Manish Kesherwani

Insights into the binding of thiosemicarbazone derivatives with human serum albumin: spectroscopy and molecular modelling studies.

4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl acetate [Ace semi],4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl propanoate [Pro semi] from the family of thiosemicarbazones derivative has been newly synthesized. It has good anticancer activity as well as antibacterial and it is also less toxic in nature, its binding characteristics are therefore of huge interest for understanding pharmacokinetic mechanism of the drug. The binding of thiosemicarbazone derivative to human serum albumin (HSA) has been investigated by studying its quenching mechanism, binding kinetics and the molecular distance (r) between donor (HSA) and acceptor (thiosemicarbazone derivative) was estimated according to Forster’s theory of non-radiative energy transfer using fluorescence spectroscopy. The binding dynamics has been elaborated using synchronous fluorescence spectroscopy, and the feature of thiosemicarbazone derivative induced structural changes of HSA has been studied by circular dichorism, Fourier transform infrared spectroscopy. Molecular modelling simulations explore the hydrophobic interaction and hydrogen bonding which stabilizes the interaction.

Identification of novel natural inhibitor for NorM – a multidrug and toxic compound extrusion transporter – an insilico molecular modeling and simulation studies

The emergence of bacterial multidrug resistance is an increasing problem in treatment of infectious diseases. An important cause for the multidrug resistance of bacteria is the expression of multidrug efflux transporters. The multidrug and toxic compound extrusion (MATE) transporters are most recently recognized as unique efflux system for extrusion of antimicrobials and therapeutic drugs due to energy stored in either Na+ or H+ electrochemical gradient. In the present study, high throughput virtual screening of natural compound collections against NorM – a MATE transporter from Neisseria gonorrhea (NorM-NG) has been carried out followed by flexible docking. The molecular simulation in membrane environment has been performed for understanding the stability and binding energetic of top lead compounds. Results identified a compound from the Indian medicinal plant “Terminalia chebula” which has good binding free energy compared to substrates (rhodamine 6 g, ethidium) and more favorable interactions with the central cavity forming active site residues. The compound has restricted movement in TM7, TM8, and TM1, thus blocking the disruption of Na+ – coordination along with equilibrium state bias towards occlude state of NorM transporter. Thus, this compound blocks the effluxing pathway of antimicrobial drugs and provides as a natural bioactive lead inhibitor against NorM transporter in drug-resistant gonorrhea.

Determination on the binding of thiadiazole derivative to human serum albumin: a spectroscopy and computational approach

4-[3-acetyl-5-(acetylamino)-2,3-dihydro-1,3,4-thiadiazole-2-yl]phenyl benzoate from the family of thiadiazole derivative has been newly synthesized. It has good anticancer activity as well as antibacterial and less toxic in nature, its binding characteristics are therefore of huge interest for understanding pharmacokinetic mechanism of the drug. The binding of thiadiazole derivative to human serum albumin (HSA) has been investigated by studying its quenching mechanism, binding kinetics and the molecular distance, r between the donor (HSA) and acceptor (thiadiazole derivative) was estimated according to Forster’s theory of non-radiative energy transfer. The Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) changes of temperature-dependent Kb was calculated, which explains that the reaction is spontaneous and exothermic. The microenvironment of HSA have also been studied using synchronous fluorescence spectroscopy, and the feature of thiadiazole derivative-induced structural changes of HSA have been carried using Fourier transform infrared spectroscopy and the Molecular modelling simulations explore the hydrophobic and hydrogen bonding interactions.

Comparison of proteomic profiles of the venoms of two of the ‘Big Four’ snakes of India, the Indian cobra (Naja naja) and the common krait (Bungarus caeruleus), and analyses of their toxins

