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Cell Chemical Biology May 2022We identify a selective nanomolar inhibitor of blood-stage malarial proliferation from a screen of microbial natural product extracts. The responsible compound, PDE-I,...
We identify a selective nanomolar inhibitor of blood-stage malarial proliferation from a screen of microbial natural product extracts. The responsible compound, PDE-I, is a precursor of the anticancer duocarmycin family that preserves the class's sequence-specific DNA binding but lacks its signature DNA alkylating cyclopropyl warhead. While less active than duocarmycin, PDE-I retains comparable antimalarial potency to chloroquine. Importantly, PDE-I is >1,000-fold less toxic to human cell lines than duocarmycin, with mitigated impacts on eukaryotic chromosome stability. PDE-I treatment induces severe defects in parasite nuclear segregation leading to impaired daughter cell formation during schizogony. Time-of-addition studies implicate parasite DNA metabolism as the target of PDE-I, with defects observed in DNA replication and chromosome integrity. We find the effect of duocarmycin and PDE-I on parasites is phenotypically indistinguishable, indicating that the DNA binding specificity of duocarmycins is sufficient and the genotoxic cyclopropyl warhead is dispensable for the parasite-specific selectivity of this compound class.
Topics: Animals; Antimalarials; Biological Products; DNA; Duocarmycins; Folic Acid Antagonists; Humans; Malaria; Parasites
PubMed: 34710358
DOI: 10.1016/j.chembiol.2021.10.005 -
Nature Communications Nov 2017GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these...
GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these proteins as cyclopropanoid cyclopropyl hydrolases (CCHs) that can catalyze the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065. Co-crystallography and molecular dynamics simulation analyses reveal that these CCHs share a conserved aromatic cage for the hydrolytic activity. Subsequent cytotoxic assays confirm that CCHs are able to protect cells against YTM. Therefore, our findings suggest that the evolutionarily conserved GyrI-like proteins confer cellular protection against diverse xenobiotics via not only binding, but also catalysis.
Topics: Alkylating Agents; Animals; Bacterial Physiological Phenomena; Binding Sites; Biocatalysis; Cell Line, Tumor; Crystallography, X-Ray; DNA; DNA Topoisomerases, Type II; Drug Resistance, Bacterial; Duocarmycins; Escherichia coli; Escherichia coli Proteins; Humans; Hydrolases; Hydrolysis; Indoles; Inhibitory Concentration 50; Jurkat Cells; Mice; Microbial Sensitivity Tests; Molecular Dynamics Simulation; Pyrroles; Recombinant Proteins; Repressor Proteins; Sequence Homology, Amino Acid; Streptomyces; Xenobiotics
PubMed: 29133784
DOI: 10.1038/s41467-017-01508-1 -
Journal of the American Chemical Society Dec 2007N-Acyl O-amino phenol derivatives of CBI-TMI and CBI-indole2 are reported as prototypical members of a new class of reductively activated prodrugs of the duocarmycin and...
N-Acyl O-amino phenol derivatives of CBI-TMI and CBI-indole2 are reported as prototypical members of a new class of reductively activated prodrugs of the duocarmycin and CC-1065 class of antitumor agents. The expectation being that hypoxic tumor environments, with their higher reducing capacity, carry an intrinsic higher concentration of "reducing" nucleophiles (e.g., thiols) capable of activating such derivatives (tunable N-O bond cleavage) and increasing their sensitivity to the prodrug treatment. Preliminary studies indicate the prodrugs effectively release the free drug in functional cellular assays for cytotoxic activity approaching or matching the activity of the free drug, yet remain essentially stable and unreactive to in vitro DNA alkylation conditions (<0.1-0.01% free drug release) and pH 7.0 phosphate buffer, and exhibit a robust half-life in human plasma (t1/2 = 3 h). Characterization of a representative O-(acylamino) prodrug in vivo indicates that they approach the potency and exceed the efficacy of the free drug itself (CBI-indole2), indicating that not only is the free drug effectively released from the inactive prodrug but also that they offer additional advantages related to a controlled or targeted release in vivo.
Topics: Alkylation; Animals; Antibiotics, Antineoplastic; Cell Line, Tumor; DNA; Duocarmycins; Humans; Indoles; Inhibitory Concentration 50; Leukemia L1210; Mice; Mice, Inbred DBA; Phenols; Prodrugs
PubMed: 18020335
DOI: 10.1021/ja075398e -
Journal of the American Chemical Society Dec 2008A unique alternative to the -spirocyclization for activation of compounds containing the duocarmycin SA alkylation subunit was established involving indole NH...
