Computational study of novel inhibitory molecule, 1-(4-((2S,3S)-3-amino-2-hydroxy-4-phenylbutyl)piperazin-1-yl)-3-phenylurea, with high potential to competitively block ATP binding to the RNA dependent RNA polymerase of SARS-CoV-2 virus.

For coronaviruses, RNA-dependent RNA polymerase (RdRp) is an essential enzyme that catalyses the replication from RNA template and therefore remains an attractive therapeutic target for anti-COVID drug discovery. In the present study, we performed a comprehensive in silico screening for 16,776 potential molecules from recently established drug libraries based on two important pharmacophores (3-amino-4-phenylbutan-2-ol and piperazine). Based on initial assessment, 4042 molecules were obtained suitable as drug candidates, which were following Lipinski's rule. Molecular docking implemented for the analysis of molecular interactions narrowed this number of compounds down to 19. Subsequent to screening filtering criteria and considering the critical parameters viz. docking score and MM-GBSA binding free energy, 1-(4-((2S,3S)-3-amino-2-hydroxy-4-phenylbutyl)piperazin-1-yl)-3-phenylurea (compound 1) was accomplished to score highest in comparison to the remaining 18 shortlisted drug candidates. Notably, compound 1 displayed higher docking score (-8.069 kcal/mol) and MM-GBSA binding free energy (-49.56 kcal/mol) than the control drug, remdesivir triphosphate, the active form of remdesivir as well as adenosine triphosphate. Furthermore, a molecular dynamics simulation was carried out (100 ns), which substantiated the candidacy of compound 1 as better inhibitor. Overall, our systematic in silico study predicts the potential of compound 1 to exhibit a more favourable specific activity than remdesivir triphosphate. Hence, we suggest compound 1 as a novel potential drug candidate, which should be considered for further exploration and validation of its potential against SARS-CoV-2 in wet lab experimental studies.Communicated by Ramasawamy H. Sarma.

Synthesis of novel indolo[3,2-c]isoquinoline derivatives bearing pyrimidine, piperazine rings and their biological evaluation and docking studies against COVID-19 virus main protease.

A series of hybrid indolo[3,2-c]isoquinoline (δ-carboline) analogs incorporating two pyrimidine and piperizine ring frameworks were synthesized. Intending biological activities and SAR we propose replacements of fluorine, methyl and methoxy of synthetic compounds for noteworthy antimicrobial, antioxidant, anticancer and anti-tuberculosis activities. Among these compounds 3a, 4a and 5e were progressively strong against E. coli and K. pneumonia. Whereas, compounds 4a, 5a and 6a with addition of various functional groups (OCH3, CH3) were excellent against S. aureus and B. subtilis. Compound 5c exhibited strong RSA and dynamic ferrous ion (Fe2+) metal chelating impact with IC50 of 7.88 ± 0.93 and 4.06 ± 0.31 µg/mL, respectively. Compound 5e was considerably cytotoxic against all cancer cells displaying activity better than the standard drug. Compounds 6b and 6e inhibited M. tuberculosis (MIC 1.0 mg/L) considerably. Molecular docking studies indicate that compounds 4d, 5a, 5b, 6b and 6f exhibited good interactions with 6LZE (COVID-19) and 6XFN (SARS-CoV-2) at active sites. The structure of the synthesized compounds were elementally analyzed using IR, 1H, 13C NMR and mass spectral information.

Novel Curcumin Mimics: Design, Synthesis, Biological Properties and Computational Studies of Piperidone-Piperazine Conjugates

3,5-Di[(E)-arylidene]-1-[3-(4-methylpiperazin-1-yl)alkyl]piperidin-4-ones 7 a-k were synthesized through dehydrohalogenation of 1-(2-chloroacyl)piperidin-4-ones 5 a-k with N-methylpiperazine (6). High antiproliferation potencies were observed by most of the synthesized agents against both HCT116 (colon) and MCF7 (breast) cancer cell lines relative to the standard references (sunitinib and 5-fluorouracil). The synthesized agents are of dual activity against topoisomerases I and II alpha however, with higher efficacy against topoisomerase II alpha rather than topoisomerase I. Flow-cytometry cell cycle studies support the observed antiproliferation properties and exhibit the capability of 1-(2-chloroacetyl)-3,5-bis[(E)-4-chlorobenzylidene]piperidin-4-one (5 e) and 3,5-bis[(E)-4-bromobenzylidene]-1-[2-(4-methylpiperazin-1-yl)acetyl]piperidin-4-one (7 g) to arrest the HCT116 cell cycle progression at G1/S and G1 phases, respectively. Noticeable anti-SARS-CoV-2 properties were observed by many synthesized agents. 3,5-Bis[(E)-4-chlorobenzylidene]-1-[3-(4-methylpiperazin-1-yl)propanoyl]piperidin-4-one (7 f) is the most effective anti-SARS-CoV-2 synthesized with high SI. Applicability of the highly effective candidates synthesized as antitumor and anti-SARS-CoV-2 is due to the safety observations against normal (RPE1 and VERO-E6) cells. QSAR models validated internally and externally, support their possibility for optimizing more hits/leads.

