric variant of macrophage colony-stimulating factor (M‑CSF) that antagonizes the c-FMS receptor. Y. Zur, L. Rosenfeld, A. Bakhman, S. Ilic, H. Hayun, A. Shahar, B. Akabayov, M. Kosloff, N. Levaot, N. Papo, (2017). Biochemical Journal, 20;474(15):2601-2617. 

Before 2017

21. Identification of DNA primase inhibitors via a combined fragment-based and virtual screening. S. Iilic, S.R. Akabayov, H. Arthanari, G. Wagner, C.C. Richardson, B. Akabayov, (2016). Scientific Reports, 6:36322.

20.  eIF4A augments Ago2-mediated Dicer-independent miRNA bogenesis and RNA interference. T. Yi, H. Arthanari, B. Akabayov, H. Song, E. Papadopolous, H.H. Qi, M. Jedrychowski, T. Guttler, C. Guo, R.E. Luna, S.P. Gygi, G. Wagner, (2015). Nature Communications, 6, 7164.

19.  Human translation initiation factor eIF4G1 possesses a low affinity ATP binding site facing the ATP-binding cleft of eIF4A in the eIF4G/eIF4A complex. S.R. Akabayov, B. Akabayov, G. Wagner, (2014). Biochemistry, 53(41):6422-5.

Starting BGU affiliation

18. Vanadate in structural biology.  S.R. Akabayov*, B. Akabayov*, (2014). Inorganica Chimica Acta, 420, 16–23.

17.  The interaction between eukaryotic initiation factor 1A and eIF5 retains eIF1 within scanning preinitiation complexes.  R.E. Luna, H. Arthanari, H. Hiraishi, B. Akabayov, L. Tang, C. Cox, M.A. Markus, L.E. Luna, Y. Ikeda, R. Watanabe, E. Bedoya, C. Yu, S. Alikhan, G. Wagner, K. Asano, (2013). Biochemistry, 2013 52(52):9510-8.

16. Molecular Crowding Enhanced ATPase Activity of the RNA Helicase eIF4A Correlates with Compaction of Its Quaternary Structure and Association with eIF4G. S.R. Akabayov, B. Akabayov, C.C. Richardson, G. Wagner, (2013). J Am Chem Soc, 135(27), 10040-10047.  (See spotlight in JACS)

15. Isolation, characterization, and aggregation of a structured bacterial matrix precursor. L. Chai, D. Romero C. Kayatekin, B. Akabayov, H. Vlamakis, R. Losick, R. Kolter, (2013). J Biol Chem, 288(44), 17559-17568.

14. Impact of macromolecular crowding on DNA replication. B. Akabayov, SR. Akabayov, S-J. Lee, G. Wagner, and CC. Richardson, (2013). Nature Communications, 4:1615.

13. An interaction between DNA polymerase and helicase is essential for the high processivity of the bacteriophage T7 replisome. AW. Kulczyk, B. Akabayov, S-J. Lee, M. Bostina, S. Berkowitz, and CC. Richardson,  (2012). J Biol Chem, 287(46):39050-60.

12. Zinc-binding domain of DNA primase modulates binding to template DNA. S-J. Lee, B. Zhu, B. Akabayov, and CC Richardson,  (2012). J Biol Chem, 287(46):39030-40.

11. Role of exposed cysteine located on the thioredoxin-binding region of gene 5 DNA polymerase of bacteriophage T7. N.Q. Tran*, S-J. Lee*, B. Akabayov*, DE. Johnson and CC. Richardson,  (2012). J Biol Chem, 287(47):39732-41.

10. The C-terminal domain of eukaryotic initiation factor 5 promotes start codon recognition by its dynamic interplay with eIF1 and eIF2β. RE. Luna, H. Arthanari, H. Hiraishi, J. Nanda, P. Martin-Marcos, M. Markus, B. Akabayov, A. Milbradt, S. Hyberts, LE. Luna, M. Reibarkh, A. Farmy, H. Seo, A. Marintchev, A. Hinnebusch, J. Lorsch, K. Asano, and G. Wagner,  (2012). Cell Reports, 1(6), 689-702.

9. Probing conformational variations at the ATPase site of the RNA helicase DbpA by high-field electron-nuclear double resonance spectroscopy. I. Kaminker, A. Sushenko, A. Potapov, S. Daube, B. Akabayov, I. Sagi and D. Goldfarb,  (2011). J Am Chem Soc, 133(39):15514-23.

8. Pyrovanadolysis: a pyrophosphorolysis-like reaction mediated by pyrovanadate and Mn-substituted DNA polymerase of bacteriophage T7. B. Akabayov, AW. Kulczyk, SR. Akabayov, C. Thiele, LW. McLaughlin, B. Beauchamp, and CC Richardson,  (2011). J Biol Chem, 19;286(33):29146-57.

7. Binding of Mn-deoxyribonucleoside triphosphates to the active site of the DNA polymerase of bacteriophage T7. B. Akabayov, C.C. Richardson,  (2011). Powder Diffraction, 2(26):159-163.

6. Conformational dynamics of bacteriophage T7 DNA polymerase and its processivity factor, Escherichia coli thioredoxin. B. Akabayov, S.R. Akabayov, S-J. Lee, A Kulczyk, S. Tabor, C.C. Richardson, (2010). Proc Natl Acad Sci USA, 107 (34) 15033-15038.

5. DNA recognition by the DNA primase of bacteriophage T7: a structure-function study of the zinc-binding domain. B. Akabayov, S-J. Lee, S.R. Akabayov, S. Rekhi, B. Zhu, C.C. Richardson,  (2009). Biochemistry, 48(8), 1763–73.

4. Key feature of the catalytic cycle of TNF-alpha converting enzyme involves communication between distal protein sites and the enzyme catalytic core. A. Solomon, B. Akabayov, M.E. Milla, I. Sagi,  (2007). Proc Natl Acad Sci USA 104 (12): 4931-6.

3. Using softer x-ray absorption spectroscopy to probe biological systems.  B. Akabayov, CJ. Doonan, IJ. Pickering, GN. George and I. Sagi,  (2005). J Synchrotron Radiat 12 (4): 392-401.

2. RNA labeling and immobilization for nano-displacement measurements: probing three dimensional RNA structures. B. Akabayov, A. Henn, M. Elbaum, I. Sagi,  (2003). IEEE TRANS Nanobioscience; 2(2):70-4.

1. The role of A1/A3 adenosine receptor activation in reduction of cardiomyocyte injury caused by hypoxic stress and in induction of apoptosis in rat cardiomyocyte cultures. A. Shainberg, N. Safran, N. Balas, KA. Jacobson, T. Zinman, A. Isaac, K. Schwab, B. Akabayov, V. Shneyvays, (2000). Adv Exp Med Biol; 486: 201-5.

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