Summary

The synthesis of metabolites from the available raw materials at the right time and when they
are needed by highly selective catalytic reaction steps in biological cells, tissues, organs and
whole organisms is a masterpiece in molecular economy. The universe of metabolites
constitutes an important small molecule domain beside the large molecule domains of the
DNA-, RNA-, protein and polysaccharide world.
The chemical synthesis of metabolites has led to spectacular advances in methodologies for
total synthesis and the high-yield preparation of the most complex molecular structures from
simple building blocks or intermediates. The applications on industrial large-scale or in
biological systems however remind us of the many challenges, bottlenecks and dead ends [1]
which may be encountered on the route from the starting material to the product: a) protection
of the macroenvironment (humans, environment, product) or the microenvironment (other
functional groups of the molecule, other molecular components or parts of the cell) may
represent challenging tasks, b) available known reactions may not be selective enough, c) no
direct synthetic route from the starting material to the product may be known, d) too many
steps and detours for the intended synthetic route may be required or a key reaction step may
turn out to be a dead-end, and e) waste growth in relation to the growth of the desired product
may create problems due to unfavourable. Since waste accumulation with each reaction step
is a common feature of production processes in chemical synthesis, increased attention to
waste is of prime importance, in addition to the traditional synthetic criteria such as product
yield and purity. The economy of a synthetic scheme on a molecular scale can be viewed from
different perspectives, but all aim at making the best use of materials and minimizing the
waste.
Biological cells use this strategy with the help of nature’s catalysts in order to avoid the
scaling of waste with the increasing amount of product as in stoichiometric reactions in
chemical synthesis. From the single reaction step perspective, selective transformations with
high resource efficiency continue to be a main focus of research in the science of synthesis.
As enzymes within a biological cell perform the required molecular transformations with
excellent selectivity, the waste is minimized and product yield maximized. The micro- and
macroeconomic value creation by natural biotransformations of raw materials on our planet
has been central to life and the knowledge of the molecular diversity of natural compounds is
far from complete despite the great progress in the understanding of metabolic pathways. The
progress in the development of databases and bioinformatic tools for metabolites and their
reaction pathways in health and disease and their linkage to the increasing number of fully
sequenced genomes is therefore of much interest [2-4]. Metabolites and natural products have
played an important role in the history of chemistry, biology and medicine and they still
matter because the continue to inspire chemists, remain a major source of human medicines
[5], lead to important biological insights and there is still a wealth of metabolites and natural
products to be discovered [6]. Metabolites have contributed to many areas of the healthcare
and medicine sector from drug discovery and early development, drug behaviour and toxico-
logy, metabolite production for preclinical & clinical studies to the active pharmaceutical
ingredients and micronutrients in therapy. Finally, metabolites and natural products have been
of great value both as tools for molecular recognition in biomedical analysis and as targets for
robust and reliable point-of-care analysis in medical routine practice. Although the metabo-
lism of drugs in biological organisms leads to therapeutically inactive molecules, there are
also cases where metabolites are generated which show higher activity against the same
pharmacological target as the parent compound [7]. It is therefore advantageous to screen
drug candidates for active metabolites already during the drug discovery and design process
[7]. The milestone discoveries of antibiotics to fight infectious diseases by pathogenic micro-
organisms have clearly demonstrated the tremendous value of microbial metabolite pro-
duction for human health [8]. Numerous human cancers show anomalies in the cell division
and its regulation, with changes in protein expression, mutations and deletions of natural
inhibitors [9], which provide interesting target sites for the development of anti-cancer drugs.
