Associate editor: D. Shugar Designing bisubstrate analog inhibitors for protein kinases Keykavous Parang a,b,1 , Philip A. Cole b, * a Department of Biomedical Sciences, College of Pharmacy, University of Rhode Island, 41 Lower College Road, Kingston, RI 02881, USA b Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA Abstract Protein kinases play critical roles in signal transduction pathways by transmitting extracellular signals across the cell membrane to distant locations in the cytoplasm and the nucleus. The development of protein kinase inhibitors has been hindered by the broad overlapping substrate specificities exhibited by these enzymes. The design of bisubstrate analog inhibitors could provide for the enhancement of specificity and potency in protein kinase inhibition. Bisubstrate analog inhibitors form a special group of protein kinase inhibitors that mimic two natural substrates/ligands and that simultaneously associate with two regions of given kinases. Most bisubstrate analogs have been designed to mimic the phosphate donor (ATP) and the acceptor components (Ser-, Thr-, or Tyr-containing peptides). Recent studies have emphasized the importance of maintaining a specific distance between these two components to achieve potent inhibition. In this review, we present a discussion of the methods for designing protein kinase inhibitors by mechanism-based approaches. Emphasis is given to bivalent approaches, with an interpretation of what has been learned from more and less successful examples. Future challenges in this area are also highlighted. D 2002 Elsevier Science Inc. All rights reserved. Keywords: Protein kinases; Src; Insulin receptor kinase; Bisubstrate inhibitor; Mechanism; Transition state Abbreviations: AdoC, adenosine-5 0 -carboxylic acid; CK, casein kinase; CDPK-1, Ca 2+ -dependent protein kinase 1; CT, C-terminal; EGFR, epidermal growth factor receptor, ( F 5 )Phe, pentafluorophenylalanine; GABA, g-aminobutyric acid; IRK, insulin receptor kinase; NT, N-terminal; PKA, protein kinase A; PKC, protein kinase C; PTK; protein tyrosine kinase; RTK, receptor tyrosine kinase; SH, Src homology. Contents 1. Introduction ............................................ 146 1.1. General structural features of protein kinases ....................... 146 1.2. General mechanistic features of protein kinases ...................... 147 2. Bisubstrate analog inhibitors (general) .............................. 148 2.1. An ideal bisubstrate analog inhibitor for protein kinases ................. 148 2.2. Different strategies in designing bisubstrate analog inhibitors for protein kinases ..... 149 2.2.1. Sulfonamides and sulfonylbenzoyl derivatives .................. 149 2.2.2. Carboxylic acid derivatives ............................ 151 2.2.3. Dipeptidyl and N-acylated peptide derivatives .................. 151 2.2.4. Phosphodiester derivatives ............................ 153 3. Conclusions ............................................ 155 Acknowledgements ........................................... 155 References ............................................... 155 0163-7258/02/$ – see front matter D 2002 Elsevier Science Inc. All rights reserved. PII:S0163-7258(02)00184-5 * Corresponding author. Tel.: 410-614-0540; fax: 410-614-7717. E-mail addresses: pcole@jhmi.edu (P.A. Cole), kparang@uri.com (K. Parang). 1 Also corresponding author. Tel.: 401-874-4471; fax: 401-874-5048. Pharmacology & Therapeutics 93 (2002) 145 – 157