Biomimetic Chemistry: Biology as an Inspiration (2008)

On the border between chemistry and biology, information can flow in both directions. Information from chemistry into biology helps us understand how biological systems work and also furnishes many of the tools needed to explore and understand biology generally. However, there is another aspect in which information from biology flows into chemistry. This inspires new chemistry based on the principles used by Nature, a field that I have named “biomimetic chemistry” (1Breslow R. Biomimetic chemistry: centenary lecture.Chem. Soc. Rev. 1972; 1: 553-580Crossref Google Scholar, 2Breslow R. Biomimetic chemistry.Pure Appl. Chem. 1994; 66: 1573-1582Crossref Scopus (51) Google Scholar, 3Breslow R. Biomimetic chemistry and artificial enzymes: catalysis by design.Acc. Chem. Res. 1995; 28: 146-153Crossref Scopus (903) Google Scholar, 4Breslow R. Biomimetic chemistry: a frontier at the chemistry/biology interface.Chem. Biol. 1998; 5: R27-R28Abstract Full Text PDF PubMed Scopus (25) Google Scholar). It mirrors an activity that humans have pursued for a long time: inventing new things inspired by what Nature does. For example, when humans were trying to decide how to fly, they examined the flying organisms, birds and insects, and realized that wings were a major and fundamental idea. However, when early inventors tried to make the wings flap the way they do in birds and insects, they discovered that there were better ways to furnish the power. People took the principle of flight using wings, but not the details of how biology actually used them. As Philip Ball has stated, a jumbo jet is not just a scaled-up pigeon (5Ball P. Stories of the Invisible: A Guided Tour of Molecules. 2001; (Oxford University Press, Oxford)Google Scholar). In biomimetic chemistry, we also take inspiration, but not blueprints, from natural chemistry. As a child, I became interested in chemistry with my first chemistry set. I was excited by the magic that occurred when iron filings were added to a blue copper sulfate solution: the iron became coated with copper, and the solution lost its color. I wanted to know more about this wonderful field and was fortunate that Max Tishler, the head of medicinal chemistry at Merck in Rahway, NJ, where I lived, was a patient of my physician father. Max gave me a college textbook on organic chemistry, by Conant and Blatt, when I was in seventh grade, and I was hooked. I loved the two facets of chemistry. On the one hand, it tries to understand the physical world, as do other sciences. However, it also creates new substances and new reactions. The synthesis of new compounds and new organized systems is a special creative aspect of chemistry, and it contrasts with such fields as astronomy and geology where there is no synthetic component. (I sometimes suggest to students that they establish the field of synthetic astronomy, a virgin area.) In high school, I set up a lab in my basement and tried to synthesize the silicon analog of benzene to see if it was also stabilized by aromaticity. I was not successful (it was made many years later by others), but my attempts did land me a position as a finalist in the Westinghouse contest. In my trip to Washington to meet with the President, I also met many other young budding scientists, some of whom are my friends to this day. At Harvard, I plunged directly into the organic chemistry course, and by my fourth year, I had taken most of the graduate courses. Thus, I went off to the medical science program at Harvard (it was the first year, and all the faculty were involved) to see what scientific path I wanted to pursue. I learned biochemistry from Jack Richards and Eric Ball and physiology and even some pathology from leaders in the field, and I earned a master's degree in medical science. However, I concluded that chemistry was still my true interest, so I went back to the chemistry department and completed my Ph.D. with Bob Woodward while keeping an eye on biology. After a 1-year postdoctoral study with Alex Todd, I came to Columbia University as an instructor. I pursued a program in both theoretically interesting chemistry (we made the simplest aromatic system and established the phenomenon of antiaromaticity) and biologically relevant chemistry. I am now a member of both the chemistry and biology departments, co-director of the Columbia Nanocenter, and one of eleven University Professors. In 1991, I won the National Medal of Science, 4 years after Max Tishler, my earliest mentor. I will focus this account on our work in biomimetic chemistry. In our first studies, I was concerned about understanding how the coenzyme thiamine diphosphate could catalyze reactions such as that in pyruvate decarboxylase, a process for which very unusual catalysis would be needed. Many chemists had speculated on possible ways in which thiamine diphosphate might catalyze such a reaction; indeed, we made a false start with one such speculation before we discovered that the thiazolium ring had a hitherto unsuspected chemistry (6Breslow R. Rapid deuterium exchange in thiazolium salts.J. Am. Chem. Soc. 1957; 79: 1762Crossref Scopus (247) Google Scholar, 7Breslow R. Mechanism of thiamine action: participation of a thiazolium zwitterion.Chem. Ind. 1957; : 893-894Google