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1.
Bioconjug Chem ; 34(1): 238-247, 2023 01 18.
Article in English | MEDLINE | ID: mdl-36516871

ABSTRACT

As a counterpart to antibody-drug conjugates (ADCs), aptamer-drug conjugates (ApDCs) have been considered a promising strategy for targeted therapy due to the various benefits of aptamers. However, an aptamer merely serves as a targeting ligand in ApDCs, whereas the antibody enables the unexpected therapeutic efficacy of ADCs through antibody-dependent cellular cytotoxicity (ADCC). In this study, we developed a tumor-specific aptamer with an effector function and used it to confirm the feasibility of more potent ApDCs. First, we designed a nucleolin (NCL)-binding G-quadruplex (GQ) library based on the ability of NCL to bind to telomeric sequences. We then identified a bifunctional GQ aptamer (BGA) inhibiting the catalytic activity of topoisomerase 1 (TOP1) by forming an irreversible cleavage complex. Our BGA specifically targeted NCL-positive MCF-7 cells, exhibiting antiproliferative activity, and this suggested that tumor-specific therapeutic aptamers can be developed by using a biased library to screen aptamer candidates for functional targets. Finally, we utilized DM1, which has a synergistic interaction with TOP1 inhibitors, as a conjugated drug. BGA-DM1 exerted an anticancer effect 20-fold stronger than free DM1 and even 10-fold stronger than AS1411 (NCL aptamer)-DM1, highlighting our approach to develop synergistic ApDCs. Therefore, we anticipate that our library might be utilized for the identification of aptamers with effector functions. Furthermore, by employing such aptamers and appropriate drugs, synergistic ApDCs can be developed for targeted cancer therapy in a manner distinct from how ADCs exhibit additional therapeutic efficacy.


Subject(s)
Aptamers, Nucleotide , DNA Topoisomerases, Type I , RNA-Binding Proteins , Humans , Aptamers, Nucleotide/pharmacology , Aptamers, Nucleotide/metabolism , MCF-7 Cells , Phosphoproteins/metabolism , RNA-Binding Proteins/drug effects , RNA-Binding Proteins/metabolism , DNA Topoisomerases, Type I/drug effects , DNA Topoisomerases, Type I/metabolism , Drug Synergism , Nucleolin
2.
Nat Commun ; 13(1): 842, 2022 02 11.
Article in English | MEDLINE | ID: mdl-35149673

ABSTRACT

In natural product discovery programs, the power of synthetic chemistry is often leveraged for the total synthesis and diversification of characterized metabolites. The synthesis of structures that are bioinformatically predicted to arise from uncharacterized biosynthetic gene clusters (BGCs) provides a means for synthetic chemistry to enter this process at an early stage. The recent identification of non-ribosomal peptides (NRPs) containing multiple ρ-aminobenzoic acids (PABAs) led us to search soil metagenomes for BGCs that polymerize PABA. Here, we use PABA-specific adenylation-domain sequences to guide the cloning of the lap BGC directly from soil. This BGC was predicted to encode a unique N-acylated PABA and thiazole containing structure. Chemical synthesis of this structure gave lapcin, a dual topoisomerase I/II inhibitor with nM to pM IC50s against diverse cancer cell lines. The discovery of lapcin highlights the power of coupling metagenomics, bioinformatics and total chemical synthesis to unlock the biosynthetic potential contained in even complex uncharacterized BGCs.


Subject(s)
Biological Products/pharmacology , DNA Topoisomerases, Type II/drug effects , DNA Topoisomerases, Type I/drug effects , Enzyme Inhibitors/pharmacology , Metagenome , Biological Products/chemistry , Biological Products/isolation & purification , Biosynthetic Pathways/genetics , Cell Line , Cell Survival/drug effects , Computational Biology , DNA Topoisomerases, Type I/metabolism , DNA Topoisomerases, Type II/metabolism , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/isolation & purification , Humans , Metagenome/genetics , Metagenomics , Multigene Family , Soil
3.
J Med Chem ; 64(24): 17572-17600, 2021 12 23.
Article in English | MEDLINE | ID: mdl-34879200

ABSTRACT

The discovery that certain indenoisoquinolines inhibit the religation reaction of DNA in the topoisomerase I-DNA-indenoisoquinoline ternary complex led to a structure-based drug design research program which resulted in three representatives that entered Phase I clinical trials in cancer patients at the National Cancer Institute. This has stimulated a great deal of interest in the design and execution of new synthetic pathways for indenoisoquinoline production. More recently, modulation of the substitution pattern and chemical nature of substituents on the indenoisoquinoline scaffold has resulted in a widening scope of additional biological targets, including RXR, PARP-1, MYC promoter G-quadruplex, topoisomerase II, estrogen receptor, VEGFR-2, HIF-1α, and tyrosyl DNA phosphodiesterases 1 and 2. Furthermore, convincing evidence has been advanced supporting the potential use of indenoisoquinolines for the treatment of diseases other than cancer. The rapidly expanding indenoisoquinoline knowledge base has provided a firm foundation for further advancements in indenoisoquinoline chemistry, pharmacology, and therapeutics.


