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.

Synthesis of Cyclotetrapeptides Analogues to Natural Products as Herbicides.

The synthesis of cyclotetrapeptides analogues of the natural products tentoxin and versicotide D was achieved in good yield by solid phase peptide synthesis (SPPS) of their linear precursors and solution phase cyclization. All the cyclopeptides and several open precursors were evaluated as herbicides. Five cyclopeptides and five lineal peptides showed a significant inhibition (>70%) of Ryegrass seed's radicle growth at 67 µg/mL. The evaluation at lower concentrations (4−11 µM) indicates two cyclopeptides analogs of tentoxin, which present one (N-Methyl-d-Phe), and two N-MeAA (N-Methyl-Ala and N-Methyl-Phe), respectively, as the most active of them, showing remarkable phytotoxic activity. In two cases, the open precursors are as active as their corresponding cyclopeptide. However, many linear peptides are inactive and their cyclization derivatives showed herbicidal activity. In addition, two cyclopeptide analogues of versicotide D showed more improved activity than the natural product. The results indicate that the peptide sequence, the amino acid stereochemistry and the presence of N-methyl group have important influence on the phytotoxic activity. Moreover, several compounds could be considered as lead candidates in the development of bioherbicides.

Synthesis and antiplasmodial assessment of nitazoxanide and analogs as new antimalarial candidates.

During the last years, the progression to control malaria disease seems to be slowed and WHO (World Health Organization) reported a modeling analysis with the prediction of the increase in malaria morbidity and mortality in sub-Saharan Africa during the COVID-19 pandemic. A rapid way to the discovery of new drugs could be carried out by performing investigations to identify drugs based on repurposing of "old" drugs. The 5-nitrothiazole drug, Nitazoxanide was shown to be active against intestinal protozoa, human helminths, anaerobic bacteria, viruses, etc. In this work, Nitazoxanide and analogs were prepared using two methodologies and evaluated against P. falciparum 3D7. A bithiazole analog, showed attractive inhibitory activity with an EC50 value of 5.9 µM, low propensity to show toxic effect against HepG2 cells at 25 µM, and no cross-resistance with standard antimalarials.

Three Methods for Peptide Cyclization Via Lactamization.

Lactamization is the key step in the synthesis of many compounds with macrocyclic structure. As the interest for these types of molecules grows in various fields such as drug discovery and nanomaterials, different methodologies to access them are being developed. Three different strategies to obtain cyclic peptides via lactamization are described in this chapter: solution-phase macrocyclization following solid-phase peptide synthesis (SPPS) of the linear precursor, SPPS and on-resin cyclization on the 2-chlorotrityl chloride (2-CTC) resin, and SPPS and on-resin cyclization by native chemical ligation on the amino-PEGA resin.

First total synthesis of versicotide A, B and C.

The syntheses of versicotides A-C, natural products containing anthranilic acid and NMe-Ala, were achieved by solid phase peptide synthesis on 2-chlorotrityl resin followed by solution phase macrocyclization. Using an oxyma additive, the difficult coupling reactions to the deactivated aromatic amine of o-aminobenzoic acid, were performed in high yield, avoiding anthranilic rearrangements or side reactions.

On-resin synthesis of cyclic peptides via tandem N-to-S acyl migration and intramolecular thiol additive-free native chemical ligation.

On-resin intramolecular native chemical ligation (NCL) assisted by N-ethylcysteine using Fmoc/SPPS to obtain cyclic peptides is described. N-terminal cysteine-containing peptides were subjected to NCL conditions leading to cyclization-cleavage reactions and consecutive S → N shift, rendering cyclic peptides in good yields and purities. The compounds were evaluated against P. falciparum 3D7.

Synthesis, Profiling, and in Vivo Evaluation of Cyclopeptides Containing N-Methyl Amino Acids as Antiplasmodial Agents.

Malaria is a major tropical disease where important needs are to mitigate symptoms and to prevent the establishment of infection. Cyclopeptides containing N-methyl amino acids with in vitro activity against erythrocytic forms as well as liver stage are presented. The synthesis, parasitological characterization, physicochemical properties, in vivo evaluation, and mice pharmacokinetics are described.

Synthesis of Cyclic Peptides as Potential Anti-Malarials.

The results from the synthesis of peptides by Fmoc/SPPS on a 2-CTC resin and then lactamization in solution or solid phase for the preparation of cyclopeptides are presented. Both procedures allow the synthesis of the desired compounds in good to very good yield and with high cyclization efficiency for on-resin macrocyclization. In addition, the activities of the corresponding cyclopeptides against the chloroquine-resistant K1 strain of Plasmodium falciparum were evaluated. Cyclo-Cys(Trt)-Gly-Thr( tBu)-Gly-Cys(Trt)-Gly showed potent in vitro and selective activity against this parasite, EC50 = 28 nM.