Scholar). The proton on carbon 2 of the thiazolium ring can be fairly readily removed to generate a zwitterion that is the catalytic species derived from thiamine diphosphate (Fig. 1). We showed that this was the species that catalyzed model reactions for the enzymatic process, in what was the likely process by which thiamine diphosphate operated biologically. Many others have since confirmed this idea. We then explored the new chemistry that this interesting and novel species implied. We showed that we could understand the stability of this species in terms of a second resonance form, a carbene, and that many other heterocyclic cationic systems could also form a related species (8Breslow R. On the mechanism of thiamine action: IV. Evidence from studies on model systems.J. Am. Chem. Soc. 1958; 80: 3719-3726Crossref Scopus (1430) Google Scholar). In the 50 years since that time, many others have used such zwitterion/carbene species to catalyze chemical reactions and also to serve as ligands for metal ions in important catalytic processes. For example, such a species is the preferred ligand in the metathesis catalyst that was part of the work winning Robert Grubbs a recent Nobel Prize in chemistry. Thus, we saw information transfer in both directions. Our work with a chemical model system made it clear how a thiazolium salt such as thiamine could catalyze the biological reactions, and indeed, this turned out to be the correct mechanism for the biochemical process. At the same time, the discovery of this hitherto unsuspected species led to unprecedented chemistry and new and useful catalytic reactions. We also explored the catalytic chemistry using thiamine analogs to see how well natural thiamine did in chemical model systems, an effort I have called “Nature appreciation.” Thiamine was the best of its close analogs for reasons that balanced reactivity and chemical stability (9Breslow R. McNelis E. Studies on model systems for thiamine action: synthesis of reactive intermediates and evidence on the function of the pyrimidine ring.J. Am. Chem. Soc. 1959; 81: 3080-3082Crossref Scopus (109) Google Scholar). In a similar vein, we later synthesized what I called iso-DNA, based on 3-deoxyribose that makes 2,5-links instead of the normal 2-deoxyribose that makes 3,5-links (10Breslow R. Sheppard T.L. Why natural DNA is based on 2′-deoxyribose, with 3′,5′-phosphodiester links.Pure Appl. Chem. 1996; 68: 2037-2041Crossref Scopus (14) Google Scholar, 11Sheppard T.L. Breslow R.C. Selective binding of RNA, but not DNA, by complementary 2′,5′-linked DNA.J. Am. Chem. Soc. 1996; 118: 9810-9811Crossref Scopus (79) Google Scholar). In a sense, we wanted to see why Nature had selected the normal DNA structure. Iso-DNA makes a much weaker double helix with its conjugate, or with the conjugate based on normal DNA, because the helix has more hydrophobic surface exposed to solvent. Thus, it is not a suitable substitute for normal DNA as a genetic material, and organisms that may have tried it would not be competitive. However, iso-DNA does make a strong heteroduplex with normal RNA, reflecting the conformation of the ribose ring relative to that in deoxyribose. Enzymes teach us many other inspiring principles. One is that geometry can dominate chemical reactivity. A good example is the conversion of lanosterol to cholesterol, in which three unactivated methyl groups are oxidatively degraded by enzymes of the class cytochrome P-450 while the much more reactive double bonds of lanosterol are left untouched until later (Fig. 2). This inspired us to develop processes we called remote oxidation, in which we attached reagents and templates to substrates that could reach far from their attachment point (from ring A of the steroid all the way to ring D at the other end) and perform selective reactions on particular spots because of the geometry imposed by our attached reagent or template (12Breslow R. Baldwin S. Flechtner T. Kalicky P. Liu S. Washburn W. Remote oxidation of steroids by photolysis of attached benzophenone groups.J. Am. Chem. Soc. 1973; 95: 3251-3262Crossref PubMed Scopus (167) Google Scholar, 13Breslow R. Corcoran R.J. Snider B.B. Remote functionalization of steroids by a radical relay mechanism.J. Am. Chem. Soc. 1974; 96: 6791-6792Crossref PubMed Scopus (75) Google Scholar). In more recent work, we have learned how to imitate the enzyme more fully, achieving geometrically controlled turnover catalysis (14Breslow R. Huang Y. Zhang X. Yang J. An artificial cytochrome P450 that hydroxylates unactivated carbons with regio- and stereoselectivity and useful catalytic turnovers.Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 11156-11158Crossref PubMed Scopus (139) Google Scholar, 15Breslow R. Artificial Enzymes. 2005; (Wiley-VCH, Weinheim, Germany)Crossref Scopus (116) Google Scholar, 16Breslow R. Artificial enzymes. In:.Artificial Enzymes. 