Subject(s)
Antineoplastic Agents/pharmacology , DNA Topoisomerases, Type I/drug effects , Drug Design , Isoquinolines/chemistry , Isoquinolines/pharmacology , Drug Screening Assays, Antitumor , Humans , Isoquinolines/chemical synthesis
4.
Arch Toxicol ; 95(12): 3787-3802, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34635930

ABSTRACT

Nevadensin, an abundant polyphenol of basil, is reported to reduce alkenylbenzene DNA adduct formation. Furthermore, it has a wide spectrum of further pharmacological properties. The presented study focuses the impact of nevadensin on topoisomerases (TOPO) in vitro. Considering the DNA-intercalating properties of flavonoids, first, minor groove binding properties (IC50 = 31.63 µM), as well as DNA intercalation (IC50 = 296.91 µM) of nevadensin, was found. To determine potential in vitro effects on TOPO I and TOPO IIα, the relaxation and decatenation assay was performed in a concentration range of 1-500 µM nevadensin. A partial inhibition was detected for TOPO I at concentrations  ≥ 100 µM, whereas TOPO IIα activity is only inhibited at concentrations  ≥ 250 µM. To clarify the mode of action, the isolating in vivo complex of enzyme assay was carried out using human colon carcinoma HT29 cells. After 1 h of incubation, the amount of TOPO I linked to DNA was significantly increased by nevadensin (500 µM), why nevadensin was characterized as TOPO I poison. However, no effects on TOPO IIα were detected in the cellular test system. As a subsequent cellular response to TOPO I poisoning, a highly significant increase of DNA damage after 2 h and a decrease of cell viability after 48 h at the same concentration range were found. Furthermore, after 24 h of incubation a G2/M arrest was observed at concentrations ≥ 100 µM by flow cytometry. The analysis of cell death revealed that nevadensin induces the intrinsic apoptotic pathway via activation of caspase-9 and caspase-3. The results suggest that cell cycle disruption and apoptotic events play key roles in the cellular response to TOPO I poisoning caused by nevadensin in HT29 cells.


Subject(s)
Apoptosis/drug effects , DNA Damage/drug effects , DNA Topoisomerases, Type I/drug effects , Flavones/poisoning , Cell Cycle/drug effects , Colonic Neoplasms/enzymology , DNA Topoisomerases, Type II/drug effects , Dose-Response Relationship, Drug , Flavones/administration & dosage , HT29 Cells , Humans , Inhibitory Concentration 50 , Poly-ADP-Ribose Binding Proteins/drug effects , Time Factors
5.
Cell Rep ; 36(10): 109666, 2021 09 07.
Article in English | MEDLINE | ID: mdl-34496254

ABSTRACT

Although axonal damage induces rapid changes in gene expression in primary sensory neurons, it remains unclear how this process is initiated. The transcription factor ATF3, one of the earliest genes responding to nerve injury, regulates expression of downstream genes that enable axon regeneration. By exploiting ATF3 reporter systems, we identify topoisomerase inhibitors as ATF3 inducers, including camptothecin. Camptothecin increases ATF3 expression and promotes neurite outgrowth in sensory neurons in vitro and enhances axonal regeneration after sciatic nerve crush in vivo. Given the action of topoisomerases in producing DNA breaks, we determine that they do occur immediately after nerve damage at the ATF3 gene locus in injured sensory neurons and are further increased after camptothecin exposure. Formation of DNA breaks in injured sensory neurons and enhancement of it pharmacologically may contribute to the initiation of those transcriptional changes required for peripheral nerve regeneration.


