Rajesh Kumar

Green and recyclable glycine nitrate (GlyNO3) ionic liquid triggered multicomponent Biginelli reaction for the efficient synthesis of dihydropyrimidinones

Herein we report the use of an amino acid ionic liquid as a green catalyst for the multicomponent synthesis of 3,4-dihydropyrimidin-2(1H)-ones in excellent yields and short reaction time. The ionic liquid is inexpensive and biodegradable and can be reused for more than ten consecutive reactions. The potential of the protocol for gram scale synthesis adds to its practical applicability.

Biocatalysts for multicomponent Biginelli reaction: bovine serum albumin triggered waste-free synthesis of 3,4-dihydropyrimidin-2-(1H)-ones.

Bovine serum albumin (BSA) promoted simple and efficient one-pot procedure was developed for the direct synthesis of 3,4-dihydropyrimidin-2(1H)-ones including potent mitotic kinesin Eg5 inhibitor monastrol under mild reaction conditions. The catalyst recyclability and gram scale synthesis have also been demonstrated to enhance the practical utility of process.

Multicomponent Diversity-Oriented Synthesis of Symmetrical and Unsymmetrical 1,4-dihydropyridines in Recyclable Glycine Nitrate (GlyNO 3 ) Ionic Liquid: A Mechanistic Insight Using Q-TOF, ESI-MS/MS**

Multicomponent reactions are compelling strategies for generating a chemically diverse set of multifunctionalized heterocyclic motifs with high atom economy, rendering the transformations green. These strategies can further become more prolific if catalyst recyclability, compatibility and exploration of precise mechanistic pathways are considered. To this end, an inexpensive and recyclable glycine nitrate (GlyNO3) ionic liquid has been efficiently employed to obtain diversely substituted symmetrical and unsymmetrical 1,4-dihydropyridines with up to 93% yields via three and four components, respectively. The catalyst recyclability and compatibility to obtain both symmetrical and unsymmetrical 1,4 DHPs under identical reaction conditions are added benefits to its practical utility. Furthermore, progress of the reaction was monitored by Q-TOF, direct infusion electrospray ionization mass spectrometry (ESI-MS), and key cationic intermediates involved in the reaction have been further identified by a tandem MS experiment (Q-TOF, ESI-MS/MS), which served as the proof of concept to the mechanistic model. This is the first report which revealed that the Hantzsch reaction predominantly follows the diketone pathway among four competing reaction pathways.

Amino acid and water-driven tunable green protocol to access S–S/C–S bonds via aerobic oxidative coupling and hydrothiolation

A green methodology utilizing a natural supplement such as L-arginine in conjunction with water and oxygen led to oxidative coupling of thiols into disulfides (S–S bond) whereas thiol–yne coupling to access vinyl sulfides (C–S bond) was facilitated in a nitrogen atmosphere. The tunable protocol offers several advantages such as low catalyst loading, high yields, clean reaction, no over-oxidation of the S–S bond besides being metal/base/waste-free. The synthesis of ubiquitous cystine and glutathione disulfide in the same catalytic system is an added advantage and the catalytic system has been recycled up to seven times.

In Silico Approach for Prediction of Antifungal Peptides

This paper describes in silico models developed using a wide range of peptide features for predicting antifungal peptides (AFPs). Our analyses indicate that certain types of residue (e.g., C, G, H, K, R, Y) are more abundant in AFPs. The positional residue preference analysis reveals the prominence of the particular type of residues (e.g., R, V, K) at N-terminus and a certain type of residues (e.g., C, H) at C-terminus. In this study, models have been developed for predicting AFPs using a wide range of peptide features (like residue composition, binary profile, terminal residues). The support vector machine based model developed using compositional features of peptides achieved maximum accuracy of 88.78% on the training dataset and 83.33% on independent or validation dataset. Our model developed using binary patterns of terminal residues of peptides achieved maximum accuracy of 84.88% on training and 84.64% on validation dataset. We benchmark models developed in this study and existing methods on a dataset containing compositionally similar antifungal and non-AFPs. It was observed that binary based model developed in this study preforms better than any model/method. In order to facilitate scientific community, we developed a mobile app, standalone and a user-friendly web server ‘Antifp’ (http://webs.iiitd.edu.in/raghava/antifp).

CancerPDF: A repository of cancer-associated peptidome found in human biofluids

CancerPDF (Cancer Peptidome Database of bioFluids) is a comprehensive database of endogenous peptides detected in the human biofluids. The peptidome patterns reflect the synthesis, processing and degradation of proteins in the tissue environment and therefore can act as a gold mine to probe the peptide-based cancer biomarkers. Although an extensive data on cancer peptidome has been generated in the recent years, lack of a comprehensive resource restrains the facility to query the growing community knowledge. We have developed the cancer peptidome resource named CancerPDF, to collect and compile all the endogenous peptides isolated from human biofluids in various cancer profiling studies. CancerPDF has 14,367 entries with 9,692 unique peptide sequences corresponding to 2,230 unique precursor proteins from 56 high-throughput studies for ~27 cancer conditions. We have provided an interactive interface to query the endogenous peptides along with the primary information such as m/z, precursor protein, the type of cancer and its regulation status in cancer. To add-on, many web-based tools have been incorporated, which comprise of search, browse and similarity identification modules. We consider that the CancerPDF will be an invaluable resource to unwind the potential of peptidome-based cancer biomarkers. The CancerPDF is available at the web address http://crdd.osdd.net/raghava/cancerpdf/.

