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Article ; Online: Microwave-Assisted Synthesis of Functionalized Carbon Nanospheres Using Banana Peels: pH-Dependent Synthesis, Characterization, and Selective Sensing Applications.

Chopra, Tavishi / Parkesh, Raman

ACS omega

2024 Volume 9, Issue 4, Page(s) 4555–4571

Abstract: This work presents a microwave-based green synthesis method for producing carbon nanospheres (CNSs) and investigates the impact of presynthesis pH on their size and assembly. The resulting CNSs are monodispersed, averaging 35 nm in size, and exhibit ... ...

Abstract	This work presents a microwave-based green synthesis method for producing carbon nanospheres (CNSs) and investigates the impact of presynthesis pH on their size and assembly. The resulting CNSs are monodispersed, averaging 35 nm in size, and exhibit notable characteristics including high water solubility, photostability, and a narrow size distribution, achieved within a synthesis time of 15 min. The synthesized CNS features functional groups such as -OH, -COOH, -NH, -C-O-C, =C-H, and -CH. This diversity empowers the CNS for various applications including sensing. The CNS exhibits a distinct UV peak at 282 nm and emits intense fluorescence at 430 nm upon excitation at 350 nm. These functionalized CNSs enable selective and specific sensing of Cu
Language	English
Publishing date	2024-01-16
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c07544
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Article ; Online: Chemical Space Exploration of DprE1 Inhibitors Using Chemoinformatics and Artificial Intelligence.

Chhabra, Sonali / Kumar, Sunil / Parkesh, Raman

ACS omega

2021 Volume 6, Issue 22, Page(s) 14430–14441

Abstract: Tuberculosis (TB), entrained ... ...

Abstract	Tuberculosis (TB), entrained by
Language	English
Publishing date	2021-05-25
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.1c01314
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Article: Corrigendum to "Exploiting cheminformatic and machine learning to navigate the available chemical space of potential small molecule inhibitors of SARS-CoV-2″ [Computational and Structural Biotechnology Journal 19 (2021) 424-438].

Kumar, Abhinit / Loharch, Saurabh / Kumar, Sunil / Ringe, Rajesh P / Parkesh, Raman

Computational and structural biotechnology journal

2023 Volume 21, Page(s) 4408

Abstract: This corrects the article DOI: 10.1016/j.csbj.2020.12.028.]. ...

Abstract	[This corrects the article DOI: 10.1016/j.csbj.2020.12.028.].
Language	English
Publishing date	2023-09-08
Publishing country	Netherlands
Document type	Published Erratum
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2023.09.002
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Article ; Online: Epigenetic drug discovery: systematic assessment of chemical space.

Loharch, Saurabh / Parkesh, Raman

Future medicinal chemistry

2019 Volume 11, Issue 21, Page(s) 2803–2819

Abstract: Aim: ...

Abstract	Aim:
MeSH term(s)	Databases, Chemical ; Drug Discovery ; Epigenesis, Genetic ; High-Throughput Screening Assays ; Humans ; Ligands ; Pharmacokinetics
Chemical Substances	Ligands
Language	English
Publishing date	2019-11-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1756-8927
ISSN (online)	1756-8927
DOI	10.4155/fmc-2019-0096
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Article ; Online: Discovery and characterization of small molecule SIRT3-specific inhibitors as revealed by mass spectrometry.

Loharch, Saurabh / Chhabra, Sonali / Kumar, Abhinit / Swarup, Sapna / Parkesh, Raman

Bioorganic chemistry

2021 Volume 110, Page(s) 104768

Abstract: Sirtuins play a prominent role in several cellular processes and are implicated in various diseases. The understanding of biological roles of sirtuins is limited because of the non-availability of small molecule inhibitors, particularly the specific ... ...

