Wynn L. Walker

Progress in the design of DNA sequence-specific lexitropsins

Sequence‐specific polyamides that bind in the minor groove of DNA are attractive candidates for antibiotics, cancer chemotherapeutics, and transcriptional antagonists. This paper reviews the progress of structure‐based design of minor‐groove‐binding polyamides, from the first structure of netropsin with DNA, to the effective linked polyamides currently under study. A theory of polyamide specificity is also reviewed, introducing methods to determine the optimal strategies for targeting a given DNA sequence within a genome of competing sequences.

Drug delivery to brain tumors

We develop a macroscopic model for delivering drug to brain tumors. The model accounts for bulk convective and diffusive transport across the blood-brain barrier and through the interstitial space. Through mathematical analysis and simulations, we assess the effects of changing parameters (within physiological bounds) on drug delivery. We find that there is an optimal treatment for convective drug delivery to the center of the tumor. We interpret this phenomenon in terms of traffic flow. The implications of our analyses on existing chemotherapeutic protocols are discussed.

Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method

We report the design of optimal linker geometries for the synthesis of stapledDNA-minor-groove-binding molecules. Netropsin, distamycin, and lexitropsinsbind side-by-side to mixed-sequence DNA and offer an opportunity for thedesign of sequence-reading molecules. Stapled molecules, with two moleculescovalently linked side-by-side, provide entropic gains and restrain theposition of one molecule relative to its neighbor. Using a free-atom simulatedannealing technique combined with a discrete mutable atom definition, optimallengths and atomic composition for covalent linkages are determined, and anovel hydrogen bond ‘zipper’ is proposed to phase two molecules accuratelyside-by-side.

A Preliminary Multiobjective Analysis of the Chemotherapeutic Benefits of Hairpin-Linked Polyamides

In this study we review a mathematical model for estimating the free energies of binding for γ-aminobutyric-acid-linked polyamides containing N-methylimidazole and N-methylpyrrole to five-and six-base-pair DNA sequences. We use the model to evaluate numerically several different conflicting design criteria, each characterizing the suitability of a polyamide as a chemotherapeutic agent, and we analyze the trade-offs existing between these criteria. This preliminary analysis presents several methodological and modeling problems in the area of multiobjective optimization. We introduce some concepts from multiobjective optimization and conclude by discussing the application of these concepts to solving these problems.

