Design and virtual screening of novel fluoroquinolone analogs as effective mutant DNA GyrA inhibitors against urinary tract infection-causing fluoroquinolone resistant Escherichia coli

Bioisosteric replacements of tyrosine kinases inhibitors to make potent and safe chemotherapy against malignant cells

The liver function test is an imperative element in chemotherapy management due to the idiosyncratic reaction of chemotherapy drugs. This study primly aimed to replace the toxic fragments of known protein tyrosine kinases inhibitors (PTKi) to develop safe and effective chemotherapy. All the current PTKi's were docked with the tyrosine kinases and metabolic enzymes to study the affinities on the target. It resulted from most of the PTKi's found higher affinity and efficacy with metabolic enzymes lead the hepatic cells damage. To overcome this limitation of PTKi's, a bioisosteric replacement strategy was achieved and conceptual analogs were designed. Specifically, the Generated pose of the Axitinib molecule showed that axitinib fragments C = C-, -C = O and NH2 produced clashes with active site residues of tyrosine kinases protein and good affinity with metabolic enzyme primes to the liver toxicity. The above said fragments were replaced with various bioisosteric groups and efficacy was measured. The resulting molecule shows improved affinity with tyrosine kinases enzyme and less interactions with metabolic enzyme were imminent molecule for the treatment of malignant cells with outside effects.Communicated by Ramaswamy H. Sarma.

Effect of co-pigments on anthocyanins of Rhododendron arboreum and insights into interaction mechanism

The impact of intermolecular copigmentation between five phenolic acids, two flavonoid and three amino acids with R. arboreum anthocyanins (ANS) and its isolated cyanidin-3-O-monoglycosides were investigated through experimental and theoretical approach. On addition of different copigments, phenolic acid induced strong hyperchromic (0.26-0.55 nm) and bathochromic shift (6.6-14.2 nm). The color intensity and stability of ANS with, storage at 4 °C & 25 °C, sunlight, oxidation and heat were evaluated by chromaticity, anthocyanin content, kinetic and structural simulation analysis. The strongest copigmentation reaction was observed with narningin (NA) and also showed high thermostability and highest half-life i.e. 3.39 h-1.24 h at 90-160 °C. The cyanidin-3-O-monoglycosides were analysed for their copigmentation effect and observations revealed that NA displayed best copigmentation effect to cyanidin-3-O-arabinoside (B) followed by cyanidin-3-O-galactoside (A), and cyanidin-3-O-rhamnoside (C). Additionally, structural simulation and steered molecular dynamics insights NA is the most favourable co-pigment involving π-π stacking and H-bonding.

Pharmacophore-based virtual screening, molecular docking and molecular dynamics simulations study for the identification of LIM kinase-1 inhibitors

LIM kinases (LIMKs) are a family of protein kinases involved in the regulation of actin dynamics. There are two isoforms of LIMKs i.e., LIMK1 and LIMK2. LIMK1 is expressed abundantly in neuronal tissues. LIMK1 plays an essential role in the degradation of dendritic spines, which are important for our higher brain functions, such as memory and learning. The inhibition of LIMK1 improves the size and density of dendritic spines and acts as a protective effect against Alzheimer's disease. In this study, we have adopted ligand-based drug design and molecular modelling methods to identify virtual hits. The pharmacophoric features of PF-00477736 were used to screen the Zinc15 compounds library. The identified hits were then passed through drug-likeliness and PAINS filters. Further, comprehensive docking and rigorous molecular dynamics simulation study afforded three virtual hits viz., ZINC504485634, ZINC16940431 and ZINC1091071. The hits showed a better docking score than the standard ligand, PF-00477736. The docking score was found to be -8.85, -7.50 and -7.68 kcal/mol. These hits exhibited optimal binding properties with the target in docking study, blood-brain barrier permeability, in silico pharmacokinetics and low predicted toxicity.Communicated by Ramaswamy H. Sarma.

