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Work in Progress

My current research program is focused on:

  • Monitoring and detection of biological threats 
  • Diagnosis of infectious diseases and cancer
  • Targeting of tumor cells

To attack these problems, I employ methods of Directed Molecular Evolution, Multivalent Phage Display and Phage Nanobiotechnology that have been developed by my group. This program is a continuation of my previous study of the Combinatorial Biochemistry and Landscape phage Libraries. 

I began my research activity in 1969 as a student at the Moscow State University in the Laboratory of Phosphor-organic Chemistry headed by Prof. E.E. Nifant'ev. My goal was to synthesize molecules that could normally operate in living cells. In my master diploma project, I developed new phosphorylation agents for synthesis of DNA, glycosyl-phosphates and other important natural compounds. After graduating from the University in 1972, I continued my research as a Ph.D. student in the Institute of Organic Chemistry, USSR Academy of Sciences, Moscow. My supervisors were Academician N.K. Kochetkov and Prof. V.N. Shibaev—internationally recognized leaders in DNA and carbohydrate chemistry. In my Ph.D. dissertation project, I studied biosynthesis of Salmonella antigens using synthetic analogs of thymidine-diphosphate-rhamnose. Results of this study were presented in 7 papers. 

Since 1977, I focused my scientific interests on directed molecular evolution, synthesis and designed reconstruction of DNA, phage display, protein drug design, and diagnostics.

Site-directed mutagenesis. The 70th revolutionized biotechnology by inventing recombinant DNA. Thus, since 1977, after establishing my laboratory in Scientific Association “Vector”, Novosibirsk (USSR), I focused my scientific interests on directed molecular evolution, designed reconstruction of DNA, phage display, protein drug design, and diagnostics. As result, my group developed first analogues of oligonucleotides inducing site-directed mutations in vitro and in vivo:

Petrenko V.A., P.I. Pozdnyakov, S.M. Kipriyanov, A.N. Boldyrev, L.N. Semenova, G.F. Sivolobova (1986) Site-localized mutagenesis directed by phosphotriester analogues of oligonucleotides. Bioorganicheskaya khimiya., 12, 289-292. Soviet Journal of Bioorganic Chemistry Engl.Tr., 1986, 12, 586-597.

Petrenko VA, Kuz'micheva GA, Tat'kov SI, Krasnoborov II, Il'ichev AA, Drutsa VL, Purmal' AA, Shabarova ZA. [Study of the mutagenic properties of oligonucleotides containing and internucleotide pyrophosphate bond using a mutation system based on phage M13]. Mol Biol (Mosk). 1991 Nov-Dec;25(6):1539-45

Petrenko V.A., S.M. Kipriyanov, A.N. Boldyrev, P.I. Pozdnyakov (1989). Mutagenesis directed by phosphotriester analogs of oligonucleotides: a way to site-specific mutagenesis in vivo]. Mol Gen Mikrobiol Virusol. 1989 Mar;(3):35-9.

Petrenko V.A., L.I. Karpenko, S.I. Tatkov, O.Yu. Smirnova, G.A. Kuzmicheva, A.A. Ilyichev (1991) Mutagenesis induced by oligonucleotide phosphotriester analogs and directed at double-stranded DNA breaks. Molekulyarnaya Genetika Mikrobiologia Virusologia., 10, 19-20.

We inventored a method allowing to introduce mutations localized in the operator-promotor regions of genome:

Gusev V.A., V.A. Karginov, V.V. Kravchenko, V.A. Petrenko, N.A. Petrov, L.N. Semenova (1981) Modification of the operator-promoter site of lambda phage DNA in the specific complex with E.coli RNA polimerase. Doklady Akademii nauk SSSR., 260, 753-756

Multivalent phage display. In 1985, George Smith published in Science his revolutionary paper describing cloning of foreign gene as a fusion to the Minor coat protein pIII of the filamentous phage fd. (Times Cited: 1,971. Later this technique was named “Phage Display”:

Smith G.P. and Petrenko V.A. (1997) Phage Display. Chemical Reviews, V.97, N2, p. 391-410.

