Prof. Amnon Albeck

Prof.
Prof. Amnon Albeck
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CV

Education

BSc, Chemistry, Bar Ilan University, 1982

PhD, Organic Chemistry, The Weizmann Institute of Science, 1988.

Post-doc, Biochemistry, Brandeis University, USA, 1990.

 

Appointments

On the faculty of the Department of Chemistry, Bar Ilan University since 1990.

Full Prof. since 2008. 

Chairman of the Department of Chemistry 2008-2011. 

Vice Rector, Bar Ilan University since October 2014

Member of the “Marcus Center for Medicinal Chemistry” at Bar Ilan. 

 

Academic & administrative Activities

At Bar Ilan

2012 – present:          Member of the University’s Committee for Interdisciplinary Studies

2011 – 2014:              Member of the University’s Appointment Committee

2011 – 2014:              Member of the Departmental Teaching Committee

2010 – present:          Member of the University’s Senate

1998 – 2008:              Member of The Academic Steering Committee, the Biophysics program

1996 – present:          Member of the University Safety Council

 

Outside Bar Ilan

2014 – present:          Member of The Board of Executives, The National Institute for Testing and Evaluation

2011 – 2013:              Member of the Fulbright Postdoctoral Fellowship Committee, the US-Israel Educational Foundation

2010 – present:           Member of the National Chemical Education Committee,  Ministry of Education

2003 – 2011:              Advisor to the GIF

2003 – 2007:              Member of The Academic Steering Committee, Carbohydrates Center, Ben Gurion University

1997 – 2000:              Member of The Board of Executives, The Israel Chemical Society

 

Publications

 

 

Recent Publications (past 10 years)

 

Ozeri, R.; Khazanov, N.; Perlman, N.; Shokhen, M.; Albeck, AEnzyme Isoselective Inhibitors: A Tool for Binding Trend AnalysisChemMedChem 20061, 631-638.

Shokhen, M.; Khazanov, N.; Albeck, AEnzyme Isoselective Inhibition: Application to Drug DesignChemMedChem 20061, 639-643.

Patchornik, G.; Albeck, AA General Approach for Antibody Purification Utilizing [Protein A-Catechol : Fe 3+] Macro-ComplexesBioconjugate. Chem. 200617, 258-260.

Sredni, B.; Geffen, R.; Duan, W.; Albeck, M.; Shalit, F.; Lander, H. M.; Kinor, N.; Sagi, O.; Albeck, A.; Yosef, S.; Brodsky, M.; Sredni-Kenigsbuch, D.; Sonino, T.; Longo, D. L.; Mattson, M. P.; Yadid, G. Multifunctional Tellurium Molecule Protects and Restores Dopaminergic Neurons in Parkinson’s Disease Models. FASEB J. 2007, 21, 1870-1883.

Brodsky, M.; Yosef S.; Rushkin G.; Albeck M.; Longo D. L.; Albeck A.; Sredni B. The Synthetic Tellurium Compound, AS101, is a Novel Inhibitor of Interleukin-1-beta Converting Enzyme. J. Interferon Cytokine Res. 2007, 27, 453-462.

Shokhen, M.; Khazanov, N.; Albeck, A. The Cooperative Effect Between Active Site Ionized Groups and Water Desolvation Controls the Alteration of Acid/Base Catalysis in Serine Proteases. ChemBioChem, 2007, 8, 1416-1421.

Frei, G. M.; Lebenthal, I.; Albeck, M,; Albeck, A.; Sredni, B. Neutral and Positively Charged Thiols Synergize the Effect of the Immunomodulator As101 as a Growth Inhibitor of Jurkat Cells, by Increasing Its Uptake. Biochem. Pharm. 2007, 74, 712-722.

Yosef, S.; Brodsky, M.; Sredni, S.; Albeck, A.; Albeck, M. Octa-O-bis-(R,R)-Tartarate Ditellurane (SAS) – a Novel Bioactive Organotellurium(IV) Compound: Synthesis, Characterization and Protease Inhibitory Activity. ChemMedChem 2007, 2, 1601-1606.

