Jóhannes Reynisson

Characteristics of known drug space. Natural products, their derivatives and synthetic drugs.

Known drug space (KDS) was analysed for the occurrence of natural products and their derivatives. A database of 1000 marketed drugs was compiled. It was found that 10% of the drugs on the market are unaltered natural products, 29% are their derivatives (semi-synthetics) and the rest (61%) have a synthetic origin. Of the natural products, and their derivatives, polycyclic drugs were the most abundant at 21% followed by simple drugs (16%) and steroids (15%). In regard to the molecular descriptors the natural products had larger statistical means and standard deviations than their synthetic counterparts. It was found that KDS occupies a larger volume in chemical space with respect to drug-like chemicals, i.e., KDS fully encompasses drug-like chemical space with the parameters of molecular weight≤800 g mol(-1), log P≤6.5, hydrogen bond acceptors≤15, hydrogen bond donors≤7, polar surface area≤180 Å2, and rotatable bonds≤17. Only 13% of the drugs analysed are outside one or more of these parameters. The definition of KDS gives drug designers a larger volume to work in compared to drug-like chemical space. However, the bulk of known drugs are found within the volume of drug-like chemical space.

DFT calculations on the electrophilic reaction with water of the guanine and adenine radical cations. A model for the situation in DNAElectronic Supplementary Information available. See http://www.rsc.org/suppdata/cp/b1/b109204a/

Using density functional theory, the H2O (modeled by OH−) addition on the C8-site of the guanine and adenine radical cations (Gua˙+/Ade˙+) is calculated to be exothermic by −75.3 and −77.7 kcal mol−1, respectively. In contrast, in the absence of the N1 proton on Gua˙+, i.e., in the case of the neutral radical (Gua(–H)˙) the H2O addition is +29.4 kcal mol−1endothermic. Similarly, in the case of the neutral adenine radical (Ade(–H)˙), the N6-deprotonated radical cation, the H2O addition is endothermic by +43.7 kcal mol−1. Related to these observations is the fact that with the radical cations, Gua˙+and Ade˙+, the positive charge density on the C8-carbon is higher than with the deprotonated forms. This means that nucleophilic attack is likely to have a lower activation energy in the case of the former than the latter. The protonated radical, Gua˙+, simulates the situation in double-stranded (ds) DNA where the transfer of the N1 proton to solvent molecules is inhibited due to its base pairing with cytosine. In contrast, in single-stranded DNA and in RNA, Gua˙+ is expected to quickly lose its N1 proton to the water phase. In comparison, with Ade˙+ in ds DNA the exocyclic N6-atom is in contact with water molecules in the major groove of the DNA double helix and thus should be able to rapidly lose a proton to a water molecule, even when it is paired with thymine. This concept provides an explanation for the experimental observation of 7,8-dihydro-8-oxoguanine (8-OGua) formation only in ds DNA and negligible formation of 7,8-dihydro-8-oxoadenine (8-OAde) in any other form of DNA.

Half-Sandwich Ruthenium(II) Biotin Conjugates as Biological Vectors to Cancer Cells

Ruthenium(II)-arene complexes with biotin-containing ligands were prepared so that a novel drug delivery system based on tumor-specific vitamin-receptor mediated endocytosis could be developed. The complexes were characterized by spectroscopic methods and their in vitro anticancer activity in cancer cell lines with various levels of major biotin receptor (COLO205, HCT116 and SW620 cells) was tested in comparison with the ligands. In all cases, coordination of ruthenium resulted in significantly enhanced cytotoxicity. The affinity of Ru(II) -biotin complexes to avidin was investigated and was lower than that of unmodified biotin. Hill coefficients in the range 2.012-2.851 suggest strong positive cooperation between the complexes and avidin. To estimate the likelihood of binding to the biotin receptor/transporter, docking studies with avidin and streptavidin were conducted. These explain, to some extent, the in vitro anticancer activity results and support the conclusion that these novel half-sandwich ruthenium(II)-biotin conjugates may act as biological vectors to cancer cells, although no clear relationship between the cellular Ru content, the cytotoxicity, and the presence of the biotin moiety was observed.

Known drug space as a metric in exploring the boundaries of drug-like chemical space

In this work, marketed drug compounds (or known drug space) were used as a metric to test the principles of eliminating parent structures of the nitrenium ion (aryl-amine/nitro compounds) as well as sulphur and halogen containing molecules from screening compound collections. Molecules containing such moieties and/or atoms have biological and physiochemical properties, which possibly make them less attractive as leads in drug development. It was found that precursors to the nitrenium ion were relatively abundant in known drug space at 14%. Thus, their simple elimination from drug-like chemical space is not advisable. Interestingly, the mutagenic potential of the nitrenium ions is linked to their stability and quantum mechanical calculations can be used to estimate it. Furthermore, 24% of drugs investigated contained sulphur atoms and around 28% were halogenated. As some sulphur containing moieties were abundant whilst others were scarce, it was deduced that it would be more effective to eliminate specific molecular scaffolds rather than all sulphur containing molecules. In conclusion, it has been shown that by statistically analysing known drug space a better understanding of the boundaries of drug-like chemical space was established which can help medicinal chemists in finding rewarding regions of chemical space.

Synthesis and biological evaluation of novel tyrosyl-DNA phosphodiesterase 1 inhibitors with a benzopentathiepine moiety.