After Smith’s publication, I was fascinated to learn if filamentous phage can tolerate multiple mutations and insertions of foreign peptides into the Major coat protein pVIII, 2,700 copies of which cover the viral DNA to form viral capsid. It was commonly believed that pVIII is extremely conservative and cannot be modified. Using methods of site-directed mutagenesis, we constructed vectors that allowed us to check this hypothesis.  Our efforts resulted in construction of the first recombinant phages with the pVIII protein fused to foreign peptides:

Ilyichev A.A., O.O. Minenkova, S.I. Tatkov, N.N. Karpyshev, A.M. Eroshkin, V.A. Petrenko, L.S. Sandakhchiev (1989) Production of a viable variant of phage M13 with incorporated foreign peptide in the major coat protein. Doklady Akademii nauk SSSR., 307, 481-483. Doklady Biochemistry (Proc. Acad. Sci. USSR)-Engl.Tr., 1989, 307, 196-198.

Kishchenko G.P., O.O. Minenkova, A.A. Ilyichev, A.D. Gruzdev, V.A. Petrenko (1991) Study of the structure of phage-M13 virions containing chimeric B-protein molecules. Molekulyarnaya biologiya., 25, 1497-1503. Molecular Biology, 1991, 25(6), 1171-1176.

Inventors of pVIII phage display. Novosibirsk, Russia (left to right):  Gregory Kishchenko, Sergey Tatkov, Alexander Il’ichev, Galina Kuzmicheva, Valery Petrenko, Olga Minenkova

These preliminary results inspired me to study filamentous phage with pVIII fusions (later named “landscape phage”) as novel engineered nanomaterials for design of synthetic vaccines, diagnostics, detectors and drug/gene delivery vectors:

Minenkova O.O., A.A. Ilyichev, G.P. Kishchenko and V.A. Petrenko (1993) Design of specific immunogen using filamentous phages as a carrier. Gene, 128, 85-88.

Petrenko V.A., Smith G.P., Gong X. and Quinn T. (1996) A library of organic landscapes on filamentous phage. Protein Engineering, V.9, N9, p. 797-801

Petrenko V.A. and Smith G.P. (2000) Phage from landscape libraries as substitute antibodies. Protein Engineering, V.13, N8, p.101-104.

Petrenko V.A., Smith G.P., Mazooji M.M. and Quinn T. (2002) Alfa-helically constrained phage display library. Protein Engineering, V.15, No.11, pp.943-950.

Petrenko V.A. and V.J. Vodyanoy (2003) Phage display for detection of biological threat agents. The Journal of Microbiological Methods, 53/2 pp. 243-252.

Brigati J., D.D. Williams, I.B. Sorokulova, V. Nanduri, I-H. Chen, C.L. Turnbough, Jr. and V.A. Petrenko (2004).  Diagnostic probes for Bacillus anthracis spores selected from a landscape phage library.  Clinical Chemistry V.50, No.11, p.1899-1906.

Phage biosensor designers (20030 left to right: Jennifer Brigati, Iryna Sorokulova, I-Hsuan Chen, Eric Olsen, Jane Mount, Valery Petrenko, Vishu Nanduri, Kelly Franz.

Petrenko V.A.  (2008). Landscape phage as a molecular recognition interface for detection devices.  Review. Microelectronics Journal.  Vol 39/2 pp 202-207.

G.A. Kuzmicheva, P.K. Jayanna, I.B. Sorokulova and V.A. Petrenko (2009) Diversity and censoring of landscape phage libraries. Protein Engineering, Design, and Selection. 2009 Jan;22(1):9-18.

Phage Nanobiotechnology. (Valery A. Petrenko and George P. Smith Eds.) RSCPublishing, 2011.

3. Cancer targeted nanomedicines.  My current interest lies in the area of cancer-targeted drug development. We first demonstrated that cancer-targeted major coat proteins isolated from preselected  landscape phages can be complexed with liposomes, micelles, nanotubes and siRNA, increasing their therapeutic effect:

Jayanna P.K., Torchilin V.P. and Petrenko V.A. (2009) Liposomes Targeted by Phage Fusion Proteins.  Nanomedicine: Nanotechnology, Biology and Medicine Volume 5, Issue 1, March 2009, Pages 83-89. Epub 2008 Oct 1.

