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Antithrombotic agents based on factor XIIa inhibitors can become a new class of drugs to manage conditions associated with thrombosis. Herein, we report identification of two novel classes of factor XIIa inhibitors. The first one is triazolopyrimidine derivatives designed on the basis of the literature aminotriazole hit and identified using virtual screening of the focused library. The second class is a spirocyclic furo[3,4-c]pyrrole derivatives identified by virtual screening of a large chemical library of drug-like compounds performed in a previous study but confirmed in vitro here. In both cases, the prediction of inhibitory activity is based on the score of the SOL docking program, which uses the MMFF94 force field to calculate the binding energy. For the best ligands selected in virtual screening of the large chemical library, postprocessing with the PM7 semiempirical quantum-chemical method was used to calculate the enthalpy of protein-ligand binding to prioritize 16 compounds for testing in enzymatic assay, and one of them demonstrated micromolar activity. For triazolopyrimidine library, 21 compounds were prioritized for the testing based on docking scores, and visual inspection of docking poses. Of these, 4 compounds showed inhibition of factor XIIa at 30 μM.

Docking and quantum-chemical methods have been used for screening of drug-like compounds from the own database of the Voronezh State University to find inhibitors the SARS-CoV-2 main protease, an important enzyme of the coronavirus responsible for the COVID-19 pandemic. Using the SOL program more than 42000 3D molecular structures were docked into the active site of the main protease, and more than 1000 ligands with most negative values of the SOL score were selected for further processing. For all these top ligands, the protein-ligand binding enthalpy has been calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. 20 ligands with the most negative SOL scores and the most negative binding enthalpies have been selected for further experimental testing. The latter has been made by measurements of the inhibitory activity against the main protease and suppression of SARS-CoV-2 replication in a cell culture. The inhibitory activity \of the compounds was determined using a synthetic fluorescently labeled peptide substrate including the proteolysis site of the main protease. The antiviral activity was tested against SARS-CoV-2 virus in the Vero cell culture. Eight compounds showed inhibitory activity against the main protease of SARS-CoV-2 in the submicromolar and micromolar ranges of the IC50 values. Three compounds suppressed coronavirus replication in the cell culture at the micromolar range of EC50 values and had low cytotoxicity. The found chemically diverse inhibitors can be used for optimization in order to obtain a leader compound, the basis of new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus.Byl proveden virtual'nyĭ skrining s ispol'zovaniem dokinga i metodov kvantovoĭ khimii lekarstvenno-podobnykh soedineniĭ bazy dannykh Voronezhskogo universiteta protiv glavnoĭ proteazy koronavirusa SARS-CoV-2, vyzvavshego pandemiiu COVID-19. Snachala byl vypolnen doking bolee 42 tysiach trekhmernykh struktur ligandov s pomoshch'iu programmy SOL. Dalee, na osnovanii otsenki svobodnoĭ énergii sviazyvaniia, vychisliaemoĭ s pomoshch'iu programmy dokinga SOL, bylo otobrano bolee tysiachi ligandov dlia vychisleniia éntal'pii sviazyvaniia belok-ligand s pomoshch'iu kvantovo-khimicheskogo poluémpiricheskogo metoda PM7 s uchetom rastvoritelia (vody) v neiavnoĭ modeli COSMO. V rezul'tate dlia éksperimental'nogo testirovaniia bylo otobrano 20 ligandov, pokazavshikh luchshie znacheniia funktsii otsenki svobodnoĭ énergii sviazyvaniia, vychislennoĭ programmoĭ SOL, i éntal'pii sviazyvaniia, vychislennoĭ kvantovo-khimicheskim metodom. V khode éksperimental'nogo testirovaniia izmeriali ingibiruiushchuiu aktivnost' soedineniĭ protiv glavnoĭ proteazy SARS-CoV-2 i podavlenie replikatsii étogo koronavirusa v kul'ture kletok. Ingibirovanie opredeliali s ispol'zovaniem peptidnogo substrata s fluorestsentnoĭ metkoĭ, vkliuchaiushcheĭ saĭt proteoliza glavnoĭ proteazy. Antivirusnuiu aktivnost' testirovali v kul'ture kletok Vero. V rezul'tate éksperimental'nogo testirovaniia 8 molekul pokazali aktivnost' po ingibirovaniiu glavnoĭ proteazy SARS-CoV-2 v submikromoliarnom i mikromoliarnom diapazonakh IC50, i 3 iz nikh podavliali replikatsiiu SARS-CoV-2 v kul'ture kletok na urovne mikromoliarnykh znacheniĭ EC50 i imeli nizkuiu tsitotoksichnost'. Naĭdennye khimicheski raznoobraznye ingibitory mogut byt' ispol'zovany dlia optimizatsii s tsel'iu polucheniia soedineniia-lidera — osnovy novykh antivirusnykh preparatov priamogo deĭstviia na koronavirus SARS-CoV-2.

