NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

The discovery of a drug requires over a decade of intensive research and financial investments – and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied their enzymatic metabolic targets, fate, and toxicity. NICEdrug.ch includes a unique fingerprint that identifies reactive similarities between drug–drug and drug–metabolite pairs. We validated the application, scope, and performance of NICEdrug.ch over similar methods in the field on golden standard datasets describing drugs and metabolites sharing reactivity, drug toxicities, and drug targets. We use NICEdrug.ch to evaluate inhibition and toxicity by the anticancer drug 5-fluorouracil, and suggest avenues to alleviate its side effects. We propose shikimate 3-phosphate for targeting liver-stage malaria with minimal impact on the human host cell. Finally, NICEdrug.ch suggests over 1300 candidate drugs and food molecules to target COVID-19 and explains their inhibitory mechanism for further experimental screening. The NICEdrug.ch database is accessible online to systematically identify the reactivity of small molecules and druggable enzymes with practical applications in lead discovery and drug repurposing.

Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches

Vassily Hatzimanikatis, Ljubisa Miskovic, Aikaterini Zisaki

Drug discovery and development is a high-risk enterprise that requires significant investments in capital, time and scientific expertise. The studies of xenobiotic metabolism remain as one of the main topics in the research and development of drugs, cosmetics and nutritional supplements. Antihypertensive drugs are used for the treatment of high blood pressure, which is one the most frequent symptoms of the patients that undergo cardiovascular diseases such as myocardial infraction and strokes. In current cardiovascular disease pharmacology, four drug clusters - Angiotensin Converting Enzyme Inhibitors, Beta-Blockers, Calcium Channel Blockers and Diuretics - cover the major therapeutic characteristics of the most antihypertensive drugs. The pharmacokinetic and specifically the metabolic profile of the antihypertensive agents are intensively studied because of the broad inter-individual variability on plasma concentrations and the diversity on the efficacy response especially due to the P450 dependent metabolic status they present. Several computational methods have been developed with the aim to: (i) model and better understand the human drug metabolism; and (ii) enhance the experimental investigation of the metabolism of small xenobiotic molecules. The main predictive tools these methods employ are rule-based approaches, quantitative structure metabolism/activity relationships and docking approaches. This review paper provides detailed metabolic profiles of the major clusters of antihypertensive agents, including their metabolites and their metabolizing enzymes, and it also provides specific information concerning the computational approaches that have been used to predict the metabolic profile of several antihypertensive drugs.

Bentham Science Publishers2015

In silico DNA-binding and rational design of ruthenium-arene anticancer drugs

Christian Gossens

Organometallic ruthenium(II)-arene (RA) antitumour compounds of the general type [Ru(II)(η6-arene)(X)2(pta)], RA-pta, and [Ru(II)(η6-arene)X(en)], RA-en, (X=leaving group; pta=1,3,5-triaza-7-phosphaadamantane, en=ethylenediamine) have been investigated computationally. The main focus has been i.e. the hydrolysis properties, ligand exchange reactions, binding to DNA and the analysis of the resulting structural perturbations. The goal of this thesis was to elucidate key steps in the reactivity of the above drugs that are not readily accessible by experimental techniques. The methodologies employed cover tailor made force fields in classical molecular dynamics (MD), density functional theory (DFT) MD simulations in implicit and explicit solvent as well as combined classical/quantum (QM/MM) MD simulations. For RA-pta compounds, binding energies between the metal centres and the surrounding ligands were calculated. The calculated energies rationalize the experimentally observed tendencies for arene loss, and show that the pta ligands are relatively strongly bound. Exchange of metal centre, methylation or protonation of the pta-ligand, or change of the arene result in significant differences in the metal-arene binding energies while leaving the metalphosphine bond strength essentially unchanged. Significantly lower binding energies and reduced hapticity are predicted for the exchange of arene by nucleobases. The latter show higher binding energies for nitrogen π-bonding than for p-bonding. No influence on the ruthenium-arene interaction was observed for RA-pta complexes bearing arenes with functionalized side chains. A combined DFT/continuum electrostatics approach has been used to estimate the protonation states and absolute pKa values of a series of RA-pta compounds and their hydrolysis products. Our results suggest that the selective in vivo activity towards cancer cells and the observed pH dependent DNA damage is due to a pH dependent activation/deactivation mechanism. In the context of rational drug design, it is hypothesised that analogues with fluorinated arene rings should result in improved selectivity towards hypoxic cancer cells. For RA-en complexes, we rationalized the chemoselectivity towards guanine. The calculated DFT binding energies for the three investigated nucleobases (G, A, C) decreases in the order G(N7) >> C(O2) ∼ C(N3) > A(N7) > G(O6) > OH2. The G(N7) complex is the most stable product due to a C6=O-HNen hydrogen bond while the corresponding C6-NH2-HNen interaction in adenine is repulsive. A study of the reaction of [(η6-benzene)Ru(en)(OH2)]2+ (1) towards the nucleobases G, A and C reveals a strong preference for a formation of an H-bonded cis vs. trans reactant adduct. Only guanine can form a thermally stable trans reactant adduct. The potential reaction sites of adenine and cytosine might loose their nucleophilicity by protonation while simultaneously the aqua leaving group of 1 is converted into an unreactive hydroxo ligand. For the reaction of 1 with guanine three different reaction pathways were identified, however, a "direct trans" reaction pathway is probably the most biologically relevant. Using classical and QM/MM MD we showed that both investigated ruthenium compounds, RA-pta and RA-en, can bind to the major groove of duplex DNA and are stable in this position. The DNA is highly flexible, adapts very fast and widens the major groove to accommodate the ruthenium complex. The local and global structural changes of the DNA (e.g. bending towards the major groove) observed for the RA-pta series are similar to those reported for cisplatin. A severe perturbation of the Watson-Crick base pairing adjacent to the binding site of RA-en was observed that can be linked to recent experimental results. Finally, a tailor made force field for RA-en was derived from our QM/MM trajectories using a force matching approach.