A unique alternative to the -spirocyclization for activation of compounds containing the duocarmycin SA alkylation subunit was established involving indole NH deprotonation and subsequent cyclopropane formation. The structural characterization of an alternative spirocyclization product, and the establishment of its relative reactivity, intrinsic reaction regioselectivity, biological activity, and DNA alkylation properties (selectivity, rate, and efficiency) including the isolation, characterization, and quantitation of its adenine N3 adduct, are disclosed.
Topics: Alkylation; Antineoplastic Agents; Cyclization; Duocarmycins; Hydrogen-Ion Concentration; Indoles; Kinetics; Pyrroles
PubMed: 19554689
DOI: 10.1021/ja806593w -
The Journal of Antibiotics Mar 1986
Review
Topics: Adenine; Alkylation; Animals; Base Sequence; Binding Sites; Cell Cycle; Chemical Phenomena; Chemistry; DNA; DNA Repair; Duocarmycins; Humans; In Vitro Techniques; Indoles; Lethal Dose 50; Leucomycins; Mice; Neoplasms, Experimental; Stereoisomerism
PubMed: 3516958
DOI: 10.7164/antibiotics.39.319 -
Biomedicines Mar 2021Despite significant advances in treatment strategies over the past decade, selective treatment of breast cancer with limited side-effects still remains a great... (Review)
Review
Despite significant advances in treatment strategies over the past decade, selective treatment of breast cancer with limited side-effects still remains a great challenge. The cytochrome P450 (CYP) family of enzymes contribute to cancer cell proliferation, cell signaling and drug metabolism with implications for treatment outcomes. A clearer understanding of CYP expression is important in the pathogenesis of breast cancer as several isoforms play critical roles in metabolising steroid hormones and xenobiotics that contribute to the genesis of breast cancer. The purpose of this review is to provide an update on how the presence of CYPs impacts on standard of care (SoC) drugs used to treat breast cancer as well as discuss opportunities to exploit CYP expression for therapeutic intervention. Finally, we provide our thoughts on future work in CYP research with the aim of supporting ongoing efforts to develop drugs with improved therapeutic index for patient benefit.
PubMed: 33809117
DOI: 10.3390/biomedicines9030290 -
Nature Chemical Biology Sep 2017Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial and antitumor properties and is the most recent addition to the CC-1065 and...
Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial and antitumor properties and is the most recent addition to the CC-1065 and duocarmycin family of natural products. Though bulky DNA lesions the size of those produced by YTM are normally removed from the genome by the nucleotide-excision repair (NER) pathway, YTM adducts are also a substrate for the bacterial DNA glycosylases AlkD and YtkR2, unexpectedly implicating base-excision repair (BER) in their elimination. The reason for the extreme toxicity of these lesions and the molecular basis for the way they are eliminated by BER have been unclear. Here, we describe the structural and biochemical properties of YTM adducts that are responsible for their toxicity, and define the mechanism by which they are excised by AlkD. These findings delineate an alternative strategy for repair of bulky DNA damage and establish the cellular utility of this pathway relative to that of NER.
Topics: Biological Products; DNA Adducts; DNA Damage; DNA Repair; Drug Resistance, Bacterial; Duocarmycins; Indoles; Molecular Structure; Pyrroles
PubMed: 28759018
DOI: 10.1038/nchembio.2439 -
Biochimica Et Biophysica Acta Jul 2002Cellular DNA is not a uniform target for DNA-reactive drugs. At the nucleotide level, drugs recognize and bind short motifs of a few base pairs. The location of drug... (Review)
Review
Cellular DNA is not a uniform target for DNA-reactive drugs. At the nucleotide level, drugs recognize and bind short motifs of a few base pairs. The location of drug adducts at the genomic level depends on how these short motifs are distributed in larger domains. This aspect, referred to as region specificity, may be critical for the biological outcome of drug action. Recent studies demonstrated that certain minor groove binding (MGB) drugs, such as bizelesin, produce region-specific lesions in cellular DNA. Bizelesin binds mainly T(A/T)(4)A sites, which are on average scarce, but occasionally cluster in distinct minisatellite regions (200-1000 bp of approximately 85-100% AT), herein referred to as AT islands. Bizelesin-targeted AT islands are likely to function as strong matrix attachment regions (MARs), domains that organize DNA loops on the nuclear matrix. Distortion of MAR-like AT islands may be a basis for the observed inhibition of new replicon initiation and the extreme lethality of bizelesin adducts (<10 adducts/cell for cell growth inhibition). Hence, long AT-islands represent a novel class of critical targets for anticancer drugs. The AT island paradigm illustrates the potential of the concept of regional targeting as an essential component of the rational design of new sequence-specific DNA-reactive drugs.