Belostotskii, A. M.; Albeck, A.; Hassner, A. Asymmetric Induction by a Remote Chiral Substituent – Computationally Determined Stereodifferentiation in Michael Additions of α-Lithiated Allyl Sulfones. Eur. J. Org. Chem. 2007, 29, 4837-4844.

Shokhen, M.; Khazanov, N.; Albeck, A. Screening of the Active Site from Water by the Incoming Ligand Triggers Catalysis and Inhibition in Serine Proteases. Proteins 2008, 70, 1578-1587.

Bechor, Y.; Albeck, A. Exocyclic Vinyl Ethers of Ketofuranosides. Tetrahedron, 2008, 64, 2080-2089.

Mirilashvili, S.; Chasid-Rubinstein, N.; Albeck, A. Optically Active g-Hydroxy Sulfone Julia Reagents for the Synthesis of Peptidyl Olefin Peptidomimetics. Eur. J. Org. Chem. 2008, 20, 3461-3464.

Gellerman, G.; Hazan, E.; Brider, T.; Traube, T.; Albeck A.; Shatzmiler, S. Facile Synthesis of Orthogonally Protected Optically Pure Keto– and Diketopiperazine Building Blocks for Combinatorial Chemistry. Int. J. Pept. Res. Ther. 2008, 14, 183-192.

Perlman, N.; Hazan, M.; Shokhen, M.; Albeck, A. Peptidyl Epoxides Extended in the P’ Direction as Cysteine Protease Inhibitors. Effect on Affinity and Mechanism of Inhibition. Bioorg. Med. Chem. 2008, 16, 9032-9039.

Levinger, S.; Sharabi, Y.; Mainfeld, A.; Albeck, A. Structural and Spatial Considerations in the N,N’-diacyl- and dicarbamoyl Bispidinone Series. J. Org. Chem. 2008, 73, 7793-7796.

Gellerman, G.; Hazan, E.; Kovaliov, M.; Albeck A.; Shatzmiler, S. Synthesis of Orthogonally Protected Optically Pure Ketopiperazine, Diketopiperazine, Ketodiazepane and 3-Aminopyrrolidone Building Blocks for Peptidomimetic Combinatorial Chemistry. Tetrahedron, 2009, 65, 1389-1396.

Shokhen, M.; Khazanov, N.; Albeck, A. Challenging a Paradigm: Theoretical Calculations of the Protonation State of the Cys25-His159 Catalytic Diad in Free Papain. Proteins 2009, 77, 916-926.

Gellerman, G.; Shitrit, S.; Shalit, T.; Ganot, O.; Albeck, A. Phenols - useful templates for the synthesis of bi-functional orthogonally protected dendron building blocks via Solid Phase Mitsunobu reaction. Tetrahedron 2010, 66, 878-886.

Mirilashvili, S.; Chasid-Rubinstein, N.; Albeck, A. Optically Active N- and C-terminal building blocks for the Synthesis of Peptidyl Olefin Peptidomimetics. Eur. J. Org. Chem. 2010, 4671-4686.

Shalit, T.; Albeck, A.; Gellerman, G. A double heteroatom Mitsunobu coupling with amino hydroxybenzoic acids on solid phase: a novel application of the Mitsunobu reaction to form dendron building blocks. Tetrahedron Lett. 2010, 51, 5988-5991.

Traube, T.; Vijayakumar, S.; Hirsch, M.; Uritsky, N.; Shokhen, M.; Albeck, A. EMBM – a New Enzyme Mechanism Based Method for Rational Design of Chemical Sites of Covalent Inhibitors. J. Chem. Info. Model. 2010, 50, 2256-2265.

Shokhen, M.; Khazanov, N.; Albeck, A. The Mechanism of Papain Inhibition by Peptidyl Aldehydes. Proteins 2011, 79, 975-985.

Shokhen, M.; Traube, T.; Vijayakumar, S.; Hirsch, M.; Uritsky, N.; Albeck, A. Differentiating Serine and Cysteine Proteases Mechanism by New Covalent QSAR Descriptors. ChemBioChem 2011, 12, 1023-1026.