Wang T, Yang S, Petrenko VA, Torchilin VP. Cytoplasmic Delivery of Liposomes into MCF-7 Breast Cancer Cells Mediated by Cell-Specific Phage Fusion Coat Protein. Mol Pharm. 2010 Aug 2;7(4):1149-58.

Wang T, Petrenko VA, Torchilin VP. Paclitaxel-Loaded Polymeric Micelles Modified with MCF-7 Cell-Specific Phage Protein: Enhanced Binding to Target Cancer Cells and Increased Cytotoxicity. Mol Pharm. 2010 Aug 2;7(4):1007-14.

Jayanna PK, Bedi D, Gillespie JW, Deinnocentes P, Wang T, Torchilin VP, Bird RC, Petrenko VA. Landscape phage fusion protein-mediated targeting of nanomedicines enhances their prostate tumor cell association and cytotoxic efficiency.  Nanomedicine: Nanotechnology, Biology, and Medicine. 2010 Aug;6(4):538-46.

Cancer fighters (2011) left to right: James Gillespie, Valery Petrenko, Tiffani O'Dell, Vasily Petrenko, Deepa Bedi, Amanda Gross, Lixia Wei.

Deepa Bedi,  Tiziana Musacchio, Olusegun A. Fagbohun, Patricia Deinnocentesa, R. Curtis Bird,  Lonnie Bookbinder,  Vladimir P. Torchilin, and Valery A. Petrenko. Delivery of siRNA into breast cancer cells via phage fusion protein-targeted liposomes. Nanomedicine: Nanotechnology, Biology, and Medicine, 7 (3): 315-323 JUN 2011.

Olusegun A. Fagbohun, Deepa Bedi, Natalia I. Grabchenko, Patricia A. Deinnocentes, Richard C. Bird, and Valery A. Petrenko. Landscape phages and their fusion proteins targeted to breast cancer cells. Protein Engineering, Design & Selection, 25(6), pp. 271-83, 2012.

Bedi D, Gillespie JW, Petrenko VA Jr, Ebner A, Leitner M, Hinterdorfer P, Petrenko VA. Targeted Delivery of siRNA into Breast Cancer Cells via Phage Fusion Proteins. Mol Pharm. 2013 Feb 4;10(2):551-9. Epub 2013 Jan 8.

Cancer Fighters (2013) left to right: Amanda Gross, James Diskin, Tiffani O'Dell, Clifford Deerman, Logan Stallings, James Gillespie,Deepa Bedi, Valery Petrenko.

 Petrenko VA, Jayanna PK. Phage protein-targeted cancer nanomedicines. FEBS Lett. 2014 Jan 21;588(2):341-9.

Bedi D, Gillespie JW, Petrenko VA. Selection of pancreatic cancer cell-binding landscape phages and their use in development of anticancer nanomedicines. Protein Eng Des Sel. 2014 Jul;27(7):235-43.

U.S. Patent 8,137,693 B2. Drug Delivery Nanocarriers Targeted by Landscape Phage. Valery A. Petrenko; Date of Patent: Mar.20, 2012. Application No. 11/536,844; Filed Sep.29, 2006; Provisional appln. No 60/722,320, filed on Sep.30, 2005

Cancer fighters (2015) left to right: Amanda Gross, Logan Stallings, Christopher Ramhold, Valery Petrenko, Anatoliy Puzyrev, James Gillespie.

    

 

As a faculty member in the Department of Pathobiology (since October 2000), I established the extramurally funded Program in the areas of Directed Molecular Evolution and Targeting. The research program includes:

  • Construction of new phage vectors and diverse phage display libraries.

  • Selection of tumor-targeting phage probes and their use for diagnosis and targeted gene and drug delivery and treatment of cancer diseases.

  • Selection and evolutionary improvement of phage-derived probes against Salmonella typhimurium, Bacillus anthracis and other food and environmental threat agents.

  • Genetically engineered self-assembling of bio-selective layers in biosensors for detection of microbial and toxic threat agents.

  • Optimization of monitoring and detection of Salmonella typhimurium, Bacillus anthracis and other threat agents by phage-derived probes immobilized on the surface of biosensors.

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