Targeting homologous recombination (HR) repair mechanism for cancer treatment: discovery of new potential UCHL-3 inhibitors via virtual screening, molecular dynamics and binding mode analysis.

UCHL3 (ubiquitin C-terminal hydrolase-L3) is a de-ubiquitinating enzyme involved in the homologous recombination repair mechanism of double-strand breaks (DBS) of the DNA. Multiple studies indicated that UCHL3 inhibitors could be used in combination therapy with high therapeutic efficacy against cancer thus highlighting the validity of directing research against UCHL3 as a druggable target in oncology. In this study, a combination of virtual screening methods was utilized to identify new potential UCHL3 inhibitors. A series of UCHL3 ligands were identified by applying a combination of cheminformatics and molecular modeling filtration techniques to a ChemBl database of over two million small molecules viz. Lipinski's Rule of Five, Veber's rule, pharmacophore model, Hierarchical molecular docking, Pan-assay Interference Compounds (PAINS) alerts, toxicity filter, and single-point Molecular mechanics Poisson/Boltzmann surface area (MM/PBSA) docking pose rescoring. This multi-layer filtration strategy led to the identification of twenty-one compounds as potential UCHL3 inhibitors that were subsequently subjected to a 50 ns molecular dynamics (MD) simulations predict the stability of their ligand-protein complexes. Furthermore, MM/PBSA calculations based on MD trajectories were performed, and the energy contribution per residue to the binding energy was calculated. Three compounds, 1, 2 and 3, were finally recognized as having the highest potential of being UCHL3 inhibitors. Therefore, those were used for binding mode analysis to the UCHL3 active site, leading to identification of four residues as key for binding viz. Pro8, Leu55, Val166, and Leu168.Communicated by Ramaswamy H. Sarma.

New antiparasitic flexible triaryl diamidines, their prodrugs and aza analogues: Synthesis, in vitro and in vivo biological evaluation, and molecular modelling studies.

Dicationic diamidines have been well established as potent antiparasitic agents with proven activity against tropical diseases like trypanosomiasis and malaria. This work presents the synthesis of new mono and diflexible triaryl amidines (6a-c, 13a,b and 17), their aza analogues (23 and 27) and respective methoxyamidine prodrugs (5, 7, 12a,b, 22 and 26). All diamidines were assessed in vitro against Trypanosoma brucei rhodesiense (T. b. r.) and Plasmodium falciparum (P. f.) where they displayed potent to moderate activities at the nanomolar level with IC50s = 11-378 nM for T. b. r. and 4-323 nM against P. f.. In vivo efficacy testing against T. b. r. STIB900 has shown the monoflexible diamidine 6c as the most potent derivative in this study eliciting 4/4 cures of infected mice for a treatment period of >60 days upon a 4 × 5 mg/kg dose i. p. treatment. Moreover, thermal melting analysis measurement ΔTm for this series of diamidines/poly (dA-dT) complexes fell between 0.5 and 19 °C with 6c showing the highest binding to the DNA minor groove. Finally, a 50 ns molecular dynamics study of an AT-rich DNA dodecamer with compound 6c revealed a strong binding complex supported by vdW and electrostatic interactions.

Triaryl dicationic DNA minor-groove binders with antioxidant activity display cytotoxicity and induce apoptosis in breast cancer.

Despite advances in cancer treatment modalities, DNA still stands as one of the targets for anticancer agents. DNA minor groove binders (MGBs) represent an important investigational chemotherapeutic class with promising cytotoxic capacity. Herein this study reports the potent cytotoxic effect of a series of repurposed flexible bis-imidamides 1-4, triaryl bis-guanidine 5 and bis-N-substituted guanidines 6,7 having a 1,4-diphenoxybenzene scaffold backbone on MCF-7 and MDA-MB-231 breast cancer cell lines. Of these compounds, imidamide 4 was chosen for further in-vitro, in-vivo and molecular dynamics (MD) studies owing to its promising anti-tumor activity, with IC50 values on MCF-7 and MDA-MB-231 breast cancer cell lines of 1.9 and 2.08 µM, respectively. Annexin V/propidium iodide apoptosis assay revealed apoptosis induction on imidamide 4 treated MCF-7 cells. RT-PCR assay results demonstrated the proapoptotic effect of compound 4 through increase of mRNA levels of the pro-apoptotic genes; p53, PUMA, and Bax, and inhibiting the anti-apoptotic Bcl-2 gene expression in MCF-7 cells. Moreover, compound 4 induced a G0/G1 cell-cycle arrest in MCF-7 in a dose-dependent manner. Corroborating in-vivo experiments on Ehrlich ascites carcinoma (EAC)-bearing mice, reflected the anticancer strength of derivative 4. For further target validation, molecular dynamics (MD) studies demonstrated an energetically favorable binding of imidamide 4 with the DNA minor groove AT rich site. In effect, imidamide 4 can be viewed as a promising hit dicationic compound with good cytotoxic and apoptotic inducing activity against breast cancer that can be adopted for future optimization.