&NA; Snake venoms are mixtures of biologically‐active proteins and peptides, and several studies have described the characteristics of some of these toxins. However, complete proteomic profiling of the venoms of many snake species has not yet been done. The Indian cobra (Naja naja) and common krait (Bungarus caeruleus) are elapid snake species that are among the ‘Big Four’ responsible for the majority of human snake envenomation cases in India. As understanding the composition and complexity of venoms is necessary for successful treatment of envenomation in humans, we utilized three different proteomic profiling approaches to characterize these venoms: i) one‐dimensional SDS‐PAGE coupled with in‐gel tryptic digestion and electrospray tandem mass spectrometry (ESI‐LC‐MS/MS) of individual protein bands; ii) in‐solution tryptic digestion of crude venoms coupled with ESI‐LC‐MS/MS; and iii) separation by gel‐filtration chromatography coupled with tryptic digestion and ESI‐LC‐MS/MS of separated fractions. From the generated data, 81 and 46 different proteins were identified from N. naja and B. caeruleus venoms, respectively, belonging to fifteen different protein families. Venoms from both species were found to contain a variety of phospholipases A2 and three‐finger toxins, whereas relatively higher numbers of snake venom metalloproteinases were found in N. naja compared to B. caeruleus venom. The analyses also identified less represented venom proteins including L‐amino acid oxidases, cysteine‐rich secretory proteins, 5′‐nucleotidases and venom nerve growth factors. Further, Kunitz‐type serine protease inhibitors, cobra venom factors, phosphodiesterases, vespryns and aminopeptidases were identified in the N. naja venom, while acetylcholinesterases and hyaluronidases were found in the B. caeruleus venom. We further analyzed protein coverage (Lys/Arg rich and poor regions as well as potential glycosylation sites) using in‐house software. These studies expand our understanding of the proteomes of the venoms of these two medically‐important species. Graphical abstract Figure. No caption available. HighlightsProteomic profiles of Naja naja and Bungarus caeruleus venom were analyzed and compared using complementary techniques.81 and 46 venom proteins were identified from N. naja and B. caeruleus venoms, respectively.Enzymatic toxins, including PLA2s and SVMPs, and non‐enzymatic toxins, such as 3FTxs, were detected in both venoms.KPIs, CVFs, PDEs, vespryns, and aminopeptidases were only found in N. naja venom.AChEs and hyaluronidases were unique to B. caeruleus venom.

Synthesis and molecular modelling studies of novel sulphonamide derivatives as dengue virus 2 protease inhibitors.

Development of antivirals for dengue is now based on rational approach targeting the enzymes involved in its life cycle. Among the targets available for inhibition of dengue virus, non-structural protein NS2B-NS3 protease is considered as a promising target for the development of anti-dengue agents. In the current study we have synthesized a series of 4-(1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)benzene-1-sulphonamide derivatives and screened for DENV2 protease activity. Compounds 16 and 19 showed IC50 of DENV2 Protease activity with 48.2 and 121.9μM respectively. Molecular docking and molecular dynamic simulation studies were carried out to know the binding mode responsible for the activity. MD simulations revealed that, NS2B/NS3 protease was more stable when it binds with the active compound. Structure optimization of the lead compounds 16 and 19 and their co-crystallization studies are underway.

Underlying the Mechanism of 5-Fluorouracil and Human Serum Albumin Interaction: A Biophysical Study

5-Fluorouracil is clinically utilized as antitumor drug to treat numerous sorts of malignancy, which is made accessible to the objective tissues in conjugation with transport protein serum albumin furthermore which is low harmful when compared to the other drugs of this family and hence its binding characteristics are therefore of prime interest. The steady state and time resolved fluorescence studies, Fourier transform infrared spectroscopy and circular dichroism studies were employed to explain the mode and the mechanism of interaction of 5FU with HSA. 5-Fluorouracil binding is characterized with one high affinity binding site, with the binding constant of the order of 104. The molecular distance r (1.23 nm) between donor (HSA) and acceptor (5-FU) was estimated according to Forsters theory of non-radiative energy transfer. The feature of 5-Fluorouracil induced structural changes of human serum albumin has been studied in detail by Raman spectroscopy, circular dichroism and Fourier transform infrared spectroscopy analysis. The binding dynamics was expounded by synchronous fluorescence spectroscopy, fluorescence lifetime measurements and molecular modelling elicits that hydrophobic interactions and hydrogen bonding, stabilizes the 5-Fluorouracil interaction with HSA.

Fasciola gigantica thioredoxin glutathione reductase: Biochemical properties and structural modeling.

Platyhelminth thioredoxin glutathione reductase (TGR) is a multifunctional enzyme that crosstalk between the conventional thioredoxin (Trx) and glutathione (GSH) system. It has been validated as a potential drug target in blood flukes. In the present study, we have performed a biochemical study on Fasciola gigantica TGR with substrates DTNB and GSSG. The Michaelis constant (Km) with DTNB was found to be 4.34±0.12μM while it was 61.15±1.50μM with GSSG. The kinetic results were compared with the TGR activities of other helminths. FgTGR showed typical hysteretic behavior with GSSG as other TGRs. We also described a homology-based structure of FgTGR. The cofactors (NADPH and FAD) and substrates (GSSG and DTNB) were docked, and two possible binding sites for substrates were identified in a single chain. The substrates were found to bind more favorably in the second site of TrxR domains. We also presented the first report on binding interaction of DTNB with a TGR. DTNB forms H-bond with His204 and Arg450 of chain A, Sec597, and Gly598 from chain B, salt-bridge with Lys124, and numerous other hydrophobic interactions. Helminth TGR represents an important enzyme in the redox and antioxidant system; hence, its inhibition can be used as an effective strategy against liver flukes.