It is interesting that natural products and metabolites continue to be important sources for new
pharmaceuticals and new lead structures in areas like oncology, infectious and metabolic
diseases. The elucidation of the metabolic pathways and molecular details of healthy and
diseased cells and their interactions during growth and development are thereby of major
interest. The highly evolved defense mechanisms utilized by microbial, plant and animal cells
can be of very valuable in defending human cells against microbial pathogens or cancer cells
with similar survival strategies as the natural attacking cells. The physicochemical properties
of drug com-pounds and their links to human oral absorption of the drug molecules are
important and the distribution of physicochemical properties like molecular weight, number
of rotatable bonds, H-bond acceptors, H-bond donors and topological polar surface area, has
been investigated for a dataset of 3566 compounds from the three pharmaceutical companies
AstraZeneca, GlaxoSmithKline and Pfizer [10].It is also interesting to know which chemical
transformations have been applied to medicinal chemistry problems within the pharmaceutical
industry, where reaction classes at the large scale [11] and at the small scale [10] correspond
well. For the small-scale synthesis of drug candidates a dataset of 7315 reactions from the
same companies has been analysed and among the broad range of synthetic methodologies
used a small number of favourite reactions has been found [10]. The remainder of the
reactions used has been found to cover a wide range of different types in order to achieve the
goal of discovering new drug candidate molecules. Heteroatom alkylation and acylation
reactions have been found to account for almost half of the reported reactions. The analysis
has also shown that protecting group manipulations account for ∼20% of reactions, whereas
C-C bond forming and heterocycle-forming reactions each account for ∼10% of reactions.
On the bioproduction part of the pharmaceutical industry, where the increased understanding
of the enzymatic reaction steps constituting pathways has provided versatile and modular
tools to apply retrosynthetic analysis and synthesize targets from renewable biological resour-
ces completely by enzymatic reaction steps [12]. Enzymatic reactions have also become one
of the most important tools for sustainable (green) chemistry, because it can catalyse other-
wise difficult reactions, reduce waste and hazards, improve yields, reduce costs by elimina-
ting multiple steps involved in complex syntheses [13]. Safety, health and environmental
improvements can be the major driving forces for the rapid growth of biocatalytic applica-
tions in various industries [14]. It is therefore of much interest to explore the boundaries and
interfaces between chemical and enzymatic reactions in order to create new bridges and over-
come bottlenecks and challenges [15]. This endeavour has also been taken up from the bio-
technological sciences, where industrial (white) biotechnology focuses on applications of bio-
technology to chemical manufacturing [16]. This cross-fertilization between biotechnology
and chemistry is quite old indeed and has led to a significant number of important industrial
biotransformations [17-35].
The recent discoveries of oncometabolites has shown the importance of linking diseases with
changes in metabolic pathways and their in-depth analysis of the molecular structure and chi-
rality [36-37]. It is of key importance that metabolites for these metabolomics studies, for
studying enzyme functions and biochemical reactions, pathways and their regulation are
synthesized. As the challenges of synthesizing densely and differentially functionalized small
molecules by classical chemical methods are significant, biocatalytic methods have been
useful [38-39].
References:
[1] R.Wohlgemuth, Molecular and Engineering Perspectives of the Biocatalysis Interface
to Chemical Synthesis, Chem.Biochem.Eng.Quarterly 25,125-134 (2011).
[2] M.Kanehisa, M.Araki, S.Goto, M.Hattori, M.Hirakawa, M.Itoh, T.Katayama,
S.Kawashima, S.Okuda, T.Tokimatsu, Y.Yamanishi, KEGG for linking genomes to
life and the environment, Nucleic Acids Research, Vol. 36, Database issue, D480–
D484, (2008).
[3] M.Kanehisa, S.Goto, M.Furumichi, M.Tanabe, M.Hirakawa, KEGG for representation
and analysis of molecular networks involving diseases and drugs, Nucleic Acids
Research, Vol. 38, Database issue D355–D360, (2010).
[4] Y.Moriya, D.Shigemizu, M.Hattori, T.Tokimatsu, M.Kotera, S.Goto, M.Kanehisa,
PathPred: an enzyme-catalyzed metabolic pathway prediction server, Nucleic Acids
Research, Vol. 38, Web Server issue, W138-W143, (2010).
[5] G.M.Cragg, P.G.Grothaus, D.J.Newman, Impact of Natural Products on Developing
New Anti-Cancer Agents, Chem.Rev. 109, 3012-3043 (2009).
[6] C.T.Walsh, M.A.Fishbach, Natural Products Version 2.0: Connecting Genes to
Molecules, J.Am.Chem.Soc. 132, 2469-2493 (2010).
