Ітеративне використання великих хімічних просторів у пошуку лікарських засобів

Aim. To demonstrate the advantages of large-scale virtual libraries generated using chemical protocols previously validated in primary steps of the drug discovery process.Results and discussion. Two validated parallel chemistry protocols reported earlier were used to create the chemical space. It was then sampled based on diversity metric, and the sample was subjected to the virtual screening on BRD4 target. Hits of virtual screening were synthesized and tested in the thermal shift assay.Experimental part. The chemical space was generated using commercially available building blocks and synthetic protocols suitable for parallel chemistry and previously reported. After narrowing it down, using MedChem filters, the resulting sub-space was clustered based on diversity metrics. Centroids of the clusters were put to the virtual screening against the BRD4 active center. 29 Hits from the docking were synthesized and subjected to the thermal shift assay with BRD4, and 2 compounds showed noticeable dTm.Conclusions. A combination of cheminformatics and molecular docking was applied to find novel potential binders for BRD4 from a large chemical space. The selected set of predicted molecules was synthesized with a 72 % success rate and tested in a thermal shift assay to reveal a 6 % hit rate. The selection can be performed iteratively to fast support of the drug discovery.Мета. Продемонструвати переваги віртуальних бібліотек великого розміру, згенерованих за валідованими раніше хімічними протоколами, на перших етапах пошуку лікарських засобів.Результати та їх обговорення. На основі двох валідованих методів синтезу, придатних для паралельної хімії, описаних раніше, було створено хімічний простір. На основі різноманітності з одержаної віртуальної бібліотеки зроблено вибірку, яку було піддано віртуальному скринінгу щодо активного центру білка BRD4. Хіти віртуального скринінгу було синтезовано й перевірено за допомогою диференційної сканувальної калориметрії.Експериментальна частина. На основі комерційно доступних вихідних реагентів та раніше репрезентованих синтетичних протоколів, придатних для паралельної хімії, згенеровано хімічний простір. Простір було зменшено за рахунок застосування медхімічних фільтрів; результатний підпростір було кластеризовано за критерієм різноманітності. Центроїди кластерів було піддано молекулярному докінгу щодо активного центру білка BRD4. Базуючись на результатах проведеного докінгу, синтезовано 29 хітів, які було піддано диференційній сканувальній калориметрії з білком BRD4; з цим 2 сполуки продемонстрували помітний зсув точки топлення.Висновки. Для пошуку нових потенційних лігандів BRD4 у великому хімічному просторі було застосовано комбінацію хемоінформатики і молекулярного докінгу. Набір молекул, що мали високу передбачену активність, було синтезовано з успішністю 72 %. Серед синтезованих сполук виявлено первинні хіти (6 % сполук). Подібний процес можна повторювати ітеративно для швидкої підтримки розроблення ліків

Towards in vivo photomediated delivery of anticancer peptides: Insights from pharmacokinetic and -dynamic data

An in vivo study of a photoswitchable cytotoxic peptide LMB040 has been undertaken on a chemically induced hepatocellular carcinoma model in immunocompetent rats. We analysed the pharmacokinetic profile of the less toxic photoform (“ring-closed” dithienylethene) of the compound in tumors, plasma, and healthy liver. Accordingly, the peptide can reach a tumor concentration sufficiently high to exert a cytotoxic effect upon photoconversion into the more active (“ring-open”) photoform. Tissue morphology, histology, redox state of the liver, and hepatic biochemical parameters in blood serum were analysed upon treatment with (i) the less active photoform, (ii) the in vivo light-activated alternative photoform, and (iii) compared with a reference chemotherapeutic 5-fluorouracil. We found that application of the less toxic form followed by a delayed in vivo photoconversion into the more toxic ring-open form of LMB040 led to a higher overall survival of the animals, and signs of enhanced immune response were observed compared to the untreated animals

A prospective compound screening contest identified broader inhibitors for Sirtuin 1

Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified

Further validation of strecker-type α-aminonitriles as a new class of potent human carbonic anhydrase II inhibitors: hit expansion within the public domain using differential scanning fluorimetry leads to chemotype refinement

Testing of an expanded, 800-compound set of analogues of the earlier described Strecker-type α-aminonitriles (selected from publicly available Enamine Ltd. Screening Collection) in thermal shift assay against bovine carbonic anhydrase (bCA) led to further validation of this new class of inhibitors and identification a new, refined chemotype represented by inhibitors with 10-improved potency

Screening of benzenesulfonamide in combination with chemically diverse fragments against carbonic anhydrase by differential scanning fluorimetry

The differential scanning fluorimetry (DSF) screening of 5.692 fragments in combination with benzenesulfonamide (BSA) against bovine carbonic anhydrase (bCA) delivered >100 hits that either caused, on their own, a significant thermal shift (ΔTm, °C) in the protein melting temperature or significantly influenced the thermal shift observed for BSA alone. Three hits based on 1,2,3-triazole moiety represent the periphery of the recently reported potent inhibitors of hCA II, IX and XII which were efficacious in vivo. Such a re-discovery of suitable BSA periphery essentially validates the new fragment-based approach to the discovery of future CAIs. Structures of other validated fragment hits are reported

Discovery of Strecker-type α-aminonitriles as a new class of human carbonic anhydrase inhibitors using differential scanning fluorimetry

<p>A new type of carbonic anhydrase inhibitors was identified via differential scanning fluorimetry (DSF) screening. The compounds displayed interesting inhibition profile against human carbonic anhydrase isoforms I, II, IX and XII with an obvious selectivity displayed by one compound toward carbonic anhydrase (CA) IX, an established anti-cancer target. A hypothetical mechanism of inhibitory action by the Strecker-type α-aminonitriles has been proposed.</p

Pros and cons of virtual screening based on public “Big Data”: In silico mining for new bromodomain inhibitors

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