2005; (Breslow, R., ed) pp. , Wiley-VCH, Weinheim, Germany: 1-35Google Scholar). The enzyme mimic we synthesized was a metalloporphyrin carrying cyclodextrin groups that would reversibly bind substrates such as steroids. These mimics of cytochrome P-450 performed selective oxidations that are of practical interest, with thousands of turnovers. The result was selective oxidation of particular C–H bonds that was hitherto possible only with natural biological enzymes. Another of the important principles that natural enzymes use is bifunctional and sometimes even multifunctional catalysis. In simple chemical reactions, such processes are rare because they would involve the collision of two or more different catalytic materials with a substrate at the same time, but of course in enzymes, the catalytic groups are part of the binding molecule. In particular, in the enzyme ribonuclease A, both the imidazole of histidine 12 and the imidazolium ion of histidine 119 play such a bifunctional catalytic role in RNA cleavage. We synthesized molecules that could perform the same kind of phosphate ester cleavage by attaching imidazole groups to the rim of a binding molecule, a cyclodextrin (17Breslow R. Anslyn E. Huang D.-L. Ribonuclease mimics.Tetrahedron. 1991; 47: 2365-2376Crossref Scopus (64) Google Scholar). With such a system, we were able to control the geometry of the process by fixing the positions where the two groups were attached. With a technique called “proton inventory,” we showed that the imidazole and imidazolium catalytic groups operated simultaneously in the cleavage process, as they do in the natural enzyme (17Breslow R. Anslyn E. Huang D.-L. Ribonuclease mimics.Tetrahedron. 1991; 47: 2365-2376Crossref Scopus (64) Google Scholar). We made an important and surprising chemical finding. It was usually believed that ribonuclease uses a basic imidazole to deliver the hydroxyl group of carbon 2 to the phosphate as the histidine 119 imidazolium ion protonates the leaving nucleoside group, but this would require that the catalytic species be positioned essentially 180° apart. Our surprising finding was that such an isomer in our artificial enzyme was the worst of the three positional isomeric catalysts, and the best one had the acid and base groups as near each other as possible, on neighboring glucose residues. This indicated that the mechanism was not a direct reaction, as is usually invoked in biochemistry textbooks, but instead a process in which water is added to the phosphate to produce what is called a phosphorane, a five-coordinated phosphorous species. At first, the imidazolium ion binds to the phosphate oxygen anion, and the water is delivered to this species by the imidazole. With further bifunctional catalysis, this phosphorane then decomposes to cleavage products in a second step. In chemical kinetic studies, we were able to show that imidazole buffers used at high concentration could catalyze the hydrolysis of uridyluridine, a fragment of RNA, and that this hydrolysis also proceeded through such a water addition to the phosphate group, rather than by a direct reaction (18Breslow R. Dong S.D. Webb Y. Xu R. Further studies on the buffer-catalyzed cleavage and isomerization of uridyluridine: medium and ionic strength effects on catalysis by morpholine, imidazole, and acetate buffers help clarify the mechanisms involved and their relationship to the mechanism used by the enzyme ribonuclease and by a ribonuclease mimic.J. Am. Chem. Soc. 1996; 118: 6588-6600Crossref Scopus (69) Google Scholar). The imidazolium ion of the buffer again binds to the phosphorus, and the imidazole of the buffer then again delivers a water molecule to this species. The process resembles that in the hydrolysis of esters and amides, in which a tetrahedral intermediate is formed first. In phosphorus chemistry, such an intermediate is instead the five-coordinated phosphorane. We pointed out that some of the evidence on the enzyme itself would be consistent with such a two-step mechanism of hydrolysis, where the water is added before the leaving group begins to depart or, in the case of the cyclization of RNA, where the C-2 hydroxyl group adds to the phosphate to make such a five-coordinated phosphorous species before the leaving group is lost in a subsequent step. It remains to be seen whether our addition mechanism proves to be correct with the enzyme, but it is certainly clear that we have learned important features of phosphate chemistry from the detailed study of an enzyme mimic inspired by ribonuclease. Not only is bifunctional catalysis (by an enzyme mimic that binds a substrate next to two well placed catalytic groups) a useful process in chemistry, it also furnishes mechanistic information not available in other ways, as it did in the case of phosphate hydrolysis. As another example, we looked at the ability of such a bifunctional catalyst to promote the enolization of a ketone in a substrate that was into a cyclodextrin R. A. of enolization using a bifunctional Am. Chem. Soc. Scopus Google Scholar). the catalysis involved one imidazole and one imidazolium group, but in this the catalyst was the one with groups apart. This detailed chemical information about how a base and a proton in the enolization of a ketone (Fig. information that was The base not the C–H but to the the is another important that biological chemistry has the of water as a reaction solvent. has much in water as an in the effort to make the of into a we saw that the hydrophobic in water can also have very useful special in chemical processes. In the artificial cytochrome P-450 enzyme mimic we used hydrophobic binding of the substrate steroid into the catalyst to the well geometry that the oxidation to a particular not the most reactive but the one that was the geometry of the (14Breslow R. Huang Y. Zhang X. Yang J. An artificial cytochrome P450 that hydroxylates unactivated carbons with regio- and stereoselectivity and useful catalytic turnovers.Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 11156-11158Crossref PubMed Scopus (139) Google Scholar, 15Breslow R. Artificial Enzymes. 2005; (Wiley-VCH, Weinheim, Germany)Crossref Scopus (116) Google Scholar, 16Breslow R. Artificial enzymes. In:.Artificial Enzymes. 2005; (Breslow, R., ed) pp. , Wiley-VCH, Weinheim, Germany: 1-35Google Scholar). In other work, we have that simple chemical reactions species with could be to high when they were performed in where hydrophobic binding the reagents to the in other organic the reactions were essentially Breslow R. selective of Am. Chem. Soc. PubMed Scopus Google Scholar). Thus, water has an for chemical reactions and processes. Not only is it it is also special in selective reactions out of what might be processes. In the course of this work, we also a way to that hydrophobic were of to the water that or the hydrophobic that this as of or detailed on hydrophobic binding of their We showed that species such as which are used as not by the of which was but instead by to the hydrophobic of the The species can between the hydrophobic and the water R. T. show that are not just Natl. Acad. Sci. U. S. A. PubMed Scopus Google Scholar). Our for this was the in biology and biochemistry of such but they inspired us to the use of such in simple chemical As part of we also showed that we could the detailed of a of important chemical reactions, a of chemistry that was hitherto by using such in water solution R. effects for reactions in water oxygen carbon of Am. Chem. Soc. PubMed Scopus Google Scholar). The of the on reaction to be directly related to the of exposed surface in the for the reactions relative to that in the Another principle from biology is that enzymes have a and a hydrophobic This hydrophobic substrates to bind into the of the enzyme and also the chemistry to from the water up bonds to and substrate and in a catalytic process, bonds be as the groups are before they can directly the chemistry or biochemistry a are not We saw this in a of artificial enzymes we synthesized Breslow R. enzyme In:.Artificial Enzymes. 2005; (Breslow, R., ed) pp. , Wiley-VCH, Weinheim, Germany: based on the first by and J. of synthetic with catalytic In:.Artificial Enzymes. 2005; (Breslow, R., pp. , Wiley-VCH, Weinheim, Germany: Scholar). Nature us how to synthesize by using phosphate coenzyme to perform a with a and we and others had for such reactions. We a model enzyme system for the process by using a hydrophobic of as the coenzyme mimic and a with an added hydrophobic as the enzyme The coenzyme into this and the substrates as well into if they hydrophobic as in the acid that formed Our system just as enzymes and with such kinetic studies, we were able to show that the hydrophobic not only the binding of the coenzyme and the it also the for the reaction the Breslow R. effects on and substrate in Am. Chem. Soc. PubMed Scopus Google Scholar). Thus, in an artificial enzyme, it is not to the catalytic groups or, for that the catalytic groups and binding it can also be important to a in medium by such a a We were of course inspired to do this by about how enzymes actually We discovered a very way to perform the of the species to be to the form by a of an acid (Fig. W. Breslow R. reactions with catalyzed by hydrophobic in the of Am. Chem. Soc. PubMed Scopus Google Scholar). This is a unusual biological process, there is an enzyme that can perform In the course of this work, we became of the that are delivered from to the by and that they have but of the We showed that we could perform a direct using such species to generate such as and with available and that we could also the to the high of needed for the synthesis of and In the account of our studies, we point out the evidence for the of reactions with and the of their (from by and have a of how first on Breslow R. synthesis and of PubMed Scopus Google Scholar). This not only the work we have but also studies in the by and It makes it clear how such in for could have occurred and made the of This is an example in which chemistry is relevant to understanding the of biology. These are some in which about biology, and sometimes the that biology can also and chemistry It is to see the in the field of biomimetic chemistry. We to know how to materials that will imitate the at in some of its The is not synthetic that is We can chemistry by to organized systems of different to new from with the of simple This is a in which chemistry is inspired by the example of the biological Thus, we have by no the of we can by biology and trying to how to imitate to imitate its principles if not its to new and chemistry. At the same time, such will to us into biological chemistry An important recent example is our of an in with Breslow R. to of this as an PubMed Scopus Google Scholar). This which we and is now as a group of It was by what we about hydrophobic and effects in enzymes. These suggest that biomimetic chemistry will have a at as as its The has established an the Breslow in Biomimetic