[7] A.Furra, Y.Z.Shu, M.Zhu, R.L.Hanson, V.Roongta, W.G.Humphries, Discovering
Drugs Through Biological Transformation: Role of Pharmacologically Active
Metabolites in Drug Discovery, J.Med. Chem. 47, 4339-4351 (2004).
[8] A.L.Demain, J.L.Adrio, Strain improvement for production of pharmaceuticals and
other microbial metabolites by fermentation, Prog. Drug Res.65, 253-289 (2008).
[9] L.Meijer, Le cycle de division cellulaire et sa regulation, Bull. Cancer 4, 41-53 (2006).
[10] S.D.Roughley, A.M.Jordan, The Medicinal Chemist’s Toolbox: An Analysis of Reac-
tions Used in the Pursuit of Drug Candidates, J.Med. Chem. 54, 3451-3479 (2011).
[11] J.S.Carey,D.Laffan, C.Thomson, M.T.Williams, Analysis of the reactions used for the
preparation of drug candidate molecules, Org.Biomol. Chem. 2337–2347 (2006).
[12] N.Horinouchi, J.Ogawa, T.Kawano, T.Sakai, K.Saito, S.Matsumoto, M.Sasaki, Y.
Makami, S.Shimizu, Biochemical retrosynthesis of 2′-deoxyribonucleosides from glu-
cose, acetaldehyde, and a nucleobase, Appl.Microbiol.Biotechnol. 71, 615-621 (2006).
[13] R.Wohlgemuth,in: Biocatalysis for Green Chemistry and Process Development, J.Tao,
R.Kazlauskas (Eds.), 2011, 277-298, John Wiley & Sons, Inc., Hoboken, New Jersey.
[14] R.Wohlgemuth, Modular and scalable biocatalytic tools for practical safety, health and
environmental improvements in the production of speciality chemicals, Biocat.
Biotransform. 25, 178-185 (2007).
[15] R.Wohlgemuth. Interfacing biocatalysis and organic synthesis J. Chem.Technol.
Biotechnol. 82, 1055–1062 (2007).
[16] R.Wohlgemuth, The locks and keys to industrial biotechnology, New Biotechnol. 25,
204-213 (2009).
[17] O.Ghisalba, H.P.Meyer, R.Wohlgemuth, Industrial Biotransformations, in: Encyclo-
pedia in Industrial Biotechnology. M.C.Flickinger (Ed.), (2010), John Wiley & Sons.
[18] M.C.R.Franssen,M.Kircher,R.Wohlgemuth, Industrial Biotechnology in the Chemical
and Pharmaceutical Industries, in: Industrial Biotechnology, Sustainable Growth and
Economic Success (2010), W.Soetaert, E.J.Vandamme, (Eds.) Wiley-VCH,Weinheim.
[19] R.Wohlgemuth, Asymmetric biocatalysis with microbial enzymes and cells, Curr.
Opin. Microbiology 13, 283-292 (2010).
[20] R.Wohlgemuth, Biocatalytic Asymmetric Oxidations with Oxygen, in: W.D.Fessner,
T.Anthonsen (Eds.), Modern Biocatalysis (2009), Wiley-VCH, Weinheim.
[21] R.Wohlgemuth, J.M.Woodley, Asymmetric Baeyer-Villiger Reactions using Whole-
Cell Biocatalysts, in:H.U.Blaser, H.J.Federsel (Eds): Large-Scale Asymmetric
 Catalysis, Wiley-VCH, Weinheim, (2010).
[22] V.Alphand, R.Wohlgemuth, Applications of Baeyer-Villiger Monooxygenases in
Organic Synthesis, Curr.Org.Chem. 14, 1928-1965 (2010).
[23] R.Wohlgemuth, Biocatalysis - key to sustainable industrial chemistry, Curr. Opin.
Biotechnol., 21, 713-724 (2010).
[24] Richter N, Neuman M, Liese A, Wohlgemuth R, Eggert T, Hummel W.
Characterisation of a recombinant NADP-dependent glycerol dehydrogenase from
Gluconobacter oxydans and its application in the production of L-glyceraldehyde,
ChemBioChem 10, 1888-1896 (2009).
[25] N.Richter, M.Neumann, A.Liese, R.Wohlgemuth, A.Weckbecker, T.Eggert, W.
