Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.

In vitro screening of large compound libraries with automated high-throughput screening is expensive and time-consuming and requires dedicated infrastructures. Conversely, the selection of DNA-encoded chemical libraries (DECLs) can be rapidly performed with routine equipment available in most laboratories. In this study, we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity-based selection of the DELopen library (open access for academics), containing 4.2 billion compounds. The identified inhibitors were peptide-like compounds containing an N-terminal electrophilic group able to form a covalent bond with the nucleophilic Cys145 of Mpro, as confirmed by x-ray crystallography. This DECL selection campaign enabled the discovery of the unoptimized compound SLL11 (IC50 = 30 nM), proving that the rapid exploration of large chemical spaces enabled by DECL technology allows for the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. As demonstrated further by x-ray crystallography, SLL11 was found to adopt a highly unique U-shaped binding conformation, which allows the N-terminal electrophilic group to loop back to the S1' subsite while the C-terminal amino acid sits in the S1 subsite. MP1, a close analog of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50 = 2.3 µM) cell lines. As peptide-like compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds will be explored in the future to improve their antiviral activity.

Heat capacity of cytisine - the drug for smoking cessation.

The characterization of cytisine (CYT) and its blends with poly(lactic acid) was performed using thermal analysis, elemental analysis, infrared spectroscopy, and powder X-ray diffractometry. The heat capacities, total enthalpy, and phase transitions of CYT were established from 1.8 to 448.15 K (-271.35 - 175 °C) by advanced thermal analysis. Data were obtained using a Quantum Design Physical Property Measurement System (PPMS) and a differential scanning calorimetry (DSC). The low-temperature heat capacity of the crystalline CYT in the range of 1.8 to 300 K (-271.35 - 26.86 °C) was measured by PPMS and fitted to a theoretical model in the low temperature region below 11 K (-262.15 °C), to orthogonal polynomials in the middle range 5 K < T < 60 K (-268.15 °C < t < -213.15 °C) and to the Debye and Einstein functions in the high range of temperature above 60 K (-213.15 °C). The liquid heat capacity was calculated based on the approximated linear regression data above the molten state of the experimental heat capacity of CYT obtained by the standard DSC measurements, and it was expressed as Cpliquid = 0.0838T + 346.78 J·K-1·mol-1. The calculated heat capacity in the solid state was extended to a higher temperature and was used, together with liquid heat capacity, as the reference baselines for the advanced thermal analysis of CYT. The PPMS and DSC/TMDSC methods are complementary methods for thermal analysis of cytisine. The PPMS method allowed determination of the equilibrium heat capacity in the solid state, which together with the equilibrium heat capacity in the liquid state allowed to analyze of the experimental apparent heat capacity of cytisine obtained based on DSC. The melting temperature and the total heat of fusion of crystalline material were established as 431.8 K (158.65 °C) and 26.5 kJ·mol-1, respectively. The solid and liquid heat capacities and transition parameters of CYT were applied to calculate total enthalpies for fully amorphous and crystalline states. Analyses of DSC and X-ray confirmed the presence of the solid-solid transition linking with not so far described a polymorphism phenomenon of CYT. Based on the thermogravimetric analysis the temperature of degradation of CYT was determined as 460.5 K (187.35 °C). Also, a preliminary thermal analysis of the blends of cytisine and poly(lactic acid) as a new candidate for drug delivery system was presented.

Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies.

The antiviral component of Paxlovid, nirmatrelvir (NIR), forms a covalent bond with Cys145 of SARS-CoV-2 nsp5. To explore NIR resistance we designed mutations to impair binding of NIR over substrate. Using 12 Omicron (BA.1) and WA.1 SARS-CoV-2 replicons, cell-based complementation and enzymatic assays, we showed that in both strains, E166V imparted high NIR resistance (∼55-fold), with major decrease in WA1 replicon fitness (∼20-fold), but not BA.1 (∼2-fold). WA1 replicon fitness was restored by L50F. These differences may contribute to a potentially lower barrier to resistance in Omicron than WA1. E166V is rare in untreated patients, albeit more prevalent in paxlovid-treated EPIC-HR clinical trial patients. Importantly, NIR-resistant replicons with E166V or E166V/L50F remained susceptible to a) the flexible GC376, and b) PF-00835231, which forms additional interactions. Molecular dynamics simulations show steric clashes between the rigid and bulky NIR t-butyl and ß-branched V166 distancing the NIR warhead from its Cys145 target. In contrast, GC376, through "wiggling and jiggling" accommodates V166 and still covalently binds Cys145. PF-00835231 uses its strategically positioned methoxy-indole to form a ß-sheet and overcome E166V. Drug design based on strategic flexibility and main chain-targeting may help develop second-generation nsp5-targeting antivirals efficient against NIR-resistant viruses.

Application of advanced thermal analysis for characterization of crystalline and amorphous phases of carvedilol.

The thermal behaviour of crystalline and amorphous carvedilol (CAR) phases was studied by advanced thermal analysis using Quantum Design Physical Property Measurement System and Differential Scanning Calorimetry. Theoretical functions describing crystalline carvedilol heat capacity at low temperatures and the Debye-Einstein function for high temperatures were obtained. Based on the experimental heat capacity values, solid and liquid baselines were established, and the state functions (H, S, G) for solid and liquid states were calculated. A comprehensive characterization of melting and glass transition processes was obtained. CAR is easily amorphizable by cooling the liquid. The residual entropy, which quantifies the extent of frozen-in disorder in the amorphous solid, for glassy CAR was estimated as 51 J·mol-1·K-1. The Kauzmann temperature (TK) was estimated based on enthalpy and entropy. Molecular motions in the amorphous phase were also studied. The activation energy for structural relaxation (Ea = 539 kJ·mol-1) and fragility parameter (m = 91) were obtained from the non-isothermal physical ageing. The isothermal physical ageing kinetics of amorphous CAR was studied by applying Kohlrausch-Williams-Watts (KWW) model. The mean molecular relaxation time constant (τKWW = 117 min) and relaxation constant (ßKWW = 0.33) were obtained. CAR was classified as a fragile glass-former. Furthermore, τKWW constant for samples aged at 303.15 K is very low, thus, the physical ageing will occur during the short- and long-term storage of amorphous CAR, potentially changing its physicochemical properties during the ageing process. However, the results of molecular mobility studies (high molecular motions) show that the relationship between molecular motions in a glassy solid and its tendency to crystallization does not seem to follow an expected pattern, i.e., no crystallization occurred by thermal treatment of glassy, supercooled liquid and liquid phases of CAR as one would expect. Modern calorimetry and quantitative thermal analysis provided the fundamental kinetic and thermodynamic information about the crystalline and amorphous states of CAR.