Abstract	Sirtuins play a prominent role in several cellular processes and are implicated in various diseases. The understanding of biological roles of sirtuins is limited because of the non-availability of small molecule inhibitors, particularly the specific inhibitors directed against a particular SIRT. We performed a high-throughput screening of pharmacologically active compounds to discover novel, specific, and selective sirtuin inhibitor. Several unique in vitro sirtuin inhibitor pharmacophores were discovered. Here, we present the discovery of novel chemical scaffolds specific for SIRT3. We have demonstrated the in vitro activity of these compounds using label-free mass spectroscopy. We have further validated our results using biochemical, biophysical, and computational studies. Determination of kinetic parameters shows that the SIRT3 specific inhibitors have a moderately longer residence time, possibly implying high in vivo efficacy. The molecular docking results revealed the differential selectivity pattern of these inhibitors against sirtuins. The discovery of specific inhibitors will improve the understanding of ligand selectivity in sirtuins, and the binding mechanism as revealed by docking studies can be further exploited for discovering selective and potent ligands targeting sirtuins.
MeSH term(s)	Drug Design ; High-Throughput Screening Assays ; Models, Molecular ; Molecular Docking Simulation ; Molecular Structure ; Protein Conformation ; Sirtuin 1/antagonists & inhibitors ; Sirtuin 1/metabolism ; Sirtuin 2/antagonists & inhibitors ; Sirtuin 2/metabolism ; Sirtuin 3/antagonists & inhibitors ; Sirtuin 3/metabolism ; Small Molecule Libraries ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Structure-Activity Relationship
Chemical Substances	Small Molecule Libraries ; Sirtuin 1 (EC 3.5.1.-) ; Sirtuin 2 (EC 3.5.1.-) ; Sirtuin 3 (EC 3.5.1.-)
Language	English
Publishing date	2021-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2021.104768
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Article ; Online: Fluorescence "Turn-Off" and Colorimetric Sensor for Fe

Sasan, Sonakshi / Chopra, Tavishi / Gupta, Annah / Tsering, Dolma / Kapoor, Kamal K / Parkesh, Raman

ACS omega

2022 Volume 7, Issue 13, Page(s) 11114–11125

Abstract: Two cyanoimidazopyridine-based sensors (SS1 and SS2) were explored for the colorimetric and fluorometric detection of ... ...

Abstract	Two cyanoimidazopyridine-based sensors (SS1 and SS2) were explored for the colorimetric and fluorometric detection of Fe
Language	English
Publishing date	2022-03-22
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.1c07193
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Article ; Online: Bifidobacterium adolescentis is intrinsically resistant to antitubercular drugs.

Lokesh, Dhanashree / Parkesh, Raman / Kammara, Rajagopal

Scientific reports

2018 Volume 8, Issue 1, Page(s) 11897

Abstract: Multiple mutations in the β subunit of the RNA polymerase (rpoβ) of Mycobacterium tuberculosis (Mtb) are the primary cause of resistance to rifamycin (RIF). In the present study, bifidobacterial rpoβ sequences were analyzed to characterize the mutations ... ...

Abstract	Multiple mutations in the β subunit of the RNA polymerase (rpoβ) of Mycobacterium tuberculosis (Mtb) are the primary cause of resistance to rifamycin (RIF). In the present study, bifidobacterial rpoβ sequences were analyzed to characterize the mutations that contribute to the development of intrinsic resistance to RIF, isoniazid, streptomycin and pyrazinamide. Sequence variations, which mapped to cassettes 1 and 2 of the rpoβ pocket, are also found in multidrug-resistant Mtb (MDR Mtb). Growth curves in the presence of osmolytes and different concentrations of RIF showed that the bacteria adapted rapidly by shortening the growth curve lag time. Insight into the adapted rpoβ DNA sequences revealed that B. adolescentis harbored mutations both in the RIF pocket and in regions outside the pocket. The minimum inhibitory concentrations (MICs) and mutant prevention concentrations (MPCs) indicated that B. longum, B. adolescentis and B. animalis are resistant to antitubercular drugs. 3D-homology modeling and binding interaction studies using computational docking suggested that mutants had reduced binding affinity towards RIF. RIF-exposed/resistant bacteria exhibited variant protein profiles along with morphological differences, such as elongated and branched cells, surface conversion from rough to smooth, and formation of a concentrating ring.
MeSH term(s)	Antitubercular Agents/metabolism ; Antitubercular Agents/pharmacology ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bifidobacterium adolescentis/drug effects ; Bifidobacterium adolescentis/genetics ; Bifidobacterium adolescentis/growth & development ; Binding Sites/genetics ; Drug Resistance, Multiple, Bacterial/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; Isoniazid/metabolism ; Isoniazid/pharmacology ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Mutation ; Protein Binding ; Protein Domains ; Pyrazinamide/metabolism ; Pyrazinamide/pharmacology ; RNA Polymerase II/chemistry ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Rifamycins/metabolism ; Rifamycins/pharmacology
Chemical Substances	Antitubercular Agents ; Bacterial Proteins ; Rifamycins ; Pyrazinamide (2KNI5N06TI) ; RNA Polymerase II (EC 2.7.7.-) ; Isoniazid (V83O1VOZ8L)
Language	English
Publishing date	2018-08-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-30429-2
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Article: Exploiting cheminformatic and machine learning to navigate the available chemical space of potential small molecule inhibitors of SARS-CoV-2.

