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Article: Exploring the anticancer potential of fluoro flavone analogues: insights from molecular docking and dynamics studies with Aurora Kinase B.

Singh, Ipsa A / Lokhande, Kiran Bharat / Swamy, K Venkateswara

2024 Volume 