Building block (chemistry)

Building block is a term in chemistry which is used to describe a virtual molecular fragment or a real chemical compound the molecules of which possess reactive functional groups.[1] Building blocks are used for bottom-up modular assembly of molecular architectures: nano-particles,[2][3] metal-organic frameworks,[4] organic molecular constructs, supra-molecular complexes.[5] Using building blocks ensures strict control of what a final compound or a (supra)molecular construct will be.[6]

Construction of complex molecular architectures is easily possible using simple building blocks

Building blocks for medicinal chemistry

In medicinal chemistry, the term defines either imaginable, virtual molecular fragments or chemical reagents from which drugs or drug candidates might be constructed or synthetically prepared.[7]

Virtual building blocks

Virtual building blocks are used in drug discovery for drug design and virtual screening, addressing the desire to have controllable molecular morphologies that interact with biological targets.[8] Of special interest for this purpose are the building blocks common to known biologically active compounds, in particular, known drugs,[9] or natural products.[10] There are algorithms for de novo design of molecular architectures by assembly of drug-derived virtual building blocks.[11]

Chemical reagents as building blocks

Organic functionalized molecules (reagents), carefully selected for the use in modular synthesis of novel drug candidates, in particular, by combinatorial chemistry, or in order to realize the ideas of virtual screening and drug design are also called building blocks.[12][13] To be practically useful for the modular drug or drug candidate assembly, the building blocks should be either mono-functionalised or possessing selectively chemically addressable functional groups, for example, orthogonally protected.[14] Selection criteria applied to organic functionalized molecules to be included in the building block collections for medicinal chemistry are usually based on empirical rules aimed at drug-like properties of the final drug candidates.[15][16] Bioisosteric replacements of the molecular fragments in drug candidates could be made using analogous building blocks.[17]

Building blocks and chemical industry

The building block approach to drug discovery changed the landscape of chemical industry which supports medicinal chemistry.[18] Major chemical suppliers for medicinal chemistry like Maybridge,[19] Chembridge,[20] Enamine[21] adjusted their business correspondingly.[22] By the end of the 1990th the use of building block collections prepared for fast and reliable construction of small-molecule sets of compounds (libraries) for biological screening became one of the major strategies for pharmaceutical industry involved in drug discovery; modular, usually one-step synthesis of compounds for biological screening from building blocks turned out to be in most cases faster and more reliable than multistep, even convergent syntheses of target compounds.[23]

There are online web-resources.

Examples

Typical examples of building block collections for medicinal chemistry are libraries of fluorine-containing building blocks.[24][25] Introduction of the fluorine into a molecule has been shown to be beneficial for its pharmacokinetic and pharmacodynamic properties, therefore, the fluorine-substituted building blocks in drug design increase the probability of finding drug leads.[26] Other examples include natural and unnatural amino acid libraries,[27] collections of conformationally constrained bifunctionalized compounds[28] and diversity-oriented building block collections.[29]

An anti-diabetic drug Saxagliptin and two building blocks BB1 and BB2 from which it could be synthesized