Subject(s)
Activating Transcription Factor 3/metabolism , Axons/metabolism , DNA Breaks/drug effects , DNA Topoisomerases, Type I/metabolism , Peripheral Nerve Injuries/metabolism , Sensory Receptor Cells/metabolism , Animals , DNA Topoisomerases, Type I/drug effects , Gene Expression/physiology , Mice, Inbred C57BL , Nerve Regeneration/drug effects , Nerve Regeneration/physiology , Neuronal Outgrowth/physiology , Sciatic Nerve/metabolism
6.
Biomed Pharmacother ; 139: 111628, 2021 Jul.
Article in English | MEDLINE | ID: mdl-33940508

ABSTRACT

Pinus kesiya Royle ex Gordon (PK), widely found in Southeast Asia, has been traditionally used for the treatment of several illnesses. Our previous studies showed that PK was highly cytotoxicity against liver cancer cells. The detailed mechanism of anticancer action of 50% hydro-ethanolic extract of PK's twig was, therefore, investigated in hepatocellular carcinoma HepG2 cells. Cytotoxicity of PK was determined by using NR assay, followed by determination of the mode of cell death by flow cytometry. The apoptosis-inducing effect was determined based on caspases activity, mitochondria membrane potential change, and expression of proteins related to apoptosis by western blot. The biomolecular alteration in the PK-treated HepG2 cells was investigated by FTIR microspectroscopy. Inhibition of topoisomerase I enzyme was determined by using DNA relaxation assay. Results showed that PK displayed high selective cytotoxicity and induced apoptosis against HepG2. FTIR microspectroscopy indicated that PK altered major biomolecules in HepG2 different from melphalan (a positive control), indicating a different mechanism of anticancer action. PK induced apoptotic cell death through the intrinsic pathway by increasing caspases 9 and 3/7 activity, increasing Bax, and decreasing Bcl-2 expression leading to mitochondrial membrane potential changes. PK also inhibited Top I and PARP activity that triggered an intrinsic apoptotic pathway. The phytochemical test presented terpenoids (i.e., α-pinene confirmed by GC-MS), alkaloids, steroids, xanthone, reducing sugar, and saponin. α-Pinene exhibited low cytotoxicity against HepG2, therefore, several terpene derivatives may work synergistically for inducing apoptosis. Our data demonstrated that PK has the potential for further study with chemotherapeutic purposes.


Subject(s)
Antineoplastic Agents, Phytogenic/pharmacology , Apoptosis/drug effects , DNA Topoisomerases, Type I/drug effects , Pinus/chemistry , Plant Extracts/pharmacology , Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use , Signal Transduction/drug effects , Caspases/metabolism , DNA Topoisomerases, Type I/genetics , Hep G2 Cells , Humans , Membrane Potential, Mitochondrial/drug effects , Plant Extracts/chemistry , Spectroscopy, Fourier Transform Infrared
7.
Expert Opin Ther Pat ; 31(6): 473-508, 2021 Jun.
Article in English | MEDLINE | ID: mdl-33475439

ABSTRACT

INTRODUCTION: Topoisomerases are important targets for therapeutic improvement in the treatment of some diseases, including cancer. Inhibitors and poisons of topoisomerase I can limit the activity of this enzyme in its enzymatic cycle. This fact implies an anticancer effect of these drugs, since most cancer cells are characterized by both a higher activity of topoisomerase I and a higher replication rate compared to non-cancerous cells. Clinically approved inhibitors include camptothecin (CPT) and its derivatives. However, their limitations have encouraged different research groups to prepare new compounds, proof of which are the numerous research works and patents, some of them in the last five years. AREAS COVERED: This review covers patent literature on topoisomerase I inhibitors and their application published between 2016-present. EXPERT OPINION: The highest contribution toward patent development has been obtained from academics or small biotechnology companies. The most important fields of innovation include the preparation of prodrugs or inhibitors combined with other agents, as biocompatible polymers or antibodies. A promising development of topoisomerase I inhibitors is expected in the next years, directed to the treatment of diverse diseases, specifically toward different types of cancer and infectious diseases, among others.


Subject(s)
Antineoplastic Agents/pharmacology , Neoplasms/drug therapy , Topoisomerase I Inhibitors/pharmacology , Animals , DNA Topoisomerases, Type I/drug effects , DNA Topoisomerases, Type I/metabolism , Drug Design , Drug Development , Humans , Neoplasms/pathology , Patents as Topic
8.
PLoS Genet ; 16(10): e1009085, 2020 10.
Article in English | MEDLINE | ID: mdl-33125364

ABSTRACT

DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA. These enzymes are widely conserved, sharing >91% amino acid identity between the closely related species Escherichia coli and Salmonella enterica serovar Typhimurium. Why, then, do E. coli and Salmonella exhibit different DNA supercoiling when experiencing the same conditions? We now report that this surprising difference reflects disparate activation of their DNA gyrases by the polyamine spermidine and its precursor putrescine. In vitro, Salmonella DNA gyrase activity was sensitive to changes in putrescine concentration within the physiological range, whereas activity of the E. coli enzyme was not. In vivo, putrescine activated the Salmonella DNA gyrase and spermidine the E. coli enzyme. High extracellular Mg2+ decreased DNA supercoiling exclusively in Salmonella by reducing the putrescine concentration. Our results establish the basis for the differences in global DNA supercoiling between E. coli and Salmonella, define a signal transduction pathway regulating DNA supercoiling, and identify potential targets for antibacterial agents.