The theoretical limits of DNA sequence discrimination of polyamides

Linked polyamides bind in the minor groove of double-stranded DNA in a partially sequence-specific maoner but have limited sequence dis criminatoty abilities, suggesting a need for design alternatives to create molecules with enhanced sequence selectivity. We present an aualysis of the theoretical limits of the DNA sequence selectivity of hypothetical sequence reading molecules as a function of their base recogition properties and sequence content of their target sequence. The analysis shows the nonobvious result that molecules containing nonspecific readers at critical positions within the molecule may have enhcuzced sequence selectivity over molecules composed entirely of base specific reading elements. We apply this result to determine optimal patterns of base recognition for molecules in order to optimize their target sequence selectivity. We also examine the effect of the length of a polyamide (Le. the number of base pairs it binds) on its sequence d&rim&tory ability and determine necessary concentration dependent constraints on the binding tiee energies in order for longer polyamides to have greater sequence specificity than shorter ones. Introauction Drugs that bind to nucleic acids, blocking transcription and replication, are important in the treatment of cancer and AIDS-related diseases. Drugs of clinical importance act by Several mechanisms: alkylating agents and platinum coordination complexes form cross-links in DNA; anthracycline antibiotics intercalate in double-stranded DNA; iron-chelating antibiotics fragment DN& and groove-binding drugs typicalIy bind in the minor groove of DNA These drugs show limited sequence specificity and bind to many sites in a typical genome, leading to harmful side effects. Recently, the search for new chemotherapeutic agents has shifted to molecules designed to target a given doublestranded DNA sequence in a pathogenic organism or neoplastic cell Some minor groove binding molecules demonstrate an ability to target a specific sequence by recognizing certain base pairs over others based on differences in structural features of the base pairs. Ewmples of minor groove binding molecules include pyrrole-amide-containing molecules such as netropsin and their imidarole-containing synthetic derivatives, known as lexitropsins. Molecules pdon to make digital/hard copies of aU or part of this material for pa~nd or classroom use is granted About fre provided that the copies are not made or distributed for profit or commercial dvantagZ, the COPYright notice, the title of the publication and its date appear, and noti= is g;~m that qyigbt is by permission ofthe AChZ Inc. To copy ofi* to republish, to post on servers or to rediiiute to k% rqirrs SpecitiC permission a&or fee. RECOMB 98 New York NY USA containing pyn-ole-amide and/or imidazole-amide repeat units joined in tandem are commonly referred to as polyamides. Ilolyamides possess two major shortcomings. First of all, while they have a strong ability to read sequences containing A and T, they exhibit limited ability to recognize sequences containing G and C. Secondly, they have a short reading name, recognizing only three to five base pairs. Such limitations contriiute to the toxicity of these agents because they may randomly bind over any region of the genome containing short stretches of A and ‘I containing base pairs. There is currently much interest in fmding ways to increase the selectivity or sequence dis criminatory capability of groove binding molecules (i.e. the specificity of the molecules for binding a given target DNA sequence while not binding other sequences). Enhanced dis crimination would increase the drug effectiveness per dose (as measured by the amount bound to a specific sequence) while mhimizbg harmful side effects as a consequence of nonspecitic binding of the dmg over the remainder of the genome. Recently it has been found that polyamide molecules can bind DNA in a sequence-specific manner in a 21 polyamideDNA stoichiometry (l-3). In this mode, the two polyamides bind to a sequence in the minor groove in a side-by-side orientation, enabling each polyamide to recognize its own strand of DNA The polyamides are positioned such that each pyrrole ring or each imidazole ring makes contact with a single base, and the two polyamides stack one on top of the other so that each base pair is adjacent to two rings, one from each polyamide strand The sequence specificity results from the different hydrogen bonding capability of pyrrole and imidazole rings: imidazole binds preferentially to guanine, and pyrrole binds to adenine, thymine, and cytosine, excluding guanine through steric hindrance. This side-by-side binding motif has strong implications for drug design. First of all, when certain polyamides bind side by side, they exhibit a strong recognition capability for G/C-rich regions (4). Secondly, the property of each molecule recognizing’ its own strand allows for more precise sequence recognition than when one molecule has to read both strands. It has also been found that covalent linkage of the two polyamides enhances the side-by-side molecular binding to DNA by ftig the relative positioning of the two molecules. Henceforth, the general term “polyamide” refers to the configuration of two individual polyamide strands wvalently link& In an earlier study (5) we developed and analyzed a linear regression model for predicting the binding i&e energies of linked polyamides for 5 and 6-base-pair DNA sequences. The calculations of this study suggested that there are serious limitations in the sequence selectivity of pyrroleand imidazole-containing polyamides and a need for considering CQpyigbt 1998 0-89791-976-9/98/3..s5.00 270 design altematives for molecules with better discriminatory is the ratio of the binding constants of the polyamide to the abiities. target and ifh sequences. In this paper we present an analysis of the theoretical limits of the DNA sequence speciEcity of hypothetical sequence m molecules as a fnuction of their base recognition pmperties and the sequence content of their target sequence. We present the counterintoitie result that molecules comaiuing nonspecik readers at critical positions withh the molecule may have enIzf2zced sequence selectivity over molecdes composed entirely of base specific reading elements. We apply this result to determine optimal patterns of base recognition for molezules in order to optimize their target sequence selectivity. We also examine the effect of the length of a polyamide (ie. the number of base p-airs it bids) on its sequence discrimhmtory ability and determine necessary concentration dependent comtmints on the biding f&e energies in order for longer polyamides to have greater sequence specificity than shorter ones. Assumptions and Terminology Relevant to the Analysis of the Emits of the Sequence Discriminatory Ability of Polyamides The term ring is used to denote a generic base binding unit and the term puiyamide refers to two identical length molecules composed of rings linked in tandem. We make the assump.tion that the free energy of binding of a polyamide to a double-stranded DNA sequence may be expressed as an additive sum of the binding free energies of each ring in the polyamide for its nearest neighbor base (and that there are no cross interactions between these rings and other bases). Modeling the Sequence Discriminatory Ability of a Molecule We begin by briefly reviewing a mathematical model for predicting the double-stranded DNA sequence disuiminatory ahiity of polyamides. For a given polyamide one can approximate e,, the fractional ocq.ancy or satnration for the ifhn-base-pair DNA sequence (where i: rauges from 1 to 4n and i=l correq~onds to the target sequence) by the following equation (6): We let Bi e{A,C,G,T) denote the single base favored by ring ri (where i.=l,..., m and m is the available number of different discrimina tory rings). For the analysis in the next section m = 2, but later we address cases when m = 3 and 4. The symbol

An analysis of a class of DNA sequence reading molecules.

denotes {A,C,G,T)\ Bi, namely the set of three bases remaking after excluding Bi. For example, if Bi = C, then

Estimation of the DNA sequence discriminatory ability of hairpin-linked lexitropsins

= {A,G,lJ. The binding of ri to its preferred base Bi is favored over the binding of ri to any of the bases in q. For this lmxmation we make the simplifying assnmption that the f&e energies of binding for ri to each of the bases in

Coevolution and subsite decomposition for the design of resistance-evading HIV-1 protease inhibitors.

are the same. This common free energy of binding to the less favored bases is used as a reference level. The difference between the fia t~~am of binding for ri to the bases in

Regular articleCoevolution and subsite decomposition for the design of resistance-evading HIV-1 protease inhibitors1

and the free energy of binding of ri to Bi is denoted by Si (so that Si > 0).

Design of B-DNA cross-linking and sequence-reading molecules

Linked polyamides are a class of designed molecules that bind in the minor groove of double-stranded DNA in a partially sequence-specific manner but have limited sequence discriminatory abilities. This suggests a need for design alternatives to create molecules with enhanced sequence specificity. In this report we present formal proofs of the theoretical limits of the DNA sequence specificity of hypothetical sequence reading molecules as a function of their base recognition properties and sequence content and length of their target sequence. We prove that molecules containing nonspecific readers at critical positions within the molecule may have enhanced sequence specificity over molecules composed entirely of base specific reading elements. We also determine optimal patterns of base recognition for molecules in order to optimize their target sequence specificity. We also examine the effect of the length of a polyamide (i.e., the number of base pairs it binds) on its sequence discriminatory ability and determine necessary concentration dependent constraints on the binding free energies in order for longer polyamides to have greater sequence specificity than shorter ones. We show that unless the discriminatory ability of a ring for its preferred base is very strong, longer polyamides do not necessarily have greater sequence specificity over shorter ones when compared at the same molar concentration.