In Vitro Physical Characterizations and Docking Studies on Carvedilol Nanocrystals

The major goal of this investigation was to prepare carvedilol nanocrystals (CRL-NCs) for better solubility, stability, and bioavailability. Using polyvinyl pyrolidine K-30 (PVP) and sodium dodecyl sulphate (SDS) as stabilisers, CRL-NCs were effectively synthesised by emulsion-diffusion, followed by the high-pressure homogenization (HPH) method. The AL classes of phase solubility curves with ideal complexes produced with stabilisers were estimated by thermodynamic parameters. The docking study was performed with the active site of a β-1 adrenoreceptor protein, and the CRLs docking score was revealed as −23.481 Kcal/mol−1. At 25 and 37 °C, the optimum interaction constant was determined for PVP (144 and 176 M−1) and SDS (102 and 121 M−1). The average particle size (PS) of the produced stable CRL-NCs is 58 nm, with a zeta potential of −27.2 ± 2.29 mV, a poly dispersibility index of 0.181 ± 0.012, a percentage yield of 78.7 ± 3.41, drug content of 96.81 ± 3.64%, and entrapment efficiency of 83.61 ± 1.80%. The morphological data also reveals that the CRL-NCs were nearly sphere shaped, with distinct and smooth surfaces. CRL-NCs were studied using X-ray diffraction (XRD), fourier transform infrared (FT-IR) spectroscopy, and differential scanning calorimetry (DSC), and the results show no chemical structural alterations, even when PS was reduced. NCs accelerate their in vitro dissolution release rate by about three times faster than CRL-MCs (microcrystals). When kept at 4 °C, the CRL-NCs exhibit good physical stability for six months. As a result, the CRL-NCs created via emulsion-diffusion followed by HPH with stabilisers can be used to increase the solubility, stability, and bioavailability of poorly soluble or lipophilic drugs.

Exploration of binding mechanism of triclosan towards cancer markers using molecular docking and molecular dynamics

The molecule 5-chloro-2-(2,4-dichlorophenoxy) phenol is well-known as Triclosan (TCS), which is also a potential endocrine disrupting synthetic chemical. TCS exposure has been connected to the control of the human enoyl-acyl carrier protein-reductase (hER), which has been linked to a range of life threatening diseases. However, other than hER, the new protein targets for TCS that are responsible for a variety of cancers are yet unclear. The goal of this work is to investigate into the protein binding patterns of TCS and proteins from various cancer signaling pathways. Discovery Studio 4.1 was used to perform molecular docking and molecular dynamics (MD) on the protein-triclosan complex. The proteins were first screened using CHARMM-based docking with a CDOCKER energy greater than -21.40 kcal/mol. The CDOCKER energies of Fas-associated death domain (FADD), Receptor-interacting protein 1 (RIP1), F-κB-inducing kinase (NIK), c-Jun N-terminal kinase (JNK), Apoptosis signal-regulating kinase 1 (ASK1), B-cell lymphoma 2 (Bcl-2), Apoptosis-inducing factor (AIF), α-tubulin, and Actin were -20.68 kcal/mol, -26.88 kcal/mol, -23.43 kcal/mol, -22.21 kcal/mol, -20.40 kcal/mol, -21.10 kcal/mol, -20.98 kcal/mol, -24.67 kcal/mol, and -23.09 kcal/mol respectively. MD was performed on the screened proteins by standard dynamics cascade tool using CHARMM Force field. The MD results were accessed using the energy-time graph, root-mean-square deviation (RMSD), and root mean square fluctuations (RMSF). The 100 conformers of α-tubulin, NIK, FADD, and RIP1 were found to have a trend of increasing RMSD, whereas Bcl-2, ASK1, AIF, Actin, and JNK proteins had lower RMSD values. In compared to FADD, AIF, and JNK, the RMSF variations of the Bcl-2, ASK1, α-tubulin, Actin, NIK, and RIP1 residues were shown to be high. Similar patterns were seen in the energy variations, which range from 1000 kcal/mol to 2000 kcal/mol. RIP1 and Bcl-2 showed more variation in the sidechain RMSF in comparison to FADD, ASK1, AIF, Actin, α-tubulin, NIK and JNK. Thus, it can be postulated that AIF and JNK proteins of apoptosis signaling pathway are pivotal in the TCS mediated reactions.

