The design and synthesis of redox core±alpha amino acid composites based on thiol±disul®de exchange mechanism and a comparative study of their zinc abstraction potential from [CCXX] boxes in proteins Subramania Ranganathan, a,b,p K. M. Muraleedharan, a Parimal Bharadwaj, c Dipankar Chatterji d and Isabella Karle e,p a Discovery Laboratory, Organic III, Indian Institute of Chemical Technology, Hyderabad 500 007, India b Jawaharlal Nehru Centre for Advanced Scienti®c Research, Bangalore 560 012, India c Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India d Molecular Biophysics Unit, Indian Institute Science, Bangalore 560 012, India e Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375-5341, USA Respectfully dedicated to Darshan Ranganathan who passed away on her 60th birthday 4 June 2001) Received 2 October 2001; revised 7 January 2002; accepted 7 February 2002 Abstract ÐThe design and synthesis of agents that can abstract zinc from their [CCXX] Ccysteine; Xcysteine/histidine) boxes by thiol± disul®de exchange-having as control, the redox parities of the core sulfur ligands of the reagent and the enzyme, has been illustrated, and their ef®ciency demonstrated by monitoring the inhibition of the transcription of calf thymus DNA by E.coli RNA polymerase, which harbors two zinc atoms in their [CCXX] boxes of which one is exchangeable. Maximum inhibition possible with removal of the exchangeable zinc was seen with redox±sulfanilamide±glutamate composite. In sharp contrast, normal chelating agents EDTA, phenanthroline) even in a thousand fold excess showed only marginal inhibition, thus supporting an exchange mechanism for the metal removal. q 2002 Elsevier Science Ltd. All rights reserved. 1. Introduction The genesis of the present work pertains to recent reports on the fact that, in the maturation of HIV virus, a 55-residue protein called nucleocapsid protein NCp7) plays a very important role in the proper packaging of HIV-RNA. Viral RNA, which provides all the information for its func- tion, can be packaged only if this protein is present. The sequence of this protein is presented in Chart 1, A. The protein contains two zinc ®nger modules, where the metal is harbored in the [CCXX] boxes. 1 Concerted efforts to remove zinc from these ef®ciently, led to the identi®cation of disul®des of the type B Chart 1) as useful agents to disrupt the NCp7 conformation by the removal of the zinc present, thus making the protein inoperative and thereby making the packaging of virions in the HIV virus defective and dysfunctional. 2 The ef®ciency with which zinc is removed from A by B, in the context of work from our laboratory, 3 provided an opportunity to design agents that could abstract zinc present in the [CCXX] boxes of enzymes, by the thiol±disul®de exchange mechanism Chart 2). 4 Thus, B Chart 1) could react with an appropriate [CCXX] box harboring zinc in proteins, to form the octahedral complexes, which could break up, effecting oxidation in the [CCXX] box with concomitant removal of B as a zinc complex. The rationalization of the overall process in this manner brings to focus, the redox parity of the S±S system present in A and B Chart 2). The redox core in B was redesigned to interact favorably with the zinc ®nger modules, by linking with diverse amino acid residues. This was considered important, since, in the removal of zinc from [CCXX] boxes, the amino acid side chains could play a major role in stabilizing the transition state, by interaction with residues present in the zinc Tetrahedron 58 2002) 2861±2874 Pergamon TETRAHEDRON 0040±4020/02/$ - see front matter q 2002 Elsevier Science Ltd. All rights reserved. PII: S0040-402002)00159-X Keywords: thiol±disul®de exchange; RNA polymerase; dithiobisbenza- mides; benzisothiazolones. p Corresponding authors. Address: Discovery Laboratory, Organic III, Indian Institute of Chemical Technology, Hyderabad 500 007, India. Tel.: 191-40-7160123x2648; fax: 191-40-7160757; e-mail: rangan@iict.ap.nic.in