Subject(s)
DNA Gyrase/genetics , DNA Topoisomerases, Type I/genetics , DNA, Superhelical/genetics , Escherichia coli/genetics , Salmonella typhimurium/genetics , DNA Gyrase/drug effects , DNA Topoisomerases, Type I/drug effects , DNA, Superhelical/drug effects , Escherichia coli/drug effects , Escherichia coli/enzymology , Magnesium/pharmacology , Putrescine/pharmacology , Salmonella typhimurium/drug effects , Salmonella typhimurium/enzymology , Spermidine/biosynthesis
9.
Bioorg Chem ; 103: 104162, 2020 10.
Article in English | MEDLINE | ID: mdl-32890988

ABSTRACT

In this work, 2'-alkoxymethyl substituted klavuzon derivatives were prepared starting from 2-methyl-1-naphthoic acid in eight steps. Anticancer potencies of the synthesized compounds were evaluated by performing MTT cell viability test over cancerous and healthy pancreatic cell lines, along with CRM1 inhibitory properties in HeLa cells by immunostaining and Topo I inhibition properties by supercoiled DNA relaxation assay. Their cytotoxic activities were also presented in hepatocellular carcinoma cells (HuH-7) derived 3D spheroids. Among the tested klavuzon derivatives, isobutoxymethyl substituted klavuzon showed the highest selectivity of cytotoxic activity against pancreatic cancer cell line. They showed potent Topo I inhibition while their CRM1 inhibitory properties somehow diminished compared to 4'-alkylsubstituted klavuzons. The most cytotoxic 2'-methoxymethyl derivative inhibited the growth of the spheroids derived from HuH-7 cell lines and PI staining exhibited time and concentration dependent cell death in 3D spheroids.


Subject(s)
DNA Topoisomerases, Type I/drug effects , Karyopherins/drug effects , Naphthalenes/chemistry , Naphthalenes/therapeutic use , Neoplasms/drug therapy , Pyrans/chemistry , Pyrans/therapeutic use , Receptors, Cytoplasmic and Nuclear/drug effects , Humans , Naphthalenes/pharmacology , Pyrans/pharmacology , Structure-Activity Relationship , Exportin 1 Protein
10.
Bioorg Chem ; 94: 103409, 2020 01.
Article in English | MEDLINE | ID: mdl-31732194

ABSTRACT

In the quest to ameliorate the camptothecin (CPT) downsides, we expedite to search for stable non-CPT analogues among 11 motifs of pyrazoloquinazolines reported. E-pharmacophore drug design approach helped filtering out pyrazolo[1,5-c]quinazolines as Topoisomerase I (TopoI) 'interfacial' inhibitors. Three compounds, 3c, 3e, and 3l were shown to be potent non-intercalating inhibitors of TopoI specifically and showed cancer cell-specific cytotoxicity in lung, breast and colon cancer cell lines. The compounds induced cell cycle arrest at S-phase, mitochondrial cell death pathway and modulated oxidative stress in cancer cells. Furthermore, a preliminary study was conducted to explore the feasibility of these compounds to be developed as dual TopoI-HDAC1 (histone deacetylase 1) inhibitors (4a) to combat resistance. Compound 4a was found to possess dual inhibitory capabilities in-vitro. Cytotoxic potential of 4a was found to be significantly higher than parent compound in 2D as well as 3D cancer cell models. Probable binding modes of 4a with TopoI and HDAC1 active sites were examined by molecular modelling.


Subject(s)
DNA Topoisomerases, Type I/drug effects , Enzyme Inhibitors/therapeutic use , Histone Deacetylases/drug effects , Quinazolines/therapeutic use , Cell Line, Tumor , Enzyme Inhibitors/chemistry , Humans , Molecular Structure , Quinazolines/chemistry
11.
Biomed Res Int ; 2019: 2514524, 2019.
Article in English | MEDLINE | ID: mdl-31815127

ABSTRACT

A- and D-ring-modified luotonin-inspired heterocycles have been synthesized and were evaluated for their activity against the viability of four cancer cell lines in vitro, namely, MCF7, HCT116, JURKAT, and NCI-H460. The analysis of results indicated that two of the synthesized derivatives displayed good inhibition against the growth of the human colon cancer HCT116 cell line, with potencies lower than but in the same order of magnitude as camptothecin (CPT). These two luotonin analogues also showed an activity similar to that of the highly potent alkaloid CPT as inhibitors of topoisomerase I and also inhibited topoisomerase II. These results show that complete planarity is not a strict requirement for topoisomerase inhibition by luotonin-related compounds, paving the way to the design of analogues with improved solubility.