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a promising target for antitumor therapy based on Top1 poison-mediated DNA damage. Several novel benzopentathiepines were synthesized and tested as inhibitors of TDP1 using a new oligonucleotide-based fluorescence assay. The benzopentathiepines have IC₅₀ values in the range of 0.2-6.0 μM. According to the molecular modeling, the conformational flexibility of the dibutylamine group of the most effective inhibitor (3d) allows it to occupy an advantageous position for effective binding compared to its cyclic counterparts. The study of cytotoxicity of these compounds revealed that all compounds cause an apoptotic cell death in MCF-7 and Hep G2 cells. Therefore the new class of very effective inhibitors of TDP1 was elaborated.

The effect of PLC-γ2 inhibitors on the growth of human tumour cells.

The phosphoinositide specific-phospholipase C-γ (PLC-γ1 and 2) enzymes are plausible anticancer targets implicated in cell motility important to invasion and dissemination of tumour cells. A host of known PLC-γ2 inhibitors were tested against the NCI60 panel of human tumour cell lines as well as their commercially available structural derivatives. A class of thieno[2,3-b]pyridines showed excellent growth arrest with derivative 3 giving GI(50) = 58 nM for the melanoma MDA-MB-435 cell line. The PLC-γ2 is uniquely expressed in haematopoietic cells and the leukaemia tumour cell lines were growth restricted on average GI(50) = 275 nM by derivative 3 indicating a specific interaction with this isoform. Furthermore, a moderate growth inhibition was found for compound classes of indoles and 1H-pyrazoles. It is likely that the active compounds do not only inhibit the PLC-γ2 isoform but other PLCs as well due to their conserved binding site. The compounds tested were identified by applying the tools of chemoinformatics, which supports the use of in silico methods in drug design.

The effect of a thieno[2,3- b ]pyridine PLC-γ inhibitor on the proliferation, morphology, migration and cell cycle of breast cancer cells

3-Amino-N-(3-chlorophenyl)-5-oxo-5,6,7,8-tetrahydrothieno[2,3-b]quinoline-2-carboxamide (compound 1) is a putative phosphoinositide specific-phospholipase C-γ (PLC-γ) enzyme inhibitor. This enzyme is a plausible anticancer target linked to cell motility, important for the invasion and dissemination of tumour cells. In this work it is shown that IC50 values of compound 1 are in the low nanomolar range against a host of breast cancer cell lines as a consequence of anti-proliferative activity. These results correlate well with previously published results (Feng et al., Eur. Med. Chem., 54, 2012, 463–469) on tumour cell viability confirming the efficacy of compound 1. Flow cytometry experiments revealed that compound 1 arrests the cell cycle in the G2/M phases. Furthermore, the morphology and cell migration for the MDA-MB-231 breast cancer cell line are severely affected by administration of compound 1, which fits the hypothesis of PLC-γ inhibition. Finally, a detailed docking study against PLC reveals that the side chains of the amino acids His356, Glu341, Arg549 and Lys438 are involved in hydrogen bonding with ligand 1 as well as a lipophilic pocket is occupied by the phenyl moiety. The results presented in this study are particularly interesting because compound 1 affects triple-negative breast cancer cells, which are difficult to treat in the clinic and are in a dire need for an effective targeted therapy. We believe that compound 1 and its thieno[2,3-b]pyridine derivatives demonstrate that such a therapy can be developed.

The physicochemical properties of a new class of anticancer fungal polysaccharides: a comparative study.

The structural and physicochemical properties of polysaccharides isolated from fungi with anticancer properties were investigated. The majority of the polysaccharides considered, have the β-d-Glcp component mostly connected by 1→3 and 1→6 linkages in the backbones and the short branches, respectively. The established parameters of lead-like, drug-like and of known dug space (KDS) were used and the repeating units of the polysaccharides exhibit some overlap with these. It was found that a unique region of chemical space is occupied by the polysaccharides, with MW: 1.0 x 10(5) to 2.5 x 10(5) g mol(-1); LogP: -3.0 x 10(3) to -1.0 x 10(3); HD: 1.0 x 10(3) to 5.0 x 10(3); HA: 5.0 x 10(3) to 1.0 x 10(4); PSA: 5.0 x 10(4) to 1.0 x 10(5) and RB: 5.0 x 10(3) to 1.0 x 10(4). These findings can be exploited in antitumor drug discovery projects.

Size estimation of chemical space: how big is it?

Objectives  To estimate the size of organic chemical space and its sub‐regions, i.e. drug‐like chemical space and known drug space (KDS).

New inhibitors of tyrosyl-DNA phosphodiesterase I (Tdp 1) combining 7-hydroxycoumarin and monoterpenoid moieties.

A number of derivatives of 7-hydroxycoumarins containing aromatic or monoterpene substituents at hydroxy-group were synthesized based on a hit compound from a virtual screen. The ability of these compounds to inhibit tyrosyl-DNA phosphodiesterase I (Tdp 1), important target for anti-cancer therapy, was studied for the first time. It was found that the 7-hydroxycoumarin derivatives with monoterpene pinene moiety are effective inhibitors of Tdp 1 with the most active derivative (+)-25c with IC50 value of 0.675μM. This compound has low cytotoxicity (CC50>100μM) when tested against human cancer cells which is crucial for presupposed application in combination with clinically established anticancer drugs. The ability of the new compounds to enhance the cytotoxicity of camptothecin, an established topoisomerase 1 poison, was demonstrated.