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Article: Assessment of activity of chalcone compounds as inhibitors of 3-chymotrypsin like protease (3CL

Mathpal, Shalini / Joshi, Tushar / Sharma, Priyanka / Pande, Veena / Chandra, Subhash

2022 Volume 33, Issue 5, Page(s) 1815–1831

Abstract: The COVID-19 is still pandemic due to emerging of various variant of concern of SARS-CoV2. Hence, it is devastating the world, causing significant economic as well as social chaos. This needs great effort to search and develop effective alternatives ... ...

Abstract	The COVID-19 is still pandemic due to emerging of various variant of concern of SARS-CoV2. Hence, it is devastating the world, causing significant economic as well as social chaos. This needs great effort to search and develop effective alternatives along with vaccination. Therefore, to continue drug discovery endeavors, we used chalcone derivatives to find an effective drug candidate against SARS-CoV2. Chalcone is a common simple scaffold that exists in many diets as well as in traditional medicine. Natural as well as synthetic chalcones have shown numerous interesting biological activities and are also effective in fighting various diseases. Hence, various computational methods were applied to find out potential inhibitors of 3CL Supplementary information: The online version contains supplementary material available at 10.1007/s11224-022-01887-2.
Language	English
Publishing date	2022-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2018832-8
ISSN	1572-9001 ; 1040-0400
ISSN (online)	1572-9001
ISSN	1040-0400
DOI	10.1007/s11224-022-01887-2
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Article: In silico screening of chalcone derivatives as promising EGFR-TK inhibitors for the clinical treatment of cancer.

Mathpal, Shalini / Joshi, Tushar / Sharma, Priyanka / Maiti, Priyanka / Nand, Mahesha / Pande, Veena / Chandra, Subhash

3 Biotech

2023 Volume 14, Issue 1, Page(s) 18

Abstract: Epidermal growth factor receptor (EGFR) promotes tumorigenic characteristics and activates cancer-associated signaling pathways such as Wnt/-catenin, transforming growth factor (TGF-β), and phosphoinositide-3-kinase (PI3K). Several inhibitors have been ... ...

Abstract	Epidermal growth factor receptor (EGFR) promotes tumorigenic characteristics and activates cancer-associated signaling pathways such as Wnt/-catenin, transforming growth factor (TGF-β), and phosphoinositide-3-kinase (PI3K). Several inhibitors have been reported to suppress the activity of EGFR and are being used in cancer treatment. However, patients in the malignant stage of cancer show resistance to those inhibitors, opening a wide space for research to discover novel inhibitors. Therefore, we carried out machine learning and virtual screening to discover novel inhibitors with high affinity against EGFR-TK. Initially, a library of 2640 chalcones were screened out using a machine-learning model developed based on the random forest algorithm, exhibiting high sensitivity and a Receiver Operating Characteristic curve (ROC area) of 0.99. Furthermore, out of the initial 2640 screened compounds, 412 compounds exhibiting potential activity are subjected to evaluation for drug-likeness properties through different filters: Blood-brain barrier penetration, Lipinski's rule, CMC-50 like rule, Veber rule, and Ghose filter, alongside Cell Line Cytotoxicity Prediction. A total of 30 compounds that successfully pass through all these filters are selected for molecular docking. Of these, 6 compounds display substantial binding affinity and closer interaction with the conserved catalytic residues of the target EGFR-TK compared to the reference molecule (erlotinib). Furthermore, molecular dynamics simulation studies were conducted on four compounds (CID-375861, CID-375862, CID-23636403, and CID-259166) to confirm the stability of the docked complexes over a 100 ns simulation trajectory. Additionally, the binding free energy calculations by MMPBSA reveal that these four chalcone compounds exhibit strong affinity towards the EGFR-TK enzyme, with binding free energies of - 65.421 kJ/mol, - 94.266 kJ/mol, - 80.044 kJ/mol, and - 79.734 kJ/mol, respectively. The findings from this investigation highlight a set of promising chalcone compounds that have the potential to be developed into effective drugs for the treatment of various cancers. Further research and development on these compounds could pave the way for novel therapeutic interventions. Supplementary information: The online version contains supplementary material available at 10.1007/s13205-023-03858-8.
Language	English
Publishing date	2023-12-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-023-03858-8
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Article ; Online: In silico

Sharma, Priyanka / Joshi, Tushar / Mathpal, Shalini / Chandra, Subhash / Tamta, Sushma

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 21, Page(s) 10543–10560

Abstract: The leaves and fruits ... ...