Subject(s)
Antineoplastic Agents/pharmacology , DNA Topoisomerases, Type II/drug effects , DNA Topoisomerases, Type I/drug effects , Poly-ADP-Ribose Binding Proteins/drug effects , Pyrroles/chemical synthesis , Pyrroles/pharmacology , Quinones/chemical synthesis , Quinones/pharmacology , Topoisomerase Inhibitors/pharmacology , Alkaloids/pharmacology , Camptothecin/analogs & derivatives , Camptothecin/chemical synthesis , Cell Line, Tumor/drug effects , Enzyme Inhibitors/pharmacology , Humans , Molecular Docking Simulation , Solubility , Structure-Activity Relationship
12.
Int J Mol Sci ; 20(21)2019 Oct 26.
Article in English | MEDLINE | ID: mdl-31717797

ABSTRACT

In the present study, a series of 4-acyloxy robustic acid derivatives were synthesized and characterized for evaluation of their anti-cancer activity. The structures of these derivatives were elucidated by mass spectra (MS) nuclear magnetic resonance spectra (NMR). The single-crystal X-ray diffraction structure of one of these compounds was obtained, for further validation of the target compound structures. The anticancer activities of the target products were evaluated against human leukemic cells HL-60, human non-small cell lung carcinoma cells A-549, human hepatic carcinoma cells SMMC-7721, human hepatocellular carcinoma cells HepG2, and human cervical carcinoma cells Hela. Three compounds among them exhibited potent in-vitro cytotoxicity and excellent DNA topoisomerase I inhibitory activity, even at 0.1 mM concentrations. The most noteworthy observation was the minor toxicity of two of these compounds to normal cells, with an activity similar to the positive control in cancerous cells. A Surflex-Dock docking study was performed to investigate the topoisomerase I activity of all compounds. Of all the other compounds, the most sensitive compound was selected for further investigation of its effect on apoptosis induction and cell cycle regulation in HL-60 cells. Our results suggest that the anticancer effects of these compounds can be attributed to their pharmacological effects on topoisomerase I, cell apoptosis, and cell cycle. These findings suggest that robustic acid derivatives could be used as potential antitumor drugs.


Subject(s)
Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/pharmacology , Isoflavones/chemistry , Pyranocoumarins/chemical synthesis , Pyranocoumarins/pharmacology , A549 Cells , Antineoplastic Agents/chemistry , Antineoplastic Agents/therapeutic use , Apoptosis/drug effects , Cell Cycle Checkpoints/drug effects , Cells, Cultured , DNA Topoisomerases, Type I/drug effects , Dalbergia/chemistry , Drug Screening Assays, Antitumor , HL-60 Cells , HeLa Cells , Hep G2 Cells , Humans , Inhibitory Concentration 50 , Isoflavones/pharmacology , Molecular Docking Simulation , Molecular Structure , Pyranocoumarins/chemistry , Pyranocoumarins/therapeutic use , Topoisomerase I Inhibitors/chemical synthesis , Topoisomerase I Inhibitors/chemistry , Topoisomerase I Inhibitors/pharmacology
13.
BMC Vet Res ; 15(1): 405, 2019 Nov 09.
Article in English | MEDLINE | ID: mdl-31706354

ABSTRACT

BACKGROUND: Canine leishmaniasis is a zoonotic disease caused by Leishmania infantum, being the dogs one of the major reservoirs of human visceral leishmaniasis. DNA topology is a consolidated target for drug discovery. In this regard, topoisomerase IB - one of the enzymes controlling DNA topology - has been poisoned by hundreds of compounds that increase DNA fragility and cell death. Aromathecins are novel molecules with a multiheterocyclic ring scaffold that have higher stability than camptothecins. RESULTS: Aromathecins showed strong activity against both forms of L. infantum parasites, free-living promastigotes and intra-macrophagic amastigotes harbored in ex vivo splenic explant cultures obtained from infected BALB/c mice. However, they prevented the relaxation activity of leishmanial topoisomerase IB weakly, which suggests that the inhibition of topoisomerase IB partially explains the antileishmanial effect of these compounds. The effect of aromathecins was also studied against a strain resistant to camptothecin, and results suggested that the trafficking of these compounds is not through the ABCG6 transporter. CONCLUSIONS: Aromathecins are promising novel compounds against canine leishmaniasis that can circumvent potential resistances based on drug efflux pumps.