The quasi-docking procedure with a combination of the classical MMFF94 force field and the PM7 quantum-chemical semiempirical method is applied for docking ligands into proteins with which they are co-crystallized. Main peculiarities of the test set of protein-ligand complexes are: a high resolution of the structures obtained from Protein Data Bank, no missed residues or atoms in the active sites of the proteins and the availability of experimentally measured protein-ligand binding free energies including separate contributions of the enthalpy and entropy terms. The goal of this work is to determine positioning accuracy of the quasi-docking by a comparison of best docked ligand poses with the respective ligand poses in the crystallized protein-ligand complexes, to estimate values of the protein-ligand binding enthalpy for the best ligand poses and to compare these values with the measured ones. The best ligand pose corresponds to the global energy minimum of the protein-ligand complex calculated with PM7 and with the COSMO continuum solvent model either in the old parameterization, COSMO, or in the recent one, COSMO2, in the quasi-docking procedure. It is found that the docking positioning accuracy is better in the case of PM7 with COSMO energy calculations than with COSMO2 calculations. The correlation between values of the calculated and experimentally measured binding enthalpy is also better, R = 0.74, for the PM7+COSMO energy.

Coagulation factor Xa and factor XIa are proven to be convenient and crucial protein targets for treatment for thrombotic disorders and thereby their inhibitors can serve as effective anticoagulant drugs. In the present work, we focused on the structure&ndash, activity relationships of derivatives of pyrrolo[3,2,1-ij]quinolin-2(1H)-one and an evaluation of their activity against factor Xa and factor XIa. For this, docking-guided synthesis of nine compounds based on pyrrolo[3,2,1-ij]quinolin-2(1H)-one was carried out. For the synthesis of new hybrid hydropyrrolo[3,2,1-ij]quinolin-2(1H)-one derivatives, we used convenient structural modification of both the tetrahydro- and dihydroquinoline moiety by varying the substituents at the C6,8,9 positions. In vitro testing revealed that four derivatives were able to inhibit both coagulation factors and three compounds were selective factor XIa inhibitors. An IC50 value of 3.68 &mu, M for was found for the best factor Xa inhibitor and 2 &mu, M for the best factor XIa inhibitor.

The Auto-Oil Programmes (1993–1996, 1997–2000) were considered a new model on how to solve environmental issue by close cooperation between the European Commission and industry, in particular the automobile and the oil industry. These programmes, in their larger context, are interesting cases to analyse the complexity of emission regulation. These cases are described in some details in this paper in order to distinguish patterns in the type of policy-making that have emerged over time. The main conclusion points to high complexity created by two types of tensions. One tension is that between the drivers of environmental policy: should it be target-based or should environmental policy serve the development of “state of the art technology”? The second tension relates to the question of the manageability of this policy area: should technical experts provide the main input for policy or should all parties that have a stake in this policy area become involved the so-called stakeholder approach? These questions illustrate the dilemmas that face the policy-makers. Different approaches or models can be distinguished over time. This results is a swing back and forth between them, best be described by the metaphor of a pendulum. This idea of shift in policy-making over time complements the existing models of European policy-making, in particular the work on policy-making by participation.