Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro.

Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence. Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy -performed in a large and diverse chemolibrary- complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening. Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 µM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12-20 µM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7-45 µM). Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known "garbage in, garbage out" machine learning principle.

A Tn antigen binding lectin from Myrsine coriacea displays toxicity in human cancer cell lines.

The Tn antigen (GalNAc-O-Ser/Thr) is one of the most specific human cancer-associated structures. In the present study we characterize the biochemical and functional properties of the Myrsine coriacea lectin (McL). We show that McL is an unusual high molecular weight highly glycosylated protein, which displays a strong Tn binding activity. The lectin exhibits in vitro inhibition of proliferation in the six cancer cell lines evaluated, in a dose-dependent manner (the strongest activity being against HT-29 and HeLa cells), whereas it does not exhibit toxicity against normal lymphocytes. McL could be exploited in the design of potential new tools for the diagnosis or treatment of cancer.

Marcación de un derivado de glucosa con 99mTc mediante la formación de un complejo Tc(V)-nitruro: estudios preliminares / Labelling of a glucose derivative with 99mTc through the formation of a Tc(V)-nitride symmetrical complex: preliminary studies

La preparación de derivados de glucosa marcados con 99mTc reviste gran interés para la evaluación del consumo de glucosa in vivo en oncología y cardiología nuclear. Este trabajo presenta la marcación de un análogo de glucosa (GLU-DTC) mediante la formación de un complejo Tc(V)-nitruro simétrico. Para ello se incorporó a la biomolécula un grupo ditiocarbamato capaz de coordinar al metal. La marcación fue realizada mediante sustitución de ligandos, obteniéndose una única especie con pureza radioquímica superior al 90 por cientp, la que se mantuvo durante al menos 4 hs. La caracterización fisicoquímica y biológica muestra que el complejo 99mTc(V)-nitruro(GLU-DTC)2 es un compuesto estable y altamente hidrofílico, aunque su unión a proteínas plasmáticas es mayor a la esperada, hecho que justificaría la alta actividad retenida en sangre y en hígado durante la evaluación biológica en ratones CD1 normales. Estos resultados indican que la marcación con 99mTc de este derivado de glucosa produce una alteración significativa de su comportamiento biológico.

The preparation of 99mTc-labeled glucose derivatives is of great interest to evaluate the in vivo glucose uptake in nuclear oncology and cardiology. This paper presents the labelling of a glucose analogue (GLU-DTC) through the formation of a Tc(V)-nitride symmetrical complex. For this purpose, a dithiocarbamate group was incorporated to the biomolecule, in order to coordinate the metal. The labelling reaction was carried out by substitution yielding a single complex with radiochemical purity above 90 percent. This complex was stable for at least 4 hours. The physicochemical and biological characterization shows that the 99mTc(V)-nitride(GLU-DTC)2 complex is a stable and highly hydrophilic compound, although its plasma protein binding is greater than expected, a fact which justifies the high activity retained in blood and liver during the biological evaluation in normal CD1 mice. These results indicate that 99mTc labelling of this glucose derivate alters significantly its biological behaviour.

Conformational analysis of phorboxazole bis-oxazole oxane fragment analogs by NMR spectroscopy and molecular modeling simulations.

We present a detailed conformational study of a simplified synthetic analog of the bis-oxazole oxane fragment found in the cytostatic agents phorboxazole A and B based on results from NMR spectroscopy and molecular modeling simulations. Complete 1H and 13C resonance assignments for the bis-oxazole oxane system were carried out through the use of COSY, HSQC, HMBC, TOCSY, and HSQC-TOCSY experiments, and its conformational preferences in solution were investigated by analysis of 3J(HH) coupling constants and NOE enhancements obtained from 1D and 2D NOESY experiments. In order to solve inconsistencies from our preliminary structural studies, simulated annealing studies were performed to thoroughly sample the phase space available to the molecule. Our results reveal that the six-membered oxane ring, which constitutes the most important moiety regarding the three-dimensional (3D) structure and flexibility of the analog, exists in rapid equilibrium between its two accessible chair conformers in an approximate ratio of 70:30. The information gathered from these studies will be of critical importance in our efforts to prepare novel compounds with phorboxazole-like structure and activity.