Subject(s)
Antiprotozoal Agents/pharmacology , Heterocyclic Compounds, 4 or More Rings/pharmacology , Leishmania infantum/drug effects , Topoisomerase I Inhibitors/pharmacology , Animals , Cell Culture Techniques , DNA Topoisomerases, Type I/drug effects , DNA Topoisomerases, Type I/metabolism , Female , Leishmania infantum/enzymology , Leishmania infantum/growth & development , Life Cycle Stages/drug effects , Mice, Inbred BALB C , Protozoan Proteins/antagonists & inhibitors , Spleen/parasitology
14.
Bioorg Med Chem Lett ; 29(23): 126714, 2019 12 01.
Article in English | MEDLINE | ID: mdl-31635931

ABSTRACT

A series of novel N-phenylbenzamide-4-methylamine acridine derivatives were designed and synthesized based initially on the structure of amsacrine (m-AMSA). Molecular docking suggested that the representative compound 9a had affinity for binding DNA topoisomerase (Topo) II, which was comparable with that of m-AMSA, and furthermore that 9a could have preferential interactions with Topo I. After synthesis of 9a and analogues 9b-9f, these were all tested in vitro and the synthesized compounds displayed potent antiproliferative activity against three different cancer cell lines (K562, CCRF-CEM and U937). Among them, compounds 9b, 9c and 9d exhibiting the highest activity with IC50 value ranging from 0.82 to 0.91 µM against CCRF-CEM cells. In addition, 9b and 9d also showed high antiproliferative activity against U937 cells, with IC50 values of 0.33 and 0.23 µM, respectively. The pharmacological mechanistic studies of these compounds were evaluated by Topo I/II inhibition, western blot assay and cell apoptosis detection. In summary, 9b effectively inhibited the activity of Topo I/II and induced DNA damage in CCRF-CEM cells and, moreover, significantly induced cell apoptosis in a concentration-dependent manner. These observations provide new information and guidance for the structural optimization of more novel acridine derivatives.


Subject(s)
Apoptosis/drug effects , DNA Topoisomerases, Type II/drug effects , DNA Topoisomerases, Type I/drug effects , Methylamines/chemical synthesis , Molecular Docking Simulation/methods , Humans , Methylamines/chemistry , Molecular Structure , Structure-Activity Relationship
15.
J Mol Biol ; 431(18): 3427-3449, 2019 08 23.
Article in English | MEDLINE | ID: mdl-31301408

ABSTRACT

Type II topoisomerases regulate DNA topology by making a double-stranded break in one DNA duplex, transporting another DNA segment through this break and then resealing it. Bacterial type IIA topoisomerase inhibitors, such as fluoroquinolones and novel bacterial topoisomerase inhibitors, can trap DNA cleavage complexes with double- or single-stranded cleaved DNA. To study the mode of action of such compounds, 21 crystal structures of a "gyraseCORE" fusion truncate of Staphyloccocus aureus DNA gyrase complexed with DNA and diverse inhibitors have been published, as well as 4 structures lacking inhibitors. These structures have the DNA in various cleavage states and appear to track trajectories along the catalytic paths of the DNA cleavage/religation steps. The various conformations sampled by these multiple "gyraseCORE" structures show rigid body movements of the catalytic GyrA WHD and GyrB TOPRIM domains across the dimer interface. Conformational changes common to all compound-bound structures suggest common mechanisms for DNA cleavage-stabilizing compounds. The structures suggest that S. aureus gyrase uses a single moving-metal ion for cleavage and that the central four base pairs need to be stretched between the two catalytic sites, in order for a scissile phosphate to attract a metal ion to the A-site to catalyze cleavage, after which it is "stored" in another coordination configuration (B-site) in the vicinity. We present a simplified model for the catalytic cycle in which capture of the transported DNA segment causes conformational changes in the ATPase domain that push the DNA gate open, resulting in stretching and cleaving the gate-DNA in two steps.