Abstract	The leaves and fruits of
MeSH term(s)	Humans ; Hypoglycemic Agents/chemistry ; Dipeptidyl-Peptidase IV Inhibitors/chemistry ; Diabetes Mellitus, Type 2/drug therapy ; Molecular Dynamics Simulation ; Molecular Docking Simulation ; Glucagon-Like Peptide 1 ; Gastric Inhibitory Polypeptide/pharmacology ; Gastric Inhibitory Polypeptide/therapeutic use ; Phytochemicals/pharmacology ; Phytochemicals/therapeutic use
Chemical Substances	Hypoglycemic Agents ; Dipeptidyl-Peptidase IV Inhibitors ; Glucagon-Like Peptide 1 (89750-14-1) ; Gastric Inhibitory Polypeptide (59392-49-3) ; Phytochemicals
Language	English
Publishing date	2021-07-06
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1944910
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Article ; Online: Genomic assortment and interactive insights of the chromosomal encoded control of cell death (

Chaudhary, Shobhi / Yadav, Mohit / Mathpal, Shalini / Chandra, Subhash / Rathore, Jitendra Singh

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 15, Page(s) 7032–7044

Abstract: In the present circumstances, toxin-antitoxin (TA) modules have a great consideration due to their elusive role in bacterial physiology. TA modules consist of a toxic part and a counteracting antitoxin part and these are abundant genetic loci harbored on ...

Abstract	In the present circumstances, toxin-antitoxin (TA) modules have a great consideration due to their elusive role in bacterial physiology. TA modules consist of a toxic part and a counteracting antitoxin part and these are abundant genetic loci harbored on bacterial plasmids and chromosomes. The control of cell death (
Language	English
Publishing date	2022-08-24
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2114940
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Article ; Online: Potent multi-target natural inhibitors against SARS-CoV-2 from medicinal plants of the Himalaya: a discovery from hybrid machine learning, chemoinformatics, and simulation assisted screening.

Maiti, Priyanka / Nand, Mahesha / Mathpal, Shalini / Wahab, Shadma / Kuniyal, Jagdish Chandra / Sharma, Priyanka / Joshi, Tushar / Ramakrishnan, Muthannan Andavar / Chandra, Subhash

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–14

Abstract: The emergence and immune evasion ability of SARS-CoV-2 Omicron strains, mainly BA.5.2 and BF.7 and other variants of concern have raised global apprehensions. With this context, the discovery of multitarget inhibitors may be proven more comprehensive ... ...

Abstract	The emergence and immune evasion ability of SARS-CoV-2 Omicron strains, mainly BA.5.2 and BF.7 and other variants of concern have raised global apprehensions. With this context, the discovery of multitarget inhibitors may be proven more comprehensive paradigm than its one-drug-to-one target counterpart. In the current study, a library of 271 phytochemicals from 25 medicinal plants from the Indian Himalayan Region has been virtually screened against SARS-CoV-2 by targeting nine virus proteins,
Language	English
Publishing date	2023-09-21
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2257333
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Article ; Online: Screening of potential bio-molecules from

Mathpal, Shalini / Sharma, Priyanka / Joshi, Tushar / Joshi, Tanuja / Pande, Veena / Chandra, Subhash

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 20, Page(s) 9885–9896

Abstract: COVID-19 caused by SARS-CoV-2 is responsible for the deaths of millions of people worldwide. It is having devastating effects on the people of all countries. In this regard, the phytochemicals of medicinal plants could be explored to prevent this disease. ...

Abstract	COVID-19 caused by SARS-CoV-2 is responsible for the deaths of millions of people worldwide. It is having devastating effects on the people of all countries. In this regard, the phytochemicals of medicinal plants could be explored to prevent this disease.
MeSH term(s)	Molecular Docking Simulation ; Molecular Dynamics Simulation ; Moringa/chemistry ; Protease Inhibitors/pharmacology ; SARS-CoV-2 ; Phytochemicals/pharmacology ; Coronavirus 3C Proteases/antagonists & inhibitors
Chemical Substances	3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Protease Inhibitors ; Phytochemicals ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2021-06-21
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1936183
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Article: Identification of Putative Elicitors From Plant Root Exudates Responsible for PsoR Activation in Plant-Beneficial

Sati, Diksha / Joshi, Tushar / Pandey, Satish Chandra / Pande, Veni / Mathpal, Shalini / Chandra, Subhash / Samant, Mukesh

Frontiers in plant science

2022 Volume 13, Page(s) 875494

Abstract: Plants and rhizobacteria are coexisting since the beginning, but the exact mechanism of communication between them remains enigmatic. The PsoR protein of plant- ... ...

Abstract	Plants and rhizobacteria are coexisting since the beginning, but the exact mechanism of communication between them remains enigmatic. The PsoR protein of plant-beneficial
Language	English
Publishing date	2022-04-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2022.875494
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Article: Identification of Zinc-Binding Inhibitors of Matrix Metalloproteinase-9 to Prevent Cancer Through Deep Learning and Molecular Dynamics Simulation Approach.

Mathpal, Shalini / Sharma, Priyanka / Joshi, Tushar / Pande, Veena / Mahmud, Shafi / Jeong, Mi-Kyung / Obaidullah, Ahmad J / Chandra, Subhash / Kim, Bonglee

Frontiers in molecular biosciences

2022 Volume 9, Page(s) 857430

Abstract: The overexpression of matrix metalloproteinase-9 (MMP-9) is associated with tumor development and angiogenesis, and hence, it has been considered an attractive drug target for anticancer therapy. To assist in drug design endeavors for MMP-9 targets, ... ...

