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Wołos A, Roszak R, Żądło-Dobrowolska A, Beker W, Mikulak-Klucznik B, Spólnik G, Dygas M, Szymkuć S, Grzybowski BA. Synthetic connectivity, emergence, and
self-regeneration in the network of prebiotic
chemistry. Science 2020; 369:369/6511/eaaw1955. [DOI: 10.1126/science.aaw1955] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/28/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022]
Abstract
The challenge of prebiotic chemistry is to
trace the syntheses of life’s key building blocks
from a handful of primordial substrates. Here we
report a forward-synthesis algorithm that
generates a full network of prebiotic chemical
reactions accessible from these substrates under
generally accepted conditions. This network
contains both reported and previously unidentified
routes to biotic targets, as well as plausible
syntheses of abiotic molecules. It also exhibits
three forms of nontrivial chemical emergence, as
the molecules within the network can act as
catalysts of downstream reaction types; form
functional chemical systems, including
self-regenerating cycles; and produce surfactants
relevant to primitive forms of biological
compartmentalization. To support these claims,
computer-predicted, prebiotic syntheses of several
biotic molecules as well as a multistep,
self-regenerative cycle of iminodiacetic acid were
validated by experiment.
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Affiliation(s)
- Agnieszka Wołos
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Rafał Roszak
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | | | - Wiktor Beker
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Barbara Mikulak-Klucznik
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Grzegorz Spólnik
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
| | - Mirosław Dygas
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
| | - Sara Szymkuć
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Bartosz A. Grzybowski
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
- Center for Soft and Living Matter of
Korea’s Institute for Basic Science (IBS), Ulsan,
South Korea
- Department of Chemistry, Ulsan
National Institute of Science and Technology,
Ulsan, South Korea
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Pícha J, Vaněk V, Buděšínský M, Mládková J, Garrow TA, Jiráček J. The development of a new class of inhibitors for betaine-homocysteine S-methyltransferase. Eur J Med Chem 2013; 65:256-75. [DOI: 10.1016/j.ejmech.2013.04.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/19/2013] [Accepted: 04/20/2013] [Indexed: 01/12/2023]
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5
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Synthesis and modifications of phosphinic dipeptide analogues. Molecules 2012; 17:13530-68. [PMID: 23154272 PMCID: PMC6268094 DOI: 10.3390/molecules171113530] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/09/2012] [Accepted: 11/12/2012] [Indexed: 01/01/2023] Open
Abstract
Pseudopeptides containing the phosphinate moiety (-P(O)(OH)CH2-) have been studied extensively, mainly as transition state analogue inhibitors of metalloproteases. The key synthetic aspect of their chemistry is construction of phosphinic dipeptide derivatives bearing appropriate side-chain substituents. Typically, this synthesis involves a multistep preparation of two individual building blocks, which are combined in the final step. As this methodology does not allow simple variation of the side-chain structure, many efforts have been dedicated to the development of alternative approaches. Recent achievements in this field are summarized in this review. Improved methods for the formation of the phosphinic peptide backbone, including stereoselective and multicomponent reactions, are presented. Parallel modifications leading to the structurally diversified substituents are also described. Finally, selected examples of the biomedical applications of the title compounds are given.
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Poreba M, Gajda A, Picha J, Jiracek J, Marschner A, Klein CD, Salvesen GS, Drag M. S1 pocket fingerprints of human and bacterial methionine aminopeptidases determined using fluorogenic libraries of substrates and phosphorus based inhibitors. Biochimie 2012; 94:704-10. [DOI: 10.1016/j.biochi.2011.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
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Bollinger M, Manzenrieder F, Kolb R, Bochen A, Neubauer S, Marinelli L, Limongelli V, Novellino E, Moessmer G, Pell R, Lindner W, Fanous J, Hoffman A, Kessler H. Tailoring of integrin ligands: probing the charge capability of the metal ion-dependent adhesion site. J Med Chem 2012; 55:871-82. [PMID: 22185640 DOI: 10.1021/jm2013826] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intervention in integrin-mediated cell adhesion and integrin signaling pathways is an ongoing area of research in medicinal chemistry and drug development. One key element in integrin-ligand interaction is the coordination of the bivalent cation at the metal ion-dependent adhesion site (MIDAS) by a carboxylic acid function, a consistent feature of all integrin ligands. With the exception of the recently discovered hydroxamic acids, all bioisosteric attempts to replace the carboxylic acid of integrin ligands failed. We report that phosphinates as well as monomethyl phosphonates represent excellent isosters, when introduced into integrin antagonists for the platelet integrin αIIbβ3. The novel inhibitors exhibit in vitro and ex vivo activities in the low nanomolar range. Steric and charge requirements of the MIDAS region were unraveled, thus paving the way for an in silico prediction of ligand activity and in turn the rational design of the next generation of integrin antagonists.
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Affiliation(s)
- Markus Bollinger
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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Pícha J, Liboska R, Buděšínský M, Jiráček J, Pawełczak M, Mucha A. Unusual activity pattern of leucine aminopeptidase inhibitors based on phosphorus containing derivatives of methionine and norleucine. J Enzyme Inhib Med Chem 2010; 26:155-61. [PMID: 20578976 DOI: 10.3109/14756366.2010.482047] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ligands containing bulky aliphatic P1 residues exhibit a high affinity towards cytosolic leucine aminopeptidase, a bizinc protease of biomedical significance. According to this specificity, a series of phosphonic and phosphinic compounds have been put forward as novel putative inhibitors of the enzyme. These phosphonic and phosphinic compounds were derivatives of methionine and norleucine as both single amino acids and dipeptides. The designed inhibitors were synthesised and tested towards the peptidase isolated from porcine kidneys using an improved separation procedure affording superior homogeneity. Unexpectedly, organophosphorus derivatives of methionine and norleucine exhibited moderate activity with K(i) values in the micromolar range.
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Affiliation(s)
- Jan Pícha
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, V.V.I., Flemingovo Nám., Praha, Czech Republic
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Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau DP, Almo SC, Raushel FM. Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase . Biochemistry 2010; 49:611-22. [PMID: 20000809 DOI: 10.1021/bi901935y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human renal dipeptidase, an enzyme associated with glutathione metabolism and the hydrolysis of beta-lactams, is similar in sequence to a cluster of approximately 400 microbial proteins currently annotated as nonspecific dipeptidases within the amidohydrolase superfamily. The closest homologue to the human renal dipeptidase from a fully sequenced microbe is Sco3058 from Streptomyces coelicolor. Dipeptide substrates of Sco3058 were identified by screening a comprehensive series of l-Xaa-l-Xaa, l-Xaa-d-Xaa, and d-Xaa-l-Xaa dipeptide libraries. The substrate specificity profile shows that Sco3058 hydrolyzes a broad range of dipeptides with a marked preference for an l-amino acid at the N-terminus and a d-amino acid at the C-terminus. The best substrate identified was l-Arg-d-Asp (k(cat)/K(m) = 7.6 x 10(5) M(-1) s(-1)). The three-dimensional structure of Sco3058 was determined in the absence and presence of the inhibitors citrate and a phosphinate mimic of l-Ala-d-Asp. The enzyme folds as a (beta/alpha)(8) barrel, and two zinc ions are bound in the active site. Site-directed mutagenesis was used to probe the importance of specific residues that have direct interactions with the substrate analogues in the active site (Asp-22, His-150, Arg-223, and Asp-320). The solvent viscosity and kinetic effects of D(2)O indicate that substrate binding is relatively sticky and that proton transfers do not occurr during the rate-limiting step. A bell-shaped pH-rate profile for k(cat) and k(cat)/K(m) indicated that one group needs to be deprotonated and a second group must be protonated for optimal turnover. Computational docking of high-energy intermediate forms of l/d-Ala-l/d-Ala to the three-dimensional structure of Sco3058 identified the structural determinants for the stereochemical preferences for substrate binding and turnover.
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Affiliation(s)
- Jennifer A Cummings
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77843, USA
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Pícha J, Buděšínský M, Fiedler P, Sanda M, Jiráček J. Synthesis of α-carboxyphosphinopeptides derived from norleucine. Amino Acids 2010; 39:1265-80. [PMID: 20349321 DOI: 10.1007/s00726-010-0561-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 03/09/2010] [Indexed: 11/25/2022]
Abstract
In the present study, we describe in detail the synthesis of a relatively rare class of phosphorus compounds, α-carboxyphosphinopeptides. We prepared several norleucine-derived α-carboxyphosphinic pseudopeptides of the general formula Nle-Ψ[PO(OH)]-Gly. These compounds could have important applications as transition state-mimicking inhibitors for methionine or leucine aminopeptidases or other enzymes. For the preparation of the key α-carboxyphosphinate protected precursors, we investigated, compared and improved two different synthetic methods described in literature: the Arbuzov reaction of a silylated N-protected phosphinic acid with a bromoacetate ester and the nucleophilic addition of a mixed O-methyl S-phenyl N-protected phosphonic acid or a methyl N-protected phosphonochloridate with tert-butyl lithioacetate. We also prepared two N-Fmoc protected synthons, Fmoc-Nle-Ψ[PO(OH)]-Gly-COOH and Fmoc-Nle-Ψ[PO(OAd)]-Gly-COOH, and demonstrated that these precursors are suitable building blocks for the solid-phase synthesis of α-carboxyphosphinopeptides.
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Affiliation(s)
- Jan Pícha
- Institute of Organic Chemistry and Biochemistry, v. v. i., Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
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