Topics: Antineoplastic Agents; Base Sequence; Benzofurans; Binding Sites; Cyclohexanecarboxylic Acids; Cyclohexenes; DNA Damage; DNA, Neoplasm; Distamycins; Drug Design; Duocarmycins; Genome, Human; Humans; Indoles; Nitrogen Mustard Compounds; Tandem Repeat Sequences; Tumor Cells, Cultured; Urea
PubMed: 12084472
DOI: 10.1016/s0925-4439(02)00093-5 -
Journal of the American Chemical Society Jan 2009The total synthesis and evaluation of iso-duocarmycin SA (5) and iso-yatakemycin (6), representing key analogues of the corresponding natural products incorporating an...
The total synthesis and evaluation of iso-duocarmycin SA (5) and iso-yatakemycin (6), representing key analogues of the corresponding natural products incorporating an isomeric alkylation subunit, are detailed. This pyrrole isomer of the natural alkylation subunit displayed an enhanced reaction regioselectivity and a 2-fold diminished stability. Although still exceptionally potent, the iso-duocarmycin SA derivatives and natural product analogues exhibited a corresponding approximate 3-5-fold reduction in cytotoxic activity [L1210 IC(50) for (+)-iso-duocarmycin SA = 50 pM and for (+)-iso-yatakemycin = 15 pM] consistent with their placement on a parabolic relationship correlating activity with reactivity. The DNA alkylation selectivity of the resulting key natural product analogues was unaltered by the structure modification in spite of the minor-groove presentation of a potential H-bond donor. Additionally, a unique ortho-spirocyclization with such derivatives was explored via the preparation, characterization, and evaluation of 34 that is incapable of the more conventional para-spirocyclization. Although 34 proved sufficiently stable for isolation and characterization, it displayed little stability in protic solvents (t(1/2) = 0.19 h at pH 3, t(1/2) = 0.20 h at pH 7), a pH-independent (H(+) independent) solvolysis rate profile at pH 3/4-7, and a much reduced cytotoxic potency, but a DNA alkylation selectivity and efficiency comparable to those of duocarmycin SA and iso-duocarmycin SA. The implications of these observations on the source of the DNA alkylation selectivity and catalysis for this class of natural products are discussed.
Topics: Alkylation; Animals; Biological Products; Cell Line, Tumor; Cell Survival; DNA; Duocarmycins; Indoles; Isomerism; Mice; Molecular Structure; Pyrroles; Solubility; Structure-Activity Relationship
PubMed: 19154178
DOI: 10.1021/ja808108q -
MAbs 2021This study describes the characterization of conjugation sites for a random, lysine conjugated 2-iminothiolane (2-IT) based antibody-drug-conjugate synthesized from an...
This study describes the characterization of conjugation sites for a random, lysine conjugated 2-iminothiolane (2-IT) based antibody-drug-conjugate synthesized from an IgG1 antibody and a duocarmycin analog-based payload-linker. Of the 80 putative lysine sites, 78 were found to be conjugated via tryptic peptide mapping and LC-HRMS. Surprisingly, seven cysteine-linked conjugated peptides were also detected resulting from the conjugation of cysteine residues derived from the four inter-chain disulfide bonds during the reaction. This unexpected finding could be attributed to the free thiols of the 2-IT thiolated antibody intermediates and/or the 4-mercaptobutanamide by-product resulting from the hydrolysis of 2-IT. These free thiols could cause the four inter-chain disulfide bonds of the antibody to scramble via intra- or inter-molecular attack. The presence of only pair of non-reactive (unconjugated) lysine residues, along with the four intact intra-chain disulfide bonds, is attributed to their poor accessibility, which is consistent with solvent accessibility modeling analysis. We also discovered a major by-product derived from the hydrolysis of the amidine moiety of the -terminus conjugate. In contrast, the amidine moiety in lysine-linked conjugates appeared stable. Based on our results, we propose plausible formation mechanisms of cysteine-linked conjugates and the hydrolysis of the -terminus conjugate, which provide scientific insights that are beneficial to process development and drug quality control.
Topics: Cysteine; Drug Discovery; Duocarmycins; Humans; Immunoconjugates; Immunoglobulin G; Lysine
PubMed: 34486490
DOI: 10.1080/19420862.2021.1974150