In vitro activity and mode of action of distamycin analogues against African trypanosomes.

Distamycin, a natural polyamide containing three heterocycle rings with a polar end, has inspired several groups to prepare synthetic analogues, which proved to have anti-trypanosomal and anti-tumoral activity. We describe the synthesis of bi and tri thiazoles amides that harbor different substitutions at their ends and the evaluation of their anti-Trypanosoma brucei activity. The most active compound 10b showed better biological activity (EC50 310 nM and selectivity index 16) than the control drug nifurtimox (EC50 15 µM and selectivity index 10). Studies on the mode of action show that the parasiticidal activity of 10b originates from disruption of lysosomal homeostasis, which is followed by release of redox active iron, an increase in oxidizing species and collapse of cell membrane integrity. In this respect, our study suggests that non-charged lipophylic distamycins destabilize cell membranes.

Chemoselective and Sequential Palladium-Catalyzed Couplings for the Generation of Stilbene Libraries via Immobilized Substrates.

A versatile palladium-catalyzed tandem synthetic sequence to afford E-stilbenes libraries has been developed. Excellent regio- and stereocontrol have been achieved by means of the sequence of Hiyama and Heck cross-couplings. Undesirable homocoupling byproducts were avoided employing immobilized substrates.

Macrocycles as potential therapeutic agents in neglected diseases.

Macrocycles possess desirable properties that make them promising candidates for the discovery of novel drugs. They present structural features to favor bioactive conformations, selectivity to the receptors, cell permeability and metabolic stability. More effective and nontoxic drugs to cure human African trypanosomiasis, Leishmaniasis and Chagas disease are needed, especially because resistance has been detected. Therefore, major efforts should be made for investigation in new bioactive compounds exhibiting different mechanisms of action. Macrocycles might fulfill the expectations for the development of new drugs to treat those diseases. In the current review, we focus on macrocycles exhibiting biological activities as antitrypanosomal and/or antileishmanial. The isolation, synthetic and biological studies of this class of compounds published from 2005 to 2014 are summarized.

Synthesis of a Microcystis aeruginosa predicted metabolite with antimalarial activity.

The synthesis of a Microcystis aeruginosa predicted metabolite analog of aerucyclamide B was performed. This hexacyclopeptide was obtained from three heterocyclic building blocks by a convergent macrocycle-assembly methodology. The compound exhibited good in vitro antiplasmodial activity (IC(50): 0.18 µM, K1, cholorquine resistant strain).

Thiazole and oxazole alkaloids: isolation and synthesis.

Thiazoles, oxazole and their corresponding reduced derivatives, thiazolines and oxazolines, are found in marine sources exhibiting significant biological activities. The isolation, synthetic, and biological studies of these natural products, covering literature from January 2007 to June 2010, are summarized.

Toward the Total Synthesis of Scleritodermin A: Preparation of the C(1)-N(15) Fragment.

The synthesis of the C(1)-N(15) fragment of the marine natural product Scleritodermin A has been accomplished through a short and stereocontrolled sequence. Highlights of this route include the synthesis of the novel ACT fragment and the formation of the alpha-keto amide linkage by the use of a highly activated alpha, beta-ketonitrile.

[Individual and ecological factors related to the geographical variability of psychological distress among small areas: a multilevel analysis in Catalonia, Spain]. / Factores individuales y del entorno asociados a la variabilidad geográfica de los trastornos psicológicos entre areas pequeñas: un análisis multinivel.

BACKGROUND: To know the geographic distribution of the prevalence of psychological distress is important for mental health services planning. This study is aimed at identifying the individual factors and those related to the area of residence which may explain the geographic variability of psychological distress (by healthcare districts) in Catalonia. METHODS: The data was taken from the 1994 Catalonian Health Survey and from the 1996 Catalonia population statistics. The prevalence of psychological distress is estimated by age and sex and by healthcare district. In a two-level logic regression model, a study is made of the relationship between the individual variables (first level: health survey n = 12,455) and those of the area of residence (second level: the healthcare district, n = 46) to the geographic distribution of the prevalence of psychological distress. RESULTS: The significant variables at individual level are in men: age (45-64 years OR: 0.63 y > 64 years OR: 0.22), working status (no work OR: 1.60), number of chronic diseases (CD) (CD = 1 OR: 1.75 CD = 2 OR: 2.06 CD = 3-5 OR: 3.36 and CD > 5 OR: 8.9). In women: age (25-44 years OR: 0.63 45-64 years OR: 0.45 and > 64 years OR: 0.32), working status (no work OR: 1.30), number of chronic diseases (CD = 1 OR: 1.75 CD = 2 OR: 2.44 CD = 3-5 OR: 4.09 and CD > 5 OR: 11.14), and also the kind of parental household in women (single-parental OR: 1.42). The variables at the level of the area of residence are in migration (men OR: 1.55 and women OR: 1.68) and unemployment (men OR: 1.07 and women OR: 1.06). CONCLUSIONS: The individual factors do not suffice to explain the geographical variability of the prevalence of psychological distress, but the characteristics of the area of residence are also important.