Subject(s)
Anti-Bacterial Agents/pharmacology , DNA Cleavage/drug effects , DNA Topoisomerases, Type I/drug effects , DNA/chemistry , Topoisomerase Inhibitors/pharmacology , Catalytic Domain , DNA/metabolism , DNA Gyrase/chemistry , DNA Gyrase/genetics , DNA Topoisomerases, Type I/chemistry , DNA Topoisomerases, Type II/chemistry , DNA Topoisomerases, Type II/drug effects , Fluoroquinolones/pharmacology , Metals , Models, Molecular , Protein Conformation , Quinolones , Staphylococcus aureus/enzymology , Topoisomerase II Inhibitors/pharmacology
16.
Inorg Chem ; 58(10): 6804-6810, 2019 May 20.
Article in English | MEDLINE | ID: mdl-31046253

ABSTRACT

The substitution-inert polynuclear platinum complexes (SI-PPCs) are now recognized as a distinct subclass of platinum anticancer drugs with high DNA binding affinity. Here, we investigate the effects of SI-PPCs containing dangling amine groups in place of NH3 as ligands to increase the length of the molecule and therefore overall charge and its distribution. The results obtained with the aid of biophysical techniques, such as total intensity light scattering, gel electrophoresis, and atomic force microscopy, show that addition of dangling amine groups considerably augments the ability of SI-PPCs to condense/aggregate nucleic acids. Moreover, this enhanced capability of SI-PPCs correlates with their heightened efficiency to inhibit DNA-related enzymatic activities, such as those connected with DNA transcription, catalysis of DNA relaxation by DNA topoisomerase I, and DNA synthesis catalyzed by Taq DNA polymerase. Thus, the addition of the dangling amine groups resulting in structures of SI-PPCs, which differ so markedly from the derivatives of cisplatin used in the clinic, appears to contribute to the overall biological activity of these molecules.


Subject(s)
Amines/chemistry , Coordination Complexes/chemistry , DNA Topoisomerases, Type I/drug effects , DNA/chemistry , Platinum Compounds/chemistry , RNA/chemistry , Taq Polymerase/antagonists & inhibitors , Antineoplastic Agents/chemistry , Microscopy, Atomic Force , Topoisomerase I Inhibitors
17.
Biochim Biophys Acta Gen Subj ; 1863(10): 1524-1535, 2019 10.
Article in English | MEDLINE | ID: mdl-31145964

ABSTRACT

BACKGROUND: Topoisomerase is a well known target to develop effective antibacterial agents. In pursuance of searching novel antibacterial agents, we have established a novel bisbenzimidazole (PPEF) as potent E. coli topoisomerase IA poison inhibitor. METHODS: In order to gain insights into the mechanism of action of PPEF and understanding protein-ligand interactions, we have produced wild type EcTopo 67 N-terminal domain (catalytic domain) and its six mutant proteins at acidic triad (D111, D113, E115). The DDE motif is replaced by alanine (A) to create three single mutants: D111A, D113A, E115A and three double mutants: D111A-D113A, D113A-E115A and D111A-E115A. RESULTS: Calorimetric study of PPEF with single mutants showed 10 fold lower affinity than that of wild type EcTopo 67 (7.32 × 106 M-1for wild type, 0.89 × 106 M-1for D111A) and 100 fold lower binding with double mutant D113A-E115A (0.02 × 106 M-1) was observed. The mutated proteins showed different CD signature as compared to wild type protein. CD and fluorescence titrations were done to study the interaction between EcTopo 67 and ligands. Molecular docking study validated that PPEF has decreased binding affinity towards mutated enzymes as compared to wild type. CONCLUSION: The overall study reveals that PPEF binds to D113 and E115 of acidic triad of EcTopo 67. Point mutations decrease binding affinity of PPEF towards DDE motif of topoisomerase. GENERAL SIGNIFICANCE: This study concludes PPEF as poison inhibitor of E. coli Topoisomerase IA, which binds to acidic triad of topoisomerase IA, responsible for its function. PPEF can be considered as therapeutic agent against bacteria.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bisbenzimidazole/pharmacology , Catalytic Domain/drug effects , DNA Topoisomerases, Type I/drug effects , Escherichia coli/enzymology , Bisbenzimidazole/metabolism , Cloning, Molecular , DNA Topoisomerases, Type I/genetics , DNA Topoisomerases, Type I/metabolism , Mutagenesis, Site-Directed , Thermodynamics
18.
Eur J Med Chem ; 162: 18-31, 2019 Jan 15.
Article in English | MEDLINE | ID: mdl-30408746

ABSTRACT

Heterocyclic compounds, such as hybrid tetrahydroquinoline and quinoline derivatives with phosphorated groups, have been prepared by multicomponent cycloaddition reaction between phosphorus-substituted anilines, aldehydes and styrenes. The antileishmanial activity of these compounds has been evaluated on both promastigotes and intramacrophagic amastigotes of Leishmania infantum. Good antileishmanial activity of functionalized tetrahydroquinolines 4a, 5a, 6b and quinoline 8b has been observed with similar activity than the standard drug amphotericin B and close selective index (SI between 43 and 57) towards L. infantum amastigotes to amphotericin B. Special interest shows tetrahydroquinolylphosphine sulfide 5a with an EC50 value (0.61 ±â€¯0.18 µM) similar to the standard drug amphotericin B (0.32 ±â€¯0.05 µM) and selective index (SI = 56.87). In addition, compound 4c shows remarkable inhibition on Leishmania topoisomerase IB. Parallel theoretical study of stereoelectronic properties, application of docking-based virtual screening methods, along with molecular electrostatic potential and predictive druggability analyses are also reported.


