Design, molecular docking, and molecular dynamics of thiourea-iron (III) metal complexes as NUDT5 inhibitors for breast cancer treatment

Identification of potential NUDT5 inhibitors from marine bacterial natural compounds via molecular dynamics and free energy landscape analysis

NUDIX hydrolase 5 (NUDT5) is an enzyme involved in the hydrolysis of nucleoside diphosphates linked to other moieties, such as ADP-ribose. This cofactor is vital in redox reactions and is essential for the activity of sirtuins and poly(ADP-ribose) polymerases, which are involved in DNA repair and genomic stability. It has been shown that NUDT5 activity can also influence NAD+ homeostasis, thereby affecting cancer cell metabolism and survival. In this regard, the discovery of NUDT5 inhibitors has emerged as a potential therapeutic approach in cancer treatment. In this study, we conducted a high-throughput virtual screening of marine bacterial compounds against the NUDT5 enzyme and four molecules were selected based on their docking scores. These compounds established strong interactions within the NUDT5 active site, with molecular analysis highlighting the key role of Trp28A and Trp46B residues. Molecular dynamics simulations over 200 ns indicated a stable behavior, in association with root mean square deviation values always below 3 Å, suggesting conformational stability. Free energy landscape analysis further supported their potential as NUDT5 inhibitors, offering avenues for novel therapeutic strategies against NUDT5-associated breast cancer.

Drug Selection and Posology, Optimal Therapies and Risk/Benefit Assessment in Medicine: The Paradigm of Iron-Chelating Drugs

The design of clinical protocols and the selection of drugs with appropriate posology are critical parameters for therapeutic outcomes. Optimal therapeutic protocols could ideally be designed in all diseases including for millions of patients affected by excess iron deposition (EID) toxicity based on personalised medicine parameters, as well as many variations and limitations. EID is an adverse prognostic factor for all diseases and especially for millions of chronically red-blood-cell-transfused patients. Differences in iron chelation therapy posology cause disappointing results in neurodegenerative diseases at low doses, but lifesaving outcomes in thalassemia major (TM) when using higher doses. In particular, the transformation of TM from a fatal to a chronic disease has been achieved using effective doses of oral deferiprone (L1), which improved compliance and cleared excess toxic iron from the heart associated with increased mortality in TM. Furthermore, effective L1 and L1/deferoxamine combination posology resulted in the complete elimination of EID and the maintenance of normal iron store levels in TM. The selection of effective chelation protocols has been monitored by MRI T2* diagnosis for EID levels in different organs. Millions of other iron-loaded patients with sickle cell anemia, myelodysplasia and haemopoietic stem cell transplantation, or non-iron-loaded categories with EID in different organs could also benefit from such chelation therapy advances. Drawbacks of chelation therapy include drug toxicity in some patients and also the wide use of suboptimal chelation protocols, resulting in ineffective therapies. Drug metabolic effects, and interactions with other metals, drugs and dietary molecules also affected iron chelation therapy. Drug selection and the identification of effective or optimal dose protocols are essential for positive therapeutic outcomes in the use of chelating drugs in TM and other iron-loaded and non-iron-loaded conditions, as well as general iron toxicity.

Computational Study of Bis-(1-(Benzoyl)-3-Methyl Thiourea) Platinum (II) Complex Derivatives as Anticancer Candidates

Background

The increasing incidence of cancer every year has resulted in cancer becoming one of the most common causes of death in the world. The most common types of cancer are breast cancer, lung cancer and prostate cancer. Thiourea is one of the compounds that have anticancer effects, and its activity can be increased by structural modifications, one of which involves making a Bis-(1-(benzoyl)-3-methyl thiourea) platinum (II) metal complex.

Purpose

This study aims to obtain platinum (II)-thiourea complex compounds that have a more stable interaction as an anticancer agent compared to cisplatin.

Methods

The methods used are computational studies with molecular docking, simulation of molecular dynamics, and prediction of pharmacokinetics and toxicity.

Results

Based on the molecular docking of the platinum (II)-thiourea complex which has the most stable interaction with lower binding energy than the native ligand and the cisplatin, namely Bis-(3-methyl-1-(naphthalene-2-carbonyl)thiourea)) Platinum (II) against breast cancer receptors (3ERT) and lung cancer (2ITO) and compounds Bis-(1-(3-chlorobenzoyl)-3-methylthiourea) Platinum (II) against prostate cancer receptors (1Z95). The evaluation results of the stability of the interaction using a 50 ns molecular dynamic simulation showed that the Bis-(1-benzoyl-3-methylthiourea) Platinum (II) which binds to the prostate cancer receptor (1Z95) has the most stable interaction. Pharmacokinetic prediction results show that the platinum (II)-thiourea complex has a good pharmacokinetic profile, but there are several compounds that are mutagenic and hepatotoxic.

Conclusion

The Bis-(1-(3,4-dichlorobenzoyl)-3-methyl thiourea) platinum (II) compounds could be a suitable anticancer agent for the lungs.

Synthesis of New Ester Derivatives of Salicylic Acid and Evaluation of Their COX Inhibitory Potential

Salicylic acid is an NSAID with serious side effects on the GIS. The side effects of salicylic acid on the GIS are slightly reduced by acetylating salicylic acid. 12 new ester analogs of salicylic acid were synthesized with high yields in this study. The chemical structures of the synthesized compounds were characterized by ¹ H-NMR, ¹³ C-NMR, and HRMS spectra. The inhibitory potential of the compounds was evaluated on COXs by in vitro and in silico studies. The COX2 inhibitory activity of the most potent inhibitor MEST1 (IC₅₀ : 0.048 μM) was found to be much higher than the COX2 inhibitory activity of aspirin (IC₅₀ : 2.60 μM). In docking studies, the strongest inhibitor among the compounds synthesized was predicted to be MEST1, with the lowest binding energy. Docking studies revealed that MEST1 extends from the hydrophobic channel to the top of the cyclooxygenase active site, forming various interactions with residues in the binding pocket.