Prediction of Cell-Penetrating Potential of Modified Peptides Containing Natural and Chemically Modified Residues

Designing drug delivery vehicles using cell-penetrating peptides is a hot area of research in the field of medicine. In the past, number of in silico methods have been developed for predicting cell-penetrating property of peptides containing natural residues. In this study, first time attempt has been made to predict cell-penetrating property of peptides containing natural and modified residues. The dataset used to develop prediction models, include structure and sequence of 732 chemically modified cell-penetrating peptides and an equal number of non-cell penetrating peptides. We analyzed the structure of both class of peptides and observed that positive charge groups, atoms, and residues are preferred in cell-penetrating peptides. In this study, models were developed to predict cell-penetrating peptides from its tertiary structure using a wide range of descriptors (2D, 3D descriptors, and fingerprints). Random Forest model developed by using PaDEL descriptors (combination of 2D, 3D, and fingerprints) achieved maximum accuracy of 95.10%, MCC of 0.90 and AUROC of 0.99 on the main dataset. The performance of model was also evaluated on validation/independent dataset which achieved AUROC of 0.98. In order to assist the scientific community, we have developed a web server “CellPPDMod” for predicting the cell-penetrating property of modified peptides (http://webs.iiitd.edu.in/raghava/cellppdmod/).

CTAB-mediated, single-step preparation of competent Escherichia coli, Bifidobacterium sp. and Kluyveromyces lactis cells

An efficient and reproducible method for transformation depends on the competency of the organism. We have developed a simple method for the preparation of competent Escherichia coli, Kluyveromyces lactis, and Bifidobacterium sp. by using a buffer containing cetyl trimethyl ammonium bromide (CTAB) and permits efficient uptake of plasmid DNA and ligation-reaction products. Cells are harvested, washed, mixed with 1–10 μg/ml CTAB, incubated, and followed by a buffer wash. For long-term storage of competent cells, bacteria may be frozen in 10% glycerol without the addition of other components. The transformation process is very simple; plasmid DNA and the cells are mixed and incubated for 5–60 min at 4 °C; no heat pulse is required, and the duration of incubation at 4 °C is not crucial.

AntiTbPdb: a knowledgebase of anti-tubercular peptides

Abstract Tuberculosis is a global menace, caused by Mycobacterium tuberculosis, responsible for millions of premature deaths every year. In the era of drug-resistant tuberculosis, peptide-based therapeutics may provide alternate to small molecule based drugs. In order to create knowledgebase, AntiTbPdb (http://webs.iiitd.edu.in/raghava/antitbpdb/), experimentally validated anti-tubercular and anti-mycobacterial peptides were compiled from literature. We curate 10 652 research articles and 35 patents to extract anti-tubercular peptides and annotate these peptides manually. This knowledgebase has 1010 entries, each entry provides extensive information about an anti-tubercular peptide such as sequence, chemical modification, chirality, nature and source of origin. The tertiary structure of these anti-tubercular peptides containing natural as well as chemically modified residues was predicted using PEPstrMOD and I-TASSER. In addition to structural information, database maintains other properties of peptides like physiochemical properties. Numerous web-based tools have been integrated for data retrieval, browsing, sequence similarity search and peptide mapping. In order to assist wide range of user, we developed a responsive website suitable for smartphone, tablet and desktop. Database URL: http://webs.iiitd.edu.in/raghava/antitbpdb/

Anthraquinone derivatives based natural dye from Rheum emodi as a probe for thermal stability of proteins: Spectroscopic and chromatographic studies

Rheum emodi is a storehouse of a large number of anthraquinone derivatives which are known for a large number of biological activities of significant potency. In this work, a study on the interactions between anthraquinone derivatives based natural dye isolated from R. emodi and different proteins has been reported for the first time, revealing the use of dye as an extrinsic probe to determine the stability of these proteins alone and in the presence of additives. The stability parameters have been evaluated as a change in the fluorescence intensity of the dye as a function of temperature due to the differential interaction of the dye with various conformations of a protein. Also, the effect of the change in polarity of the solvent on the fluorescence emission spectra of dye was studied where high quantum yield was observed in alcohol as compared to water. The RP-HPLC characterization of the dye revealed the presence of anthraquinones glycosides as main compounds in it. Thus, natural dyes may be used as biosensors to follow the conformational changes in proteins.