Factores individuales y del entorno asociados a la variabilidad geográfica de los trastornos psicológicos entre áreas pequeñas: un análisis multinivel / Individual and ecological factors related to the geographical variability of psychological distress among small areas: a multilevel analysis in Catalonia, Spain

Fundamento: Para planificar las necesidades de servicios sanitarioses fundamental conocer la distribución de la morbilidad portrastornos psicológicos en el territorio así como los factores que ladeterminan. El objetivo es identificar los factores que pueden explicarla variabilidad geográfica de estos trastornos en Cataluña.Métodos: Los datos proceden de la Encuesta de Salud de l994 yde la estadística de población de l996 para Cataluña. Se estima la prevalenciade trastornos psicológicos por edad y sexo y por sector sanitario.En un modelo de regresión logística a dos niveles se estudia laasociación entre las variables individuales (primer nivel: Encuestade Salud n=12.455) y las de la zona de residencia (segundo nivel: elsector sanitario, n= 46) con la prevalencia de trastornos psicológicos.Resultados: Las variables individuales que influyen en las diferenciasentre sectores son: la edad (45-64 años OR:0,63 y >64 años:OR:0,22), la situación laboral (no trabaja OR:1,60) y el número detrastornos crónicos (TC) (TC=1 OR: 1,75 TC=2 OR: 2,06 TC=3-5OR:3,36 y TC>5 OR: 8,9) en hombres. En las mujeres, además deestas variables (edad 25-44 años OR: 0,63 45-64 años OR:0,45 y >64años OR: 0,32 la situación laboral no trabaja OR:1,30 y el número detrastornos crónicos (TC) TC=1 OR: 1,75 TC=2 OR: 2,44 TC=3-5OR:4,09 y TC>5 OR: 11,14), influye el tipo de hogar (monoparentalOR: 1,42). Las variables a nivel de la zona de residencia son la proporciónde inmigración (hombres OR:1,55 y mujeres OR:1,68) y dedesempleo (hombres OR:1,07 y mujeres OR:1,06).Conclusiones: Los factores individuales no son suficientes paraexplicar la variabilidad geográfica de la prevalencia de los trastornospsicológicos, ya que también influyen las características de la zonade residencia

Background: To know the geographic distribution of the prevalenceof psychological distress is important for mental healthservices planning. This study is aimed at identifying the individualfactors and those related to the area of residence which may explainthe geographic variability of psychological distress (by healthcaredistricts) in Catalonia.Methods: The data was taken from the 1994 Catalonian HealthSurvey and from the 1996 Catalonia population statistics. The prevalenceof psychological distress is estimated by age and sex and byhealthcare district. In a two-level logic regression model, a study ismade of the relationship between the individual variables (first level:health survey n=12,455) and those of the area of residence (secondlevel: the healthcare district, n=46) to the geographic distribution ofthe prevalence of psychological distress.Results: The significant variables at individual level are in men:age (45-64 years OR:0,63 y >64 years OR: 0,22), working status (nowork OR:1,60) , number of chronic diseases (CD) (CD=1 OR: 1,75CD=2 OR: 2,06 CD=3-5 OR:3,36 and CD>5 OR: 8,9). In women:age (25-44 years OR: 0,63 45-64 years OR:0,45 and >64 years OR:0,32), working status (no work OR:1,30), number of chronic diseases(CD=1 OR: 1,75 CD=2 OR: 2,44 CD=3-5 OR:4,09 and CD>5OR: 11,14), and also the kind of parental household in women (single-parental OR: 1,42). The variables at the level of the area of residenceare inmigration (men OR:1,55 and women OR:1,68) andunemployment (men OR:1,07 and women OR:1,06).Conclusions: The individual factors do not suffice to explain thegeographical variability of the prevalence of psychological distress,but the characteristics of the area of residence are also important

Synthesis and biological evaluation of simplified mycothiazole analogues.

Thiazoline and oxazoline analogues of the natural product mycothiazole were synthesized from a common intermediate and evaluated in vitro against HCT-15 colon cancer cells and L(4) larvae of nematode Nippostrongylus brasiliensis. The nature of the heterocyclic moiety seems to modulate the cytotoxic or anthelmintic activity.