EPFL2007

Small Molecule Based Approaches to Inhibit Macrophage Migration Inhibitory Factor (MIF) Activities and Elucidate its Role in Health and Disease

Hajer Ouertatani-Sakouhi

Macrophage migration inhibitory factor (MIF) is a major mediator in innate immunity and inflammation and a potential therapeutic target in multiple inflammatory, infectious and autoimmune diseases including cancer. Current therapeutic strategies for targeting MIF focus on modulating its biological activities using anti-MIF neutralizing antibodies or developing inhibitors of its tautomerase activity. Although the identity of its natural substrate remains unknown, several small molecule inhibitors have been reported to be effective inhibitors of MIF tautomerase activity in vitro. All these inhibitors were identified by rational design and structure-activity studies based on the structure of the catalytic site and/or non physiologic substrates of MIF. The lack of suitable high-throughput screening (HTS) assays has hindered the screening of chemical libraries and discovery of more diverse inhibitors. Motivated by the goal of discovering diverse classes of MIF inhibitors that modulate MIF activity specific targeting of its biochemical, conformation and quaternary structure properties, both activity based endpoint and kinetic HTS assays were developed, optimized and performed on diverse set of libraries. Using the endpoint assay, out of 15440 compounds screened, twelve novel inhibitors of MIF's catalytic activity (∼ 0.1% hit rate) with IC50s in the range of 1.5 to 15.5 µM were identified and validated. The interaction site and mechanism of action of all these inhibitors were defined using structure activity studies and a battery of biochemical and biophysical methods, including mass spectrometry, light scattering, and NMR. The effect on MIF biological activities was also examined on MIF-mediated glucocorticoid overriding and MIF-induced Akt phosphorylation. Using the kinetic-based activity assay, we screened 80,000 small molecules and identified and validated thirteen novel inhibitors of MIF catalytic activity with inhibition constant (Ki,app) values ranging from 0.5 to 13 µM. According to the structure and potency some of these molecules could be of great therapeutic potential. The MIF inhibitors emerging from these studies could be divided into four classes: 1) molecules that covalently modify the catalytic site at the N-terminal proline residue, Pro1 which could be classified into 5 groups; 2) a novel class of catalytic site inhibitors, 3) a class of trimer destabilizing inhibitors. These findings demonstrate the potential of HTS assays as attractive means to identify novel classes of MIF inhibitors as lead drug candidates and/or chemical tools for elucidating the biochemical and structural bases underlying the multifunctionality of MIF's in health and disease. Having these molecules in hand, will advance our understanding of protein-protein interactions mechanism for MIF oligomerization and may help to elucidate the role of MIF enzymatic activity in health and disease.