Computational Lock and Key and Dynamic Trajectory Analysis of Natural Biophors Against COVID-19 Spike Protein to Identify Effective Lead Molecules

New pandemic infection of coronaviridae family virus spread to more than 210 countries with total infection of 1,136,851 and 62,955 (4.6%) deaths until 5th April 2020. Which stopped the regular cycle of humankind but the nature is consistently running. There is no micro molecule remedy found yet to restore the regular life of people. Hence, we decided to work on natural biophores against the COVID proteins. As a first step, major phytoconstituents of antiviral herbs like Leucas aspera, Morinda citrifolia, Azadirachta indica, Curcuma longa, Piper nigrum, Ocimum tenuiflorum, and Corallium rubrum collected and performed the lock and key analysis with major spike protein of COVID-19 to find the best fitting lead biophore using computational drug design platform. The results of protocol run showed, phytoconstituents of Morinda citrifolia and Leucas aspera were found lower binding energy range of - 55.18 to - 25.34 kcal/mol, respectively and compared with Hydroxychloroquine (HCQ) (- 24.29 kcal/mol) and Remdesivir (- 25.38 kcal/mol). The results conclude that, core skeletons chromen, anthracene 9, 11 dione and long-chain alkyl acids/ester-containing biophores showen high stable antagonistic affinity with S-protein. Which leads the breakdown of spike protein and ACE2 receptor complex formation and host mechanism of corono virus. In addition, the dynamic trajectory analysis confirmed the complete denaturation of spike protein by the molecule 4-(24-hydroxy-1-oxo-5-n-propyltetracosanyl)-phenol from Leucas aspera and stability of spike-ligand complex. These biophores will aid the researcher to fabricate new promising analogue and being recommended to assess its COVID-19 treatment.

Environmentally Friendly Quinolones Design for a Two-Way Choice between Biotoxicity and Genotoxicity through Double-Activity 3D-QSAR Model Coupled with the Variation Weighting Method

Quinolone (QN) antibiotics are widely used, which lead to their accumulation in soil and toxic effects on ryegrass in pasture. In this study, we employed ryegrass as the research object and selected the total scores of 29 QN molecules docked with two resistant enzyme structures, superoxide dismutase (SOD, PDB ID: 1B06) and proline (Pro, PPEP-2, PDB ID: 6FPC), as dependent variables. The structural parameters of QNs were used as independent variables to construct a QN double-activity 3D-QSAR model for determining the biotoxicity on ryegrass by employing the variation weighting method. This model was constructed to determine modification sites and groups for designing QNs molecules. According to the 3D contour map of the model, by considering enrofloxacin (ENR) and sparfloxacin (SPA) as examples, 23 QN derivatives with low biotoxicity were designed, respectively. The functional properties and environmental friendliness of the QN derivatives were predicted through a two-way selection between biotoxicity and genotoxicity before and after modification; four environmentally friendly derivatives with low biotoxicity and high genotoxicity were screened out. Mixed toxicity index and molecular dynamics methods were used to verify the combined toxicity mechanism of QNs on ryegrass before and after modification. By simulating the combined pollution of ENR and its derivatives in different soils (farmland, garden, and woodland), the types of combined toxicity were determined as partial additive and synergistic. Binding energies were calculated using molecular dynamics. The designed QN derivatives with low biotoxicity, high genotoxicity, and environmental friendliness can highly reduce the combined toxicity on ryegrass and can be used as theoretic reserves to replace QN antibiotics.

Pectin co-functionalized dual layered solid lipid nanoparticle made by soluble curcumin for the targeted potential treatment of colorectal cancer

The investigation is to increase the cytotoxicity of soluble curcumin (SC) by loading it onto pectin and skimmed milk powder (SMP) dual layered solid lipid nanoparticles (DL-SLN). The DL-SLN exhibited significantly higher encapsulation efficiency (83.94 ± 6.16), better stability (90 days), and sustained the drug release in different gastro intestional (GI) environments upto 72 h. Molecular docking revealed that the Vander Waals (57420.669 Kcal^-mol^-1) and electrostatic (-197.533) bonds were involved in the DL-SLN complex formation. The in vivo toxicity of DL-SLN was performed by the zebrafish model, the cell cycle arrest at G₂/M phase (64.34 %) by flow cytometry, and western blot investigation was recognized molecular level cell death using SW480 cells. Pharmacokinetic (PK) evaluation (Cmax-5.78 ± 3.26 μg/mL; Tmax-24 h) and organ distribution studies confirmed that the co-functionalized pectin based SLN could efficiently improve the oral bioavailability (up to 72 h) of curcumin (CMN) on colon-targeted release.

The synthesis and biological evaluation of virtually designed fluoroquinolone analogs against fluoroquinolone-resistantEscherichia coliintended for UTI treatment

Synthesis and evaluvate the supercoiling activity of the virtually screened novel fluoroquinolone analogs against fluoroquinolone-resistantEscherichia colifor the treatment of urinary tract infections (UTIs).