Kumar, Abhinit / Loharch, Saurabh / Kumar, Sunil / Ringe, Rajesh P / Parkesh, Raman

Computational and structural biotechnology journal

2020 Volume 19, Page(s) 424–438

Abstract: The current life-threatening and tenacious pandemic eruption of coronavirus disease in 2019 (COVID-19) has posed a significant global hazard concerning high mortality rate, economic meltdown, and everyday life distress. The rapid spread of COVID-19 ... ...

Abstract	The current life-threatening and tenacious pandemic eruption of coronavirus disease in 2019 (COVID-19) has posed a significant global hazard concerning high mortality rate, economic meltdown, and everyday life distress. The rapid spread of COVID-19 demands countermeasures to combat this deadly virus. Currently, there are no drugs approved by the FDA to treat COVID-19. Therefore, discovering small molecule therapeutics for treating COVID-19 infection is essential. So far, only a few small molecule inhibitors are reported for coronaviruses. There is a need to expand the small chemical space of coronaviruses inhibitors by adding potent and selective scaffolds with anti-COVID activity. In this context, the huge antiviral chemical space already available can be analysed using cheminformatic and machine learning to unearth new scaffolds. We created three specific datasets called "antiviral dataset" (N = 38,428) "drug-like antiviral dataset" (N = 20,963) and "anticorona dataset" (N = 433) for this purpose. We analyzed the 433 molecules of "anticorona dataset" for their scaffold diversity, physicochemical distributions, principal component analysis, activity cliffs, R-group decomposition, and scaffold mapping. The scaffold diversity of the "anticorona dataset" in terms of Murcko scaffold analysis demonstrates a thorough representation of diverse chemical scaffolds. However, physicochemical descriptor analysis and principal component analysis demonstrated negligible drug-like features for the "anticorona dataset" molecules. The "antiviral dataset" and "drug-like antiviral dataset" showed low scaffold diversity as measured by the Gini coefficient. The hierarchical clustering of the "antiviral dataset" against the "anticorona dataset" demonstrated little molecular similarity. We generated a library of frequent fragments and polypharmacological ligands targeting various essential viral proteins such as main protease, helicase, papain-like protease, and replicase polyprotein 1ab. Further structural and chemical features of the "anticorona dataset" were compared with SARS-CoV-2 repurposed drugs, FDA-approved drugs, natural products, and drugs currently in clinical trials. Using machine learning tool DCA (DMax Chemistry Assistant), we converted the "anticorona dataset" into an elegant hypothesis with significant functional biological relevance. Machine learning analysis uncovered that FDA approved drugs, Tizanidine HCl, Cefazolin, Raltegravir, Azilsartan, Acalabrutinib, Luliconazole, Sitagliptin, Meloxicam (Mobic), Succinyl sulfathiazole, Fluconazole, and Pranlukast could be repurposed as effective drugs for COVID-19. Fragment-based scaffold analysis and R-group decomposition uncovered pyrrolidine and the indole molecular scaffolds as the potent fragments for designing and synthesizing the novel drug-like molecules for targeting SARS-CoV-2. This comprehensive and systematic assessment of small-molecule viral therapeutics' entire chemical space realised critical insights to potentially privileged scaffolds that could aid in enrichment and rapid discovery of efficacious antiviral drugs for COVID-19.
Language	English
Publishing date	2020-12-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2020.12.028
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Article ; Online: Quinoxalinone substituted pyrrolizine (4h)-induced dual inhibition of AKT and ERK instigates apoptosis in breast and colorectal cancer by modulating mitochondrial membrane potential.