References
  1. H.H. Szmant (1989). Organic Building Blocks of the Chemical Industry. New York: John Wiley & Sons.
  2. L. Zang; Y. Che; J.S. Moore (2008). "One-Dimensional Self-Assembly of Planar π-Conjugated Molecules: Adaptable Building Blocks for Organic Nanodevices". Acc. Chem. Res. 41 (12): 1596–1608. doi:10.1021/ar800030w. PMID 18616298.
  3. J.M.J. Fréchet (2003). "Dendrimers and other dendritic macromolecules: From building blocks to functional assemblies in nanoscience and nanotechnology". J. Polym. Sci. A Polym. Chem. 41 (23): 3713–3725. Bibcode:2003JPoSA..41.3713F. doi:10.1002/pola.10952.
  4. O. K. Farha; C. D. Malliakas; M.G. Kanatzidis; J.T. Hupp (2010). "Control over Catenation in Metal−Organic Frameworks via Rational Design of the Organic Building Block". J. Am. Chem. Soc. 132 (3): 950–952. doi:10.1021/ja909519e. PMID 20039671.
  5. A.J. Cairns; J.A. Perman; L. Wojtas; V.Ch. Kravtsov; M.H. Alkordi; M.Eddaoudi; M.J. Zaworotko (2008). "Supermolecular Building Blocks (SBBs) and Crystal Design: 12-Connected Open Frameworks Based on a Molecular Cubohemioctahedron". J. Am. Chem. Soc. 130 (5): 1560–1561. doi:10.1021/ja078060t. PMID 18186639.
  6. R.S. Tu; M. Tirrell (2004). "Bottom-up design of biomimetic assemblies". Adv. Drug Deliv. Rev. 56 (11): 1537–1563. doi:10.1016/j.addr.2003.10.047. PMID 15350288.
  7. G. Schneider; M.-L. Lee; M. Stahl; P. Schneider (2000). "De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks". J. Comput.-Aided Mol. Des. 14 (5): 487–494. Bibcode:2000JCAMD..14..487S. doi:10.1023/A:1008184403558. PMID 10896320. S2CID 12380240.
  8. J. Wang; T. Hou (2010). "Drug and Drug Candidate Building Block Analysis". J. Chem. Inf. Model. 50 (1): 55–67. doi:10.1021/ci900398f. PMID 20020714. S2CID 24607262.
  9. A. Kluczyk; T. Popek; T. Kiyota; P. de Macedo; P. Stefanowicz; C. Lazar; Y. Konishi (2002). "Drug Evolution: p-Aminobenzoic Acid as a Building Block". Curr. Med. Chem. 9 (21): 1871–1892. doi:10.2174/0929867023368872. PMID 12369873.
  10. R.Breinbauer; I. R. Vetter; H.Waldmann (2002). "From Protein Domains to Drug Candidates—Natural Products as Guiding Principles in the Design and Synthesis of Compound Libraries". Angewandte Chemie International Edition. 41 (16): 2878–2890. doi:10.1002/1521-3773(20020816)41:16<2878::AID-ANIE2878>3.0.CO;2-B. PMID 12203413.
  11. G. Schneider; U. Fechner (2005). "Computer-based de novo design of drug-like molecules". Nat. Rev. Drug Discov. 4 (8): 649–663. doi:10.1038/nrd1799. PMID 16056391. S2CID 2549851.
  12. A. Linusson; J. Gottfries; F. Lindgren; S. Wold (2000). "Statistical Molecular Design of Building Blocks for Combinatorial Chemistry". J. Med. Chem. 43 (7): 1320–1328. doi:10.1021/jm991118x. PMID 10753469.
  13. G. Schneider; H.-J. Böhm (2002). "Virtual screening and fast automated docking methods". Drug Discovery Today. 7 (1): 64–70. doi:10.1016/S1359-6446(01)02091-8. PMID 11790605.
  14. A.N. Shivanyuk; D.M. Volochnyuk; I.V. Komarov; K.G. Nazarenko; D.S. Radchenko; A. Kostyuk; A.A. Tomachev (2007). "Conformationally restricted monoprotected diamines as scaffolds for design of biologically active compounds and peptidomimetics". Chimica Oggi/Chemistry Today. 25 (3): 12–13.
  15. I. Muegge (2003). "Selection criteria for drug-like compounds". Med. Res. Rev. 23 (3): 302–321. doi:10.1002/med.10041. PMID 12647312. S2CID 6236984.
  16. F.W. Goldberg; J.G. Kettle; T. Kogej; M.W.D. Perry; N.P. Tomkinson (2015). "Designing novel building blocks is an overlooked strategy to improve compound quality". Drug Discovery Today. 20 (1): 11–17. doi:10.1016/j.drudis.2014.09.023. PMID 25281855.
  17. A.V. Tymtsunik; V.A. Bilenko; S.O. Kokhan; O.O. Grygorenko; D.M. Volochnyuk; I.V. Komarov (2012). "1-Alkyl-5-((di)alkylamino) Tetrazoles: Building Blocks for Peptide Surrogates". J. Org. Chem. 77 (2): 1174–1180. doi:10.1021/jo2022235. PMID 22171684.
  18. "A MARKET GROWS, BLOCK BY BLOCK. Pharmaceutical building-block business attracts firms from ACROSS THE GLOBE". Chem. Eng. News. 89 (18): 16–18. 2011. doi:10.1021/cen-v089n018.p016.
  19. "Maybridge building blocks and reactive intermediates".
  20. "Building Blocks: Key Facts".
  21. "Building Blocks for Drug Discovery".
  22. Lowe, Derek (2010-03-18). "Good Suppliers – And The Other Guys".
  23. J. Drews (2000). "Drug Discovery: A Historical Perspective". Science. 287 (5460): 1960–1964. Bibcode:2000Sci...287.1960D. doi:10.1126/science.287.5460.1960. PMID 10720314.
  24. M Schlosser (2006). "CF3-Bearing Aromatic and Heterocyclic Building Blocks". Angewandte Chemie International Edition. 45 (33): 5432–5446. doi:10.1002/anie.200600449. PMID 16847982.
  25. V.S. Yarmolchuk; O.V. Shishkin; V.S. Starova; O.A. Zaporozhets; O. Kravchuk; S. Zozulya; I.V. Komarov; P.K. Mykhailiuk (2013). "Synthesis and Characterization of β-Trifluoromethyl-Substituted Pyrrolidines". Eur. J. Org. Chem. 2013 (15): 3086–3093. doi:10.1002/ejoc.201300121.
  26. I. Ojima (2009). Fluorine in Medicinal Chemistry and Chemical Biology. Blackwell Publishing. doi:10.1002/9781444312096.fmatter.
  27. I.V. Komarov; A.O. Grigorenko; A.V. Turov; V.P. Khilya (2004). "Conformationally rigid cyclic α-amino acids in the design of peptidomimetics, peptide models and biologically active compounds". Russian Chemical Reviews. 73 (8): 785–810. Bibcode:2004RuCRv..73..785K. doi:10.1070/rc2004v073n08abeh000912.
  28. O.O. Grygorenko; D.S. Radchenko; D.M. Volochnyuk; A.A. Tolmachev; I.V. Komarov (2011). "Bicyclic Conformationally Restricted Diamines". Chem. Rev. 111 (9): 5506–5568. doi:10.1021/cr100352k. PMID 21711015.
  29. S.L. Schreiber (2009). "Organic chemistry: Molecular diversity by design". Nature. 457 (7226): 153–154. Bibcode:2009Natur.457..153S. doi:10.1038/457153a. PMID 19129834.
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