Gellerman, G.; Waintraub, S.; Albeck, A.; Gaisin, V. One-Pot Synthesis of Novel Antiproliferative 9-Aminoacridines. Eur. J. Org. Chem. 2011, 22, 4176-4182.

Redko, B.; Albeck, A.; Gellerman, G. Facile synthesis and antitumor activity of novel N(9) methylated AHMA analogs. New J. Chem. 2012, 36, 2188-2191.

Uritsky, N.; Shokhen, M.; Albeck, A. The catalytic machinery of rhomboid proteases. Combined MD and QM simulations. J. Chem. Theory Comput. 2012, 8, 4663-4671.

Cohen, M.; Bretler, U.; Albeck, A. Peptidyl cyclopropenones: reversible inhibitors, irreversible inhibitors, or substrates of cysteine proteases? Protein Sci. 2013, 22, 788-799.

Sharabi-Ronen, Y.; Levinger, S.; Ben-Dahan Lellouche, M.; Albeck, A. Anti-neoplastic Activity of 1,3-Diaza-2-functionalized-adamantan-6-one Compounds Against Melanoma Cells. Med. Chem. 2014, 10, 27-37.

Traube, T.; Shokhen, M.; Albeck, A. Application of EMBM for Structure-Based Design of Warheads for Protease Inhibitors. Mol. Inf. 2014, 33, 36-42.

Traube, T.; Shokhen, M.; Albeck, A. A New Method for Filtering of Reactive “Warheads” of Transition-State Analog Protease Inhibitors. Eur. J. Med. Chem. 2014, 77, 134-138.

Shokhen, M.; Hirsch, M.; Khazanov, N.; Ozeri, R.; Perlman, N.; Traube, T.; Vijayakumar, S.; Albeck, A. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Hydrolases. Isr. J. Chem. 2014, 54, 1137-1151.

Gilad, Y.; Firer, M. A.; Rozovsky, A.; Ragozin, E.; Redko, B.; Albeck, A.; Gellerman, G. "Switch off/switch on" regulation of drug cytotoxicity by conjugation to a cell targeting peptide. Eur. J. Med. Chem. 2014, 85, 139-146.

Rozovsky, A.; Regozin, E.; Oron-Herman, M.; Albeck, A.; Gellerman, G. Synthesis of novel antitumor carbazole-amonafide structural hybrids. Eur J Org Chem 2015, 1811-1818.

Zats, G. M.; Kovaliov, M.; Albeck, A.; Shatzmiller, S. Antimicrobial Benzodiazepine-Based Short Cationic Peptidomimetics. J Pept Sci 2015, 21, 512-519.

Lapidot, I.; Albeck, A.; Gellerman, G.; Shatzmiller, S.; Grynszpan, F. 1,4-Dihydropyridine Cationic Peptidomimetics with Antibacterial Activity. Int J Pept Res Ther 2015, 21, 243-247.

Redko, B.; Ragozin, E.; Bazylevich, A.; Tuchinsky, H.; Albeck, A.; Shekhter Zahavi, T.; Oron-Herman, M.; Kostenich, G.; Gellerman, G. Synthesis, drug release and biological evaluation of new anticancer drug-bioconjugates containing somatostatin backbone cyclic analog as a targeting moiety. Pept Sci 2015, 104, 743-752.

Gilad, Y.; Noy, E.; Senderowitz, H.; Albeck, A.; Firer, M. A.; Gellerman, G. Synthesis, biological studies and molecular dynamics of new anticancer RGD-based peptide conjugates for targeted drug delivery. Bioorg Med Chem 2016, 24, 294-303.

Lapidot, I.; Baranes, D.; Pinhasov, A.; Gellerman, G.; Albeck, A.; Grynszpan, F.; Shatzmiller, S. E. alpha-Aminoisobutyric acid leads a fluorescent syn-bimane LASER probe across the blood-brain barrier. Med Chem 2016, 12, 48-53.

Uritsky, N.; Shokhen. M.; Albeck, A. Stepwise vs. Concerted Mechanism in General Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2016, 55, 1680-1684.

