Dr. Petukhov laboratory

Department of Medicinal Chemistry and Pharmacognosy


A short outline of the BEProFL approach is provided here.


Chemical biology, medicinal chemistry, computer-aided molecular design, photoaffinity labeling, and drug discovery targeting epigenetics:

1. Our histone deacetylase (HDAC) publications related to discovery of HDAC photoreactive probes (PRP), novel isoform selective HDAC inhibitors, and use of HDAC PRPs to study structure of deacetylase complexes, specifically HDAC3-SMRT, can be found here.

2. Discovery of HDAC isoform selective inhibitors for a variety of diseases and conditions

Hepatatis B visrus:

3. Our HBV pilot studies were recently supported by the Areas of Excellence Program at UIC and the NIH/NIAID.



1. Small molecule inhibitors of pantothenate synthesis against M. tuberculosis

2. Small molecule inhibitors of malate synthase against M. tuberculosis

Alzheimer's disease:

3. Tools for AD Research: Design of BACE2 Ligands

List of publications referenced by PubMed

Selected publications (out of more than 55, Pubmed links only):

  1. Abdelkarim, H.; Brunsteiner, M.; Neelarapu, R.; Bai, H.; Madriaga, A.; van Breemen, R. B.; Blond, S. Y.; Gaponenko, V.; Petukhov, P. A. Photoreactive "Nanorulers" Detect a Novel Conformation of Full Length HDAC3-SMRT Complex in Solution. ACS Chem Biol 2013, 8, 2538-2549. PMCID: PMC3880688.
  2. Vaidya, A. S.; Neelarapu, R.; Bai, H.; Madriaga, A.; Mendonca, E.; Brunsteiner, M.; van Breemen, R.; Blond, S. Y.; Petukhov, P. A. Novel Histone Deacetylase 8 Ligands without a Bidentate Zinc Chelating Group: Exploring an Upside-down Binding Pose. Bioorg. Med. Chem. Lett. 2012, 22, 6621-6627. PMCID: PMC3472134
  3. Vaidya, A. S.; Karumudi, B.; Mendonca, E.; Madriaga, A.; Abdelkarim, H.; van Breemen, R.; Petukhov, P. A. Design, synthesis, modeling, biological evaluation and photoaffinity labeling studies of novel series of photoreactive benzamide probes for histone deacetylase 2. Bioorg. Med. Chem. Lett. 2012, 22, 5025-5030. PMCID: PMC3401313
  4. Neelarapu, R.; Petukhov, P. A. A One-Pot Selective Synthesis of N-Boc Protected Secondary Amines: Tandem Direct Reductive Amination/N-Boc Protection. Tetrahedron 2012, 68, 7056-7062. PMCID: PMC3404846
  5. Brunsteiner, M.; Petukhov, P. A. Insights from comprehensive multiple receptor docking to HDAC8. J. Mol. Model. 2012, 18, 3927-3939. PMCID: PMC3565472
  6. Neelarapu, R.; Holzle, D. L.; Velaparthi, S.; Bai, H.; Brunsteiner, M.; Blond, S. Y.; Petukhov, P. A. Design, Synthesis, Docking, and Biological Evaluation of Novel Diazide-containing Isoxazole- and Pyrazole-based Histone Deacetylase Probes. J. Med. Chem. 2011, 54 (13), pp 4350–4364. PMC3466118.
  7. He, B.; Velaparthi, S.; Pieffet, G.; Pennington, C.; Mahesh, A.; Holzle, D. L.; Brunsteiner, M.; van Breemen, R.; Blond, S. Y.; Petukhov, P. A. Binding ensemble profiling with photoaffinity labeling (BEProFL) approach: mapping the binding poses of HDAC8 inhibitors. J. Med. Chem. 2009, 52, 7003-13. PMCID: PMC2789734
  8. Pieffet, G.; Petukhov, P.A. Parameterization of aromatic azido group: Application for Photoaffinity Probe in Molecular Dynamics Studies. Journal of Molecular Modeling 2009, 15, 1291-1297. PMID: 19288146
  9. Chirapu, S. R.; Pachaiyappan, B.; Nural, H. F.; Cheng, X.; Yuan, H.; Lankin, D. C.; Abdul-Hay, S. O.; Thatcher, G. R.; Shen, Y.; Kozikowski, A. P.; Petukhov, P. A. Molecular Modeling, Synthesis and Activity Studies of Novel Biaryl and Fused-Ring BACE1 Inhibitors. Bioorg. Med. Chem. Lett. 2009, 19, 264-274. PMC2643073
  10.  Velaparthi, S.; Brunsteiner, M.; Uddin, R.; Wan, B.; Franzblau, S. G.; Petukhov, P. A. 5-tert-butyl-N-pyrazol-4-yl-4,5,6,7-tetrahydrobenzo[d]isoxazole-3-carboxamide derivatives as novel potent inhibitors of Mycobacterium tuberculosis pantothenate synthetase: initiating a quest for new antitubercular drugs. J. Med. Chem. 2008, 51, 1999-2002. PMID: 18335974
  11. Yuan, H.; Petukhov, P. A. Improved 3D-QSAR CoMFA of the dopamine transporter blockers with multiple conformations using the genetic algorithm. Bioorganic & Medicinal Chemistry Letters 2006, 16, 6267-72. PMID: 17027270
  12. Yuan, H.; Petukhov, P. A. Computational evidence for the ligand selectivity to the alpha4beta2 and alpha3beta4 nicotinic acetylcholine receptors. Bioorganic & Medicinal Chemistry 2006, 14, 7936-42. PMID: 16919961

Other publications