Subject(s)
Antiprotozoal Agents/chemistry , DNA Topoisomerases, Type I/drug effects , Leishmania infantum/drug effects , Phosphorus/chemistry , Quinolines/chemistry , Humans , Molecular Docking Simulation , Molecular Structure , Quinolines/pharmacology , Quinolines/therapeutic use
19.
Anticancer Res ; 39(1): 135-144, 2019 Jan.
Article in English | MEDLINE | ID: mdl-30591450

ABSTRACT

BACKGROUND/AIM: The identification of a series of oxadiazole-based compounds, as promising antiproliferative agents, has been previously reported. The aim of this study was to explore the SAR of newly-synthesized oxadiazole derivatives and identify their molecular targets. MATERIALS AND METHODS: A small library of 1,2,5-oxadiazole derivatives was synthetized and their antiproliferative activity was tested by the MTT assay. Their interaction with topoisomerase I was evaluated and a molecular docking study was performed. RESULTS: Several candidates showed cytotoxicity towards two human tumor cell lines, HCT-116 (colorectal carcinoma) and HeLa (cervix adenocarcinoma). Some derivatives exhibited inhibitory effects on the catalytic activity of topoisomerase I and this effect was supported by docking studies. CONCLUSION: The enzyme inhibition results, although not directly related to cytotoxicity, suggest that a properly modified 1,2,5 oxadiazole scaffold could be considered for the development of new anti-topoisomerase agents.


Subject(s)
Cell Proliferation/drug effects , Molecular Docking Simulation , Neoplasms/drug therapy , Oxadiazoles/chemistry , DNA Topoisomerases, Type I/drug effects , Drug Screening Assays, Antitumor , HCT116 Cells , HeLa Cells , Humans , Neoplasms/pathology , Oxadiazoles/chemical synthesis , Oxadiazoles/pharmacology , Structure-Activity Relationship
20.
mBio ; 8(5)2017 10 03.
Article in English | MEDLINE | ID: mdl-28974621

ABSTRACT

Inflammatory responses, while essential for pathogen clearance, can also be deleterious to the host. Chemical inhibition of topoisomerase 1 (Top1) by low-dose camptothecin (CPT) can suppress transcriptional induction of antiviral and inflammatory genes and protect animals from excessive and damaging inflammatory responses. We describe the unexpected finding that minor DNA damage from topoisomerase 1 inhibition with low-dose CPT can trigger a strong antiviral immune response through cyclic GMP-AMP synthase (cGAS) detection of cytoplasmic DNA. This argues against CPT having only anti-inflammatory activity. Furthermore, expression of the simian virus 40 (SV40) large T antigen was paramount to the proinflammatory antiviral activity of CPT, as it potentiated cytoplasmic DNA leakage and subsequent cGAS recruitment in human and mouse cell lines. This work suggests that the capacity of Top1 inhibitors to blunt inflammatory responses can be counteracted by viral oncogenes and that this should be taken into account for their therapeutic development.IMPORTANCE Recent studies suggest that low-dose DNA-damaging compounds traditionally used in cancer therapy can have opposite effects on antiviral responses, either suppressing (with the example of CPT) or potentiating (with the example of doxorubicin) them. Our work demonstrates that the minor DNA damage promoted by low-dose CPT can also trigger strong antiviral responses, dependent on the presence of viral oncogenes. Taken together, these results call for caution in the therapeutic use of low-dose chemotherapy agents to modulate antiviral responses in humans.


Subject(s)
DNA Topoisomerases, Type I/drug effects , Immunity, Innate/drug effects , Nucleotides, Cyclic/metabolism , Simian virus 40/drug effects , Topoisomerase I Inhibitors/pharmacology , Animals , Antigens, Viral, Tumor/genetics , Antigens, Viral, Tumor/immunology , Antiviral Agents/pharmacology , Camptothecin/pharmacology , Cell Line , Coculture Techniques , DNA Damage , DNA Topoisomerases, Type I/metabolism , Fibroblasts/drug effects , Fibroblasts/virology , Humans , Inflammation , Mice , Simian virus 40/immunology , Simian virus 40/physiology , Virus Diseases/drug therapy , Virus Diseases/immunology , Virus Diseases/virology
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