Hummel, Characterization of a whole-cell catalyst co-expressing glycerol dehydro-
genase and glucose dehydrogenase and its application in the synthesis of L-glyceral-
dehyde, Biotech.Bioeng. 106, 541-552 (2010).
[26] U.Schell, R.Wohlgemuth, J.M.Ward, Synthesis of pyridoxamine 5’-phosphate using
an MBA:pyruvate transaminase as biocatalyst, J.Mol.Catal. B:Enz. 59, 279-285(2009).
[27] J.Ward, R.Wohlgemuth, High-Yield Biocatalytic Amination Reactions in Organic
Synthesis, Curr.Org.Chem. 14, 1914-1927 (2010).
[28] R.Wohlgemuth, C2-Ketol elongation by transketolase-catalyzed asymmetric synthesis,
J.Mol.Catal. B: Enz. 61, 23-29 (2009).
[29] J.Shaeri, I.Wright, E.B.Rathbone, R.Wohlgemuth, J.M.Woodley, Characterization of
enzymatic D-xylulose 5-phosphate synthesis, Biotech.Bioeng. 101,761-767 (2008).
[30] R.Wohlgemuth, M.E.B.Smith, P.A.Dalby, J.M.Woodley, Transketolases, in: Encyclo-
pedia of Industrial Biotechnology, M.C.Flickinger(Ed.), Wiley, Hoboken, NJ, 2010.
[31] J.Shaeri, R.Wohlgemuth, J.M.Woodley, Semiquantitative Process Screening for the
Biocatalytic Synthesis of d-Xylulose-5-phosphate, Org.Proc.Res.Dev. 10, 605-610
(2006).
[32] R.Wohlgemuth, Tools and ingredients for the biocatalytic synthesis of carbohydrates
and Glycoconjugates, Biocat. Biotransform. 26, 42-48 (2008).
[33] R.Wohlgemuth, Large-Scale Applications of Hydrolases in Biocatalytic Asymmetric
Synthesis, in: H.U.Blaser, H.J.Federsel (Eds): Large-Scale Asymmetric Catalysis,
Wiley-VCH, Weinheim (2010).
[34] R.Wohlgemuth, Tools for Selective Enzyme Reaction Steps in the Synthesis of
Laboratory Chemicals, Eng.Life Sci. 6, 577-583 (2006).
[35] R.Wohlgemuth, Product Recovery,in: Comprehensive Biotechnology, 2nd ed., 2011,
edited by M.Moo-Young, M.Butler, C.Webb, A.Moreira, B.Grodzinski, Z.F.Cui,
S.Agathos, Elsevier, Amsterdam, Netherlands.
[36] L.Dang, D.W.White, S.Gross, B.D.Bennett, M.A.Bittinger, E.M.Driggers, V.R.Fantin,
H.G.Jang, S.Jin, M.C.Keenan, K.M.Marks, R.M.Prins, P.S.Ward, K.E.Yen, L.M.Liau,
J.D.Rabinowitz, L.C.Cantley, C.B.Thompson, M.G.VanderHeiden, S.M.Su, Cancer-
associated IDH1 mutations produce 2-hydroxyglutarate, Nature 462, 739 (2009).
[37] P.S.Ward, J.Patel, D.R.Wise, O.Abdel-Wahab, B.D.Bennett, H.A.Coller, J.R.Cross,
V.R.Fantin, C.V.Hedvat, A.E.Perl, J.D.Rabinowitz, M.Carroll, S.M.Su, K.A.Sharp,
R.L. Levine, C.B.Thompson, The Common Feature of Leukemia-Associated IDH1
and IDH2 Mutations Is a Neomorphic Enzyme Activity Converting α-Ketoglutarate to
2-Hydroxyglutarate, Cancer Cell 17, 225-234 (2010).
[38] R.Wohlgemuth, Tools and ingredients for the biocatalytic synthesis of metabolites,
Biotechnol. J. 9, 1253-1255 (2009).
[39] P.Jani,J.Emmert, R.Wohlgemuth, Process analysis of macrotetrolide biosynthesis
during fermentation by means of direct infusion LC-MS, Biotechnology Journal 3,
202-208 (2008).