LinChemIn: Route ArithmeticOperations on Digital Synthetic Routes

Computational tools are revolutionizing our understanding and prediction of chemical reactivity by combining traditional data analysis techniques with new predictive models. These tools extract additional value from the reaction data corpus, but to effectively convert this value into actionable knowledge, domain specialists need to interact easily with the computer-generated output. In this application note, we demonstrate the capabilities of the open-source Python toolkit LinChemIn, which simplifies the manipulation of reaction networks and provides advanced functionality for working with synthetic routes. LinChemIn ensures chemical consistency when merging, editing, mining, and analyzing reaction networks. Its flexible input interface can process routes from various sources, including predictive models and expert input. The toolkit also efficiently extracts individual routes from the combined synthetic tree, identifying alternative paths and reaction combinations. By reducing the operational barrier to accessing and analyzing synthetic routes from multiple sources, LinChemIn facilitates a constructive interplay between artificial intelligence and human expertise

Protein-DNA interactions of potentially improved RVD loops for targeting guanine.

<p>(<b>A</b>) Wild type (N12-N13) alone (grey) and superposed to: (<b>B</b>) N12-N13K mutant (yellow), (<b>C</b>) N13K-G14* mutant (green) and (<b>D</b>) N13*-G14K mutant (magenta).</p

Simulation details for each system.

<p>Simulation details for each system.</p

TAL topology and RVD-to-DNA code.

<p>(<b>A</b>) Sequence of a TAL protein: type III secretion system tag (T3SS-tag, violet), tandem-repeat domain (blue), nuclear localization signal (NLS, yellow) and acidic transcriptional activation domain (AD, green). The amino acid sequence of a single repeat is shown, highlighting the RVD region (X12 and X13). The secondary structure is reported underneath; the kink induced by P27 is represented as a break in the α2 rod. (<b>B</b>) Natural occurrence of the known RVDs is reported together with the targeted DNA base to highlight RVD selectivity <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080261#pone.0080261-Moscou1" target="_blank">[4]</a>. While some RVDs target only a single base (<i>e.g.</i> HD and ND), others have shared affinities (<i>e.g.</i> NN and N*). (<b>C</b>) Representative structure of one repeat as extracted from the 3V6T structure; relevant molecular information is highlighted.</p

Protein-DNA binding energies for modified targets of repeat 7 (N*) of the PthXo1 system (TAL[22.5]/P1).

<p>The base pairs corresponding to each category are: wild type (CG), mutated (TA) and 5-methylcytosine (mCG). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080261#pone.0080261.s013" target="_blank">Methods S1</a> for details.</p

Schematic representation of the TAL-DNA interface.

<p>(<b>A</b>) Cartoon representation of one single repeat interacting with DNA. The <i>oxyanion clip</i> (G14, K16 and Q17) interacts with the phosphate group of the <i>(i-1)^th</i> base, thus fixing the position of the X13 side-chain with respect to the <i>i^th</i> base and freezing its structural fluctuation. Dashed circles indicate the interaction radii of different X13 residues, sorted by side-chain size: the inner circle corresponds to G13/*13, while the others are represented by the outer circle. Only loci α, β and γ are sampled by the side-chains of X13, resulting in incomplete molecular differentiation. (<b>B</b>) Pharmacophore-like model for the nucleobases discussed in the text (left). Dots represent sites with variable properties across nucleobases; colours are used to highlight the characteristics of the substituents: green for pyridine-like (H-bond acceptor) nitrogen atoms, blue for pyrrole-like and amine (H-bond donor) nitrogen atoms, grey for methyl groups, and red for carbonyl oxygen atoms. On the right, relative molecular electrostatic potential (MEP) maps for the corresponding nucleobases are reported. Calculations were performed at the QM level on methyl-capped purines (N9) and pyrimidines (N1) (red  =  −5.0 k_BT/e, blue  =  5.0 k_BT/e, isovalue 4.0 E⁻⁴).</p

Structural and energetic features of TAL-DNA interaction.