Amin, Tanzeeba / Sharma, Rajneesh Paul / Mir, Khalid Bashir / Slathia, Nancy / Chhabra, Sonali / Tsering, Dolma / Kotwal, Pankul / Bhagat, Madhulika / Nandi, Utpal / Parkesh, Raman / Kapoor, Kamal K / Goswami, Anindya

European journal of pharmacology

2023 Volume 957, Page(s) 175945

Abstract: AKT and ERK 1/2 play a pivotal role in cancer cell survival, proliferation, migration, and angiogenesis. Therefore, AKT and ERK 1/2 are considered crucial targets for cancer intervention. In this study, we envisaged the role of AKT and ERK signaling in ... ...

Abstract	AKT and ERK 1/2 play a pivotal role in cancer cell survival, proliferation, migration, and angiogenesis. Therefore, AKT and ERK 1/2 are considered crucial targets for cancer intervention. In this study, we envisaged the role of AKT and ERK signaling in apoptosis regulation in presence of compound 4h, a novel synthetic derivative of quinoxalinone substituted spiropyrrolizines exhibiting substantial antiproliferative activity in various cancer cell lines. Structurally 4h is a spiropyrrolizine derivative. Molecular docking analysis revealed that compound 4h shows strong binding affinity with AKT-1 (-9.5 kcal/mol) and ERK2 (-9.0 kcal/mol) via binding at allosteric sites of AKT and active site of ERK2. The implications of 4h binding with these two survival kinases resulted in the obstruction for ATP binding, hence, hampering their phosphorylation dependent activation. We demonstrate that 4h mediated apoptotic induction via disruption in the mitochondrial membrane potential of MCF-7 and HCT-116 cells and 4h-mediated inhibition of survival pathways occurred in a wild type PTEN background and is diminished in PTEN
MeSH term(s)	Animals ; Mice ; Apoptosis/drug effects ; Breast Neoplasms/drug therapy ; Cell Line, Tumor ; Cell Proliferation ; Colorectal Neoplasms/drug therapy ; Extracellular Signal-Regulated MAP Kinases/antagonists & inhibitors ; Membrane Potential, Mitochondrial/drug effects ; Mitogen-Activated Protein Kinase 3/metabolism ; Molecular Docking Simulation ; Proto-Oncogene Proteins c-akt/antagonists & inhibitors ; Pyrroles/pharmacology ; Quinoxalines/pharmacology ; Humans
Chemical Substances	Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24) ; Mitogen-Activated Protein Kinase 3 (EC 2.7.11.24) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Pyrroles ; Quinoxalines
Language	English
Publishing date	2023-08-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80121-5
ISSN	1879-0712 ; 0014-2999
ISSN (online)	1879-0712
ISSN	0014-2999
DOI	10.1016/j.ejphar.2023.175945
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Article ; Online: Transcription factors and cognate signalling cascades in the regulation of autophagy.

Chandra, Vemika / Bhagyaraj, Ella / Parkesh, Raman / Gupta, Pawan

Biological reviews of the Cambridge Philosophical Society

2016 Volume 91, Issue 2, Page(s) 429–451

Abstract: Autophagy is a process that maintains the equilibrium between biosynthesis and the recycling of cellular constituents; it is critical for avoiding the pathophysiology that results from imbalance in cellular homeostasis. Recent reports indicate the need ... ...

Abstract	Autophagy is a process that maintains the equilibrium between biosynthesis and the recycling of cellular constituents; it is critical for avoiding the pathophysiology that results from imbalance in cellular homeostasis. Recent reports indicate the need for the design of high-throughput screening assays to identify targets and small molecules for autophagy modulation. For such screening, however, a better understanding of the regulation of autophagy is essential. In addition to regulation by various signalling cascades, regulation of gene expression by transcription factors is also critical. This review focuses on the various transcription factors as well as the corresponding signalling molecules that act together to translate the stimuli to effector molecules that up- or downregulate autophagy. This review rationalizes the importance of these transcription factors functioning in tandem with cognate signalling molecules and their interfaces as possible therapeutic targets for more specific pharmacological interventions.
MeSH term(s)	Animals ; Autophagy/drug effects ; Autophagy/physiology ; Gene Expression Regulation/physiology ; Signal Transduction/physiology ; Transcription Factors/physiology
Chemical Substances	Transcription Factors
Language	English
Publishing date	2016-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1423558-4
ISSN	1469-185X ; 0006-3231 ; 1464-7931
ISSN (online)	1469-185X
ISSN	0006-3231 ; 1464-7931
DOI	10.1111/brv.12177
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