Identification of new BACE1 inhibitors using Pharmacophore and Molecular dynamics simulations approach

Inhibition of β-Secretase (BACE1) is crucial for the treatment of Alzheimers disease (AD). Availability of BACE1 crystal structures in both apo and complexed forms enables to find structure-based BACE1 inhibitors for controlling AD. There are two catalytic aspartates (ASP32 and ASP228) presents in the active domain of BACE1. In order to understand the binding mechanism and structure-activity relationship of amidine-containing BACE1 inhibitors, molecular docking, and pharmacophore and 3D-QSAR studies have been carried out with 34 amidine derivatives to develop a pharmacophore model. Pharmacophore-based virtual screening (PBVS) has been performed against BACE1 (PDB ID: 2FDP), using three chemical databases (CoCoCo, Enamine, Zinc), which yielded 6000 hit compounds. These compounds were further analyzed using structure-based docking in hierarchical filtering approaches of Glide such as HTVS, SP, and XP precision modes. The docking results show that binding orientations of the inhibitors at Asp dyad active site amino acid residues of β-Secretase. Results from glide XP docking and induced fit docking showed that four leads (Lead1, Lead3, Lead4 and Lead5) have good interactions with the target protein in comparison with cocrystal (amino-ethylene BACE1 inhibitor). Further, molecular dynamics (MD) simulation for these leads bound with BACE1 shows conformational stability and difference in dynamical flap behaviors of the active site with cocrystal inhibitor. Binding free energetic using MM-GB/SA approaches suggest lead 1 and lead 3 has comparably favorable binding to cocrystal inhibitor. Thus, the present study emphasizes these leads for an effective drug to treat Alzheimer disease.

Drug-Target Interactions: Prediction Methods and Applications

Identifying the interactions between drugs and target proteins is a key step in drug discovery. This not only aids to understand the disease mechanism, but also helps to identify unexpected therapeutic activity or adverse side effects of drugs. Hence, drug-target interaction prediction becomes an essential tool in the field of drug repurposing. The availability of heterogeneous biological data on known drug-target interactions enabled many researchers to develop various computational methods to decipher unknown drug-target interactions. This review provides an overview on these computational methods for predicting drug-target interactions along with available webservers and databases for drug-target interactions. Further, the applicability of drug-target interactions in various diseases for identifying lead compounds has been outlined.

Identification of novel Nicotinamide Phosphoribosyltransferase (NAMPT) inhibitors using computational approaches

Nicotinamide Phosphoribosyltransferase (NAMPT) is a rate-limiting enzyme in the biosynthesis of NAD. Cancer cells have elevated poly [ADP-Ribose] polymerase 1 (PARP) activity as well as the immense necessity of ATP: thereby consuming NAD at a higher rate than normal tissues. The perturbation of these intracellular processes is more sensitive and highly dependent on NAMPT to maintain the required NAD levels. Functional inhibition of NAMPT is, therefore, a promising drug target in therapeutic oncology. In this study, the importance of intermolecular contacts was realized based on contact occupancy and favorable energetic from molecular dynamic simulation to discern non-critical contacts of four different classes of potential NAMPT inhibitor bound complexes. Further, pharmacophore modeling, molecular docking, a quantum mechanical properties and MD simulation, as well as active site residual network communication were employed to identify potential leads. Present studies identified two leads, 2 and 3 which have better binding free energy compared to known inhibitors and showed stable hydrogen bonding and hydrophobic contacts with β barrel cavity lining residues in the active site of the dimer interface (A′B). Lead 2 containing fluorene as central core and lead 3 having phenyl-benzamide as a core showed stable moiety which was observed from electronic property analysis. Active site residual communication in identified leads bound complex also showed similarity to known inhibitor complexes. Compounds containing these moieties were not reported until now against NAMPT inhibition and can be considered as novel cores for future development of drugs to inhibit NAMPT function.