Gilad, Y.; Noy, E.; Senderowitz, H.; Albeck, A.; Firer, M. A.; Gellerman, G. Dual-drug RGD conjugates provide enhanced cytotoxicity of melanoma and non-small lung cancer cells. Pept Sci 2016, 106, 160-171. 

Ragozin, E.; Redko, B.; Tuchinsky, E.; Rozovsky, A.; Albeck, A.; Grynszpan, F.; Gellerman, G. Bio-Labile Peptidyl Delivery Systems Towards Sequential Drug Release. Pept Sci 2016, 106, 119-132.

Silberman, A.; Kalechman, Y.; Hircsh, S.; Erlich, Z.; Sredni, B.; Albeck, A. The anti cancer activity of organotelluranes: potential role in integrin inactivation. ChemBioChem 2016, 17, 918-927.

Levinger, S.; Hirsch, S.; Albeck, A. Lithium Aluminum Hydride Assay Suitable for the Organic Chemistry Laboratory. ChemistrySelect 2016, 1, 756-758.

Gilad, Y.; Waintraub, S.; Albeck, A.; Gellerman, G. Synthesis of novel protected Nα(ω-Drug) amino acid building units for facile preparation of anticancer drug-conjugates. Int. J. Pept. Res. Ther. 2016, 22, 301-316.

Zer-Aviv, P.; Shubely, M.; Moskovits, Y.; Viskind, O.; Albeck, A.; Vertommen, D.; Ruthstein, S.; Shokhen, M.; Gruzman, A. A new oxopiperazin-based peptidomimetic molecule inhibits prostatic acid phosphatase secretion and induces prostate cancer cells apoptosis. ChemistrySelect 2016, 1, 4658-4667.

Silberman, A.; Albeck, M.; Sredni, B.; Albeck, A. The ligand substitution reactions of the tellurium compound AS-101 in physiological aqueous and alcoholic solutions. Inorg Chem 2016, 55, 10847-10850.

Courses

Past and present:

 

84-205 Organic Chemistry 1

84-206 Organic Chemistry 2

84-305 Organic Chemistry Lab 2

84-364 Secondary Metabolism

84-964 Enzyme Catalysis and Mechanisms

84-965 Enzymatic Catalysis: Methods for Research, Control and Development 

80-236 Organic Chemistry 2 for Biology-major students

80-380 Biochemistry of enzymatic systems

80-757 Organic Chemistry lab for pre-med students

80-759 Organic Chemistry 2 for pre-med students

Research

 

 

Organic chemistry, Peptides and peptidomimetics, Biochemistry, Enzymology, Enzyme mechanisms, Enzyme inhibition, Proteases, Computational biochemistry.

 

Particular research areas (projects):

  1. Organic synthesis, peptides and peptidomimetics: amino acid- and peptide bond replacement, N- and C-terminal functional groups.
  2. Enzyme catalysis and inhibition mechanisms. The catalytic machinery of proteases, acid-base catalysis, pKa and protonation state of catalytic residues, the mechanism of inhibition by unique inhibitors.
  3. Development of inhibitors for enzymes with potential therapeutic applications.
  4. Computational biochemistry: enzyme mechanisms, development of computer-assisted drug design  tools and their implication in inhibitor- and drug design.

 

Interesting? Want to learn more?

Our research focuses on understand enzyme mechanism and inhibition and to design and develop drugs targeted towards enzymes. The research is interdisciplinary in nature, combining synthetic organic chemistry, biochemistry, enzymology, computational chemistry, and cellular biology.

 

Enzyme Reaction Mechanisms

Understanding the mode of action of enzymes at the molecular level has important potential applications, as it opens up possibilities to selectively control or modulate such activities. This approach is essential for basic research, as well as for the development of new drugs and other biologically active compounds.

We study proteolytic enzymes, enzymes that hydrolyze (cleave) proteins and peptides which are involved in many biological processes. The research combines experimental research with computational biochemistry. Experiments include biochemical analysis, enzyme kinetics, chemical synthesis, and analytical techniques such as NMR and X-ray crystallography.

How does acid/base catalysis in serine proteases really work?