Computational study of furosemide-piperazine (FS – PZ) and 2,3,5,6-tetramethylpyrazine (FS-TP) co-crystals

Co-crystals are well-known for their applications in pharmaceutical chemistry. In this current manuscript, we have conducted a DFT analysis of two Co-Crystals of furosemide with piperazine (FS-PZ) and with 2,3,5,6-tetramethylpyrazine (FS-TP). The non-covalent interactions and structural, electronic, topological properties, and solvent effects are investigated in detail. The hyper-conjugative interactions and delocalization of charge are explored along with a molecular electrostatic potential map (MEP) and frontier molecular orbital (FMO) analysis. The Ab initio molecular dynamics studies showed that the co-crystals FS-TP is more stable than FS-PZ. Docking suggested that the co-crystals show biological activity and hence can be a good inhibitor against the absorption of inhibitors. Molecular dynamics (MD) simulations were carried out in three replicates to determine the stability and convergence of SARS-CoV-2 main protease (PDB ID: 6YB7) with FS-PZ and FS-TP co-crystals. We found that the structure of proteins was stable during simulation in ligand-bound conformations.

Comparison of LC-MS and LC-DAD Methods of Detecting Abused Piperazine Designer Drugs.

Recreational use of piperazine designer drugs is a serious threat to human health. These compounds act on the body in a similar fashion to illegal drugs. They induce psychostimulatory effects as well as visual and auditory hallucinations to varying degrees. In many cases of poisoning and deaths, the presence of two or even several psychoactive substances have been demonstrated. Piperazine derivatives are often found in such mixtures and pose a great analytical problem during their identification. Additionally, some piperazine derivatives can be detected in biological material as a result of metabolic changes to related drugs. Therefore, it is necessary to correctly identify these compounds and ensure repeatability of determinations. This article presents a comparison of the methods used to detect abused piperazine designer drugs using liquid chromatography in combination with a diode-array detector (LC-DAD) or mass spectrometer (LC-MS). Each of methods can be used independently for determinations, obtaining reliable results in a short time of analysis. These methods can also complement each other, providing qualitative and quantitative confirmation of results. The proposed methods provide analytical confirmation of poisoning and may be helpful in toxicological diagnostics.

Identification of SARS-CoV-2 Spike Palmitoylation Inhibitors That Results in Release of Attenuated Virus with Reduced Infectivity.

The spike proteins of enveloped viruses are transmembrane glycoproteins that typically undergo post-translational attachment of palmitate on cysteine residues on the cytoplasmic facing tail of the protein. The role of spike protein palmitoylation in virus biogenesis and infectivity is being actively studied as a potential target of novel antivirals. Here, we report that palmitoylation of the first five cysteine residues of the C-terminal cysteine-rich domain of the SARS-CoV-2 S protein are indispensable for infection, and palmitoylation-deficient spike mutants are defective in membrane fusion. The DHHC9 palmitoyltransferase interacts with and palmitoylates the spike protein in the ER and Golgi and knockdown of DHHC9 results in reduced fusion and infection of SARS-CoV-2. Two bis-piperazine backbone-based DHHC9 inhibitors inhibit SARS-CoV-2 S protein palmitoylation and the resulting progeny virion particles released are defective in fusion and infection. This establishes these palmitoyltransferase inhibitors as potential new intervention strategies against SARS-CoV-2.

Novel piperazine based compounds as potential inhibitors for SARS-CoV-2 Protease Enzyme: Synthesis and molecular docking study.

Structurally diverse piperazine-based compounds hybrid with thiadiazole, isatin or with sulfur/nitrogen, functionalities were synthesized. The structures of the new compounds were established based on their spectral data and elemental analysis. The physicochemical, bioactivity scores and pharmacokinetic behavior of all the prepared ligands were evaluated using in silico computational tools. The new piperazine ligands have been screened for their inhibition activity against SARS-CoV-2 protease enzyme using molecular docking analysis. The docking studies showed that all the ligands have been docked with negative dock energy onto the target protease protein. Moreover, Molecular interaction studies revealed that SARS-CoV-2 protease enzyme had strong hydrogen bonding interactions with piperazine ligands. The present in silico study thus, provided some guidance to facilitate drug design targeting the SARS-CoV-2 main protease.