Abstract	The overexpression of matrix metalloproteinase-9 (MMP-9) is associated with tumor development and angiogenesis, and hence, it has been considered an attractive drug target for anticancer therapy. To assist in drug design endeavors for MMP-9 targets, an
Language	English
Publishing date	2022-03-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.857430
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Article ; Online: Structure-based screening of novel lichen compounds against SARS Coronavirus main protease (Mpro) as potentials inhibitors of COVID-19.

Joshi, Tanuja / Sharma, Priyanka / Joshi, Tushar / Pundir, Hemlata / Mathpal, Shalini / Chandra, Subhash

Molecular diversity

2020 Volume 25, Issue 3, Page(s) 1665–1677

Abstract: The outbreak of SARS-CoV-2 and deaths caused by it all over the world have imposed great concern on the scientific community to develop potential drugs to combat Coronavirus disease-19 (COVID-19). In this regard, lichen metabolites may offer a vast ... ...

Abstract	The outbreak of SARS-CoV-2 and deaths caused by it all over the world have imposed great concern on the scientific community to develop potential drugs to combat Coronavirus disease-19 (COVID-19). In this regard, lichen metabolites may offer a vast reservoir for the discovery of antiviral drug candidates. Therefore, to find novel compounds against COVID-19, we created a library of 412 lichen compounds and subjected to virtual screening against the SARS-CoV-2 Main protease (Mpro). All the ligands were virtually screened, and 27 compounds were found to have high affinity with Mpro. These compounds were assessed for drug-likeness analysis where two compounds were found to fit well for redocking studies. Molecular docking, drug-likeness, X-Score, and toxicity analysis resulting in two lichen compounds, Calycin and Rhizocarpic acid with Mpro-inhibiting activity. These compounds were finally subjected to molecular dynamics simulation to compare the dynamics behavior and stability of the Mpro after ligand binding. The binding energy was calculated by MM-PBSA method to determine the intermolecular protein-ligand interactions. Our results showed that two compounds; Calycin and Rhizocarpic acid had the binding free energy of - 42.42 kJ mol/1 and - 57.85 kJ mol/1 respectively as compared to reference X77 (- 91.78 kJ mol/1). We concluded that Calycin and Rhizocarpic acid show considerable structural and pharmacological properties and they can be used as hit compounds to develop potential antiviral agents against SARS-CoV-2. These lichen compounds may be a suitable candidate for further experimental analysis.
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Coronavirus 3C Proteases/metabolism ; Drug Evaluation, Preclinical ; Lichens/chemistry ; Lichens/metabolism ; Ligands ; Molecular Docking Simulation ; Protease Inhibitors/chemistry ; Protease Inhibitors/metabolism ; Protease Inhibitors/pharmacology ; Protein Conformation ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology
Chemical Substances	Antiviral Agents ; Ligands ; Protease Inhibitors ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-06-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-020-10118-x
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Article ; Online: Using Chou's 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors.

Pundir, Hemlata / Joshi, Tanuja / Joshi, Tushar / Sharma, Priyanka / Mathpal, Shalini / Chandra, Subhash / Tamta, Sushma

Molecular diversity

2020 Volume 25, Issue 3, Page(s) 1731–1744

Abstract: Recently emerged SARS-CoV-2 is the cause of the ongoing outbreak of COVID-19. It is responsible for the deaths of millions of people and has caused global economic and social disruption. The numbers of COVID-19 cases are increasing exponentially across ... ...

Abstract	Recently emerged SARS-CoV-2 is the cause of the ongoing outbreak of COVID-19. It is responsible for the deaths of millions of people and has caused global economic and social disruption. The numbers of COVID-19 cases are increasing exponentially across the world. Control of this pandemic disease is challenging because there is no effective drug or vaccine available against this virus and this situation demands an urgent need for the development of anti-SARS-CoV-2 potential medicines. In this regard, the main protease (Mpro) has emerged as an essential drug target as it plays a vital role in virus replication and transcription. In this research, we have identified two novel potent inhibitors of the Mpro (PubChem3408741 and PubChem4167619) from PubChem database by pharmacophore-based high-throughput virtual screening. The molecular docking, toxicity, and pharmacophore analysis indicate that these compounds may act as potential anti-viral candidates. The molecular dynamic simulation along with the binding free energy calculation by MMPBSA showed that these compounds bind to Mpro enzyme with high stability over 50 ns. Our results showed that two compounds: PubChem3408741 and PubChem4167619 had the binding free energy of - 94.02 kJ mol
MeSH term(s)	Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Coronavirus 3C Proteases/metabolism ; Drug Evaluation, Preclinical ; Molecular Docking Simulation ; Protease Inhibitors/chemistry ; Protease Inhibitors/metabolism ; Protease Inhibitors/pharmacology ; Protein Conformation ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Thermodynamics ; User-Computer Interface
Chemical Substances	Protease Inhibitors ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-10-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-020-10148-5
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