 

Computational Methods development

Computational tools are very instrumental in enzyme mechanism studies. One of the most usefull methods is QM/MM, which combines in an itterative process QM calculations on a smal active-site molecular cluster and MM calculations for the rest of the protein and its environment. We developed a new methodology, MD-QM/SCRF(VS), which combines molecular dynamics (MD) simulations with quantum mechanical (QM) calculations of the enzyme. In the QM calculations the enzyme is treated as a two layer system: the inner layer, a large molecular cluster simulating the enzyme active site, is explicitly calculated. The outer layer, the rest of the protein and its environment, is treated as a uniform continuum, a "virtual solvent (VS)", characterized by a dielectric constant which is calibrated by experimental data. This methodology has some advantages over common computational tools. It has been successfully applied for the study of structure, protonation states, pKa values and detailed molecular-level mechanisms of enzyme catalysis and inhibition.  

 

The QM/SCRF(VS) concept

 

 

Drug Design and Delivery

This research involves the design and synthesis of enzyme inhibitors, drug candidates and drug delivery systems, as well as evaluation of their activity at various levels, from in-vitro studies to in-vivo animal model experiments.

One project, in collaboration with Prof. Gary Gellerman from Ariel University, focuses on the development of novel methodologies for the preparation of targeted multi-drug delivery systems, with the aim to recruit anti cancer drugs and drug candidates that failed clinical trials due to their toxicity.

Another project, with Prof. Ilana Nathan from Ben Gurion University and Soroka Medical Center, concentrates on understanding basic biological processes involved in necrotic cell death and on the development of protease inhibitors to treat necrosis. This project has produced very encouraging in-vivo results in three animal model systems.

A decade-long collaboration with Prof. Michael Albeck and Prof. Benjamin Sredni from Bar Ilan University deals with the development of tellurium-based bioactive compounds as potential anti-cancer and anti-viral drugs. Here, too, animal studies demonstrated the therapeutic potential of these compounds.

Other projects in the pharmaceutical field and in an industrial application are underway in our lab.

Representative 3D structure of an enzyme active site (cyan) interacting with its inhibitor (magenta). The structure emerged from computational studies. 

 

Computer-Assisted Drug Design Tools Development

One central research direction in our lab involves the development of novel computer-assisted drug design (CADD) tools to assist medicinal chemists and the pharmaceutical industry in the design of new bioactive compounds. In a project that may help to overcome the problem of mutational drug resistance, led by Prof. Michael Shokhen in our lab, we develop computational tools for the design of new antibacterial and antiviral drugs based on enzyme inhibitors. Common drug design tools deal with non-covalent inhibitors, which eventually suffer from mutational drug resistance. The emergence of resistant bacterial and viral strains, as well as cancer cells, has become a major problem in modern medicine. The methodology we develop is applicable to transition-state analog enzyme inhibitors. These reversible covalent inhibitors interact directly with the catalytic machinery of the enzyme, which is not subject to mutations. While the common CADD tools are either structure-based or ligand / pharmacophore-based methodologies, our approach can be classified as a mechanism-based drug design tool. Indeed, our previous mechanistic studies on enzyme catalysis and inhibition provided the basis for the development of this novel CADD methodology.

A description of the EMBM methodology for virtual screening and rational design of protease inhibitors. 

 

Peptidomimetics

Peptide analogs, in which one or more functionalities have been altered, are promising for many applications in drug development, diagnostics, and mechanistic studies. We develop innovative synthetic methods for the preparation of such peptide analogs, applying them for the synthesis of novel enzyme inhibitors.

These inhibitors may serve mechanistic research goals, or may be developed for drug discovery projects. Their functional alterations may include the introduction of reactive functional groups to covalently interact with a target enzyme, conversion of a peptide bond to a metabolically stable isostere, or design of scaffolds that mimic small peptides.

Chemo-enzymatic synthesis of a variety of optically active functionalized building blocks for peptidomimetics (red) from a single optically active precursor (blue), obtained by a stereoselective enzymatic hydrolysis of a prochiral starting material (green). 

 

Looking to the Future

As a research group that combines both experimental and computational research tools, and that emphasizes both basic-mechanistic and applied research, we are committed to the improvement and further development of our drug design computational methodologies and their application in practical drug development projects. Ongoing projects as well as future projects are expected to yield biochemical information and bioactive compounds that together will provide the grounds for the development of new drugs.

 

Research Group

 

 

Current group members

Dr. Shlomo Levinger, Research associate

Dr. Michael Shokhen, Research associate

Dr. Sveta Furman, lab manager

 

Neta Uritski, Ph.D. student

Avinoam Isac, Ph.D. student

Kobi Wolfman, Ph.D. student

Noga Kaufman, M.Sc. student

Golda Houri, M.Sc. student

Ron Schwartz, M.Sc. student

 

 

Past group members

Graduate students

Rachel Klimovsky, M.Sc. (1993)

Limor Weiss, M.Sc. (1995)

Gary Estreicher, M.Sc. (1995)

Shulamit Fluss, M.Sc. (1995)

Hana Weitman, M.Sc. (1995)

Eduard Rogatsky, Ph.D. (1998)

Sharon Kliper, Ph.D. (1999)

Rachel Persky, Ph.D. (1999)

Nurit Perlman, Ph.D. (2000)

Oded Meroz, M.Sc. (2000)

Sima Mirilshvili, M.Sc. (2000)

Revital Yefidoff, Ph.D. (2002)

Nadia Silverman, Ph.D. (2004)

Yosi Bechor, Ph.D. (2004)

Rachel Nakash, Ph.D. (2005)

Sigal Yosef, Ph.D. (2005)

Sima Mirilshvili, Ph.D. (2005)

Shira Adler, M.Sc. (2005)

Alexander Mainfeld, M.Sc. (2005)

Naama Hassid, M.Sc. (2006)

Hani Algawi, M.Sc. (2007)

Miri Ben Dahan, M.Sc. (2007)

Marianna Kishinevsky, Ph.D. (2008)

Tamar Traube, M.Sc. (2008)

Meital Cohen, Ph.D. (2008)

Netaly Hazanov, Ph.D. (2008)

Maya Chazan, Ph.D. (2008)

Tamara Brider, M.Sc. (2008)

Rami Kriger, M.Sc. (2008)

Miriam Nakash, M.Sc. (2008)

Avraham Klein, M.Sc. (2009)

Marina Kobaliov, M.Sc. (2009)

Galina Zats, M.Sc. (2009)

Tzachi Shalit, M.Sc. (2009)

Moran Gilboa, M.Sc. (2010)

Uriel Bartler, M.Sc. (2010)

Yifat Sharabi-Ronen, Ph.D. (2010)

Keren Schultz, Ph.D. (2010).

Miri Ben Dahan, Ph.D. (2011)

Sagiv Waintraub, M.Sc. (2011)

Yosef Gilad, M.Sc. (2012)

Michal Hirsch, M.Sc. (2012)

Boris Redko, M.Sc. (2012)

Sofia Levi, M.Sc. (2012)

Rami Kriger, Ph.D. (2013)

Keti Lerman, Ph.D. (2013)

Elena Ragozin, M.Sc. (2013)

Naama Rubinstein, Ph.D. (2014)

Tamar Traube, Ph.D. (2014)

Marina Yarovoy, M.Sc. (2014)

Alon Zilberman, Ph.D. (2014)

Inbal Lapidot, Ph.D. (2014)

Shira Hirsch, M.Sc. (2014)

Alex Rozovsky, M.Sc. (2015)

Sigal Patael, Ph.D. (2015)

Yosef Gilad, Ph.D. (2016)

Tzachi Shalit, Ph.D. (2016)

Avinoam Isac, M.Sc. (2016)

Ayelet Gedalya-Bremer, M.Sc. (2016)

Ruti Bornestein, M.Sc. (2016)

Moran Mazuz, Ph.D. (2016)

Boris Redko, Ph.D. (2016)

Malki Ginzberg, M.Sc (2016)

 

Post-doctoral fellows

Nurit Perlman (2000-2001)

Guy Patchornic (2004)

Sigal Yosef (2004-2005)

Vijayakumar Subramaniam (2008-2010)

 

Former lab manager

Dr. Sigal Patael, 2015-2017