<p>(<b>A</b>) Mean residue fluctuation (RMSD) computed for the DNA-bound and <i>apo</i> states of the 11.5-repeats TAL system (TAL[11.5]/P1 and TAL[11.5]/P1-apo); averages are performed over all the repeats; bars represent standard deviations. The same trend is observed for all simulated systems (<i>cf. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080261#pone.0080261.s005" target="_blank">Figure S5</a>). (<b>B</b>) Contribution to the total DNA-binding energy from different sections of TAL subdivided by type and calculated on the DNA-bound 22.5-repeat TAL system (TAL[22.5]/P1) using MM/GBSA (Number of residues contributing to each type: G13 = 6, N13 = 2, I13 = 7, D13 = 5, G14/K16/Q17 = 20, others = 600, N-terminus = 97). Repeats containing a deletion at position X13 have been excluded from the statistics. (<b>C</b>) Per repeat mean energy contribution to the total DNA-binding energy; averages are performed over all the repeats of the DNA-bound 22.5-repeat TAL system (TAL[22.5]/P1). Repeats containing a deletion at X13 position have been excluded from the statistics. The complete binding energy profile is reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080261#pone.0080261.s009" target="_blank">Figure S9</a>.</p

TAL repeats architecture.

<p>(<b>A</b>) Top view of bound TAL along the DNA axis showing the N-terminus (structure from 3UGM). (<b>B</b>) Side view of bound TAL displayed from the N-terminus (bottom) to the C-terminus (top) (structure from 3UGM). (<b>C</b>) TAL without DNA and the RVDs explicitly depicted (laying on the inner-side of the super-helix). The orange line represents the DNA axis. The protein is orientated from N-terminus (bottom) to C-terminus (top). A larger pitch compared to the bound structure is clearly observable (structure from 3V6P). Protein: grey; DNA: orange.</p

Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase

Type II topoisomerase (topoII) is a metalloenzyme targeted by clinical antibiotics and anticancer agents. Here, we integrate existing structural data with molecular simulation and propose a model for the yet uncharacterized structure of the reactant state of topoII. This model describes a canonical two-metal-ion mechanism and suggests how the metals could rearrange at the catalytic pocket during enzymatic turnover, explaining also experimental evidence for topoII inhibition. These results call for further experimental validation

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

The stereospecific oxidative decomposition of urate into allantoin is the core of purine catabolism in many organisms. The spontaneous decomposition of upstream intermediates and the nonenzymatic racemization of allantoin lead to an accumulation of (<i>R</i>)-allantoin, because the enzymes converting allantoin into allantoate are specific for the (<i>S</i>) isomer. The enzyme allantoin racemase catalyzes the reversible conversion between the two allantoin enantiomers, thus ensuring the overall efficiency of the catabolic pathway and preventing allantoin accumulation. On the basis of recent crystallographic and biochemical evidence, allantoin racemase has been assigned to the family of cofactor-independent racemases, together with other amino acid racemases. A detailed computational investigation of allantoin racemase has been carried out to complement the available experimental data and to provide atomistic insight into the enzymatic action. Allantoin, the natural substrate of the enzyme, has been investigated at the quantum mechanical level, in order to rationalize its conformational and tautomeric equilibria, playing a key role in protein–ligand recognition and in the following catalytic steps. The reaction mechanism of the enzyme has been elucidated through quantum mechanics/molecular mechanics (QM/MM) calculations. The potential energy surface investigation, carried out at the QM/MM level, revealed a stepwise reaction mechanism. A pair of cysteine residues promotes the stereoinversion of a carbon atom of the ligand without the assistance of cofactors. Electrostatic fingerprint calculations are used to discuss the role of the active site residues in lowering the p<i>K</i>_a of the substrate. The planar unprotonated intermediate is compared with the enolic allantoin tautomer observed in the active site of the crystallized enzyme. Finally, the enzymatic catalysis featured by allantoin racemase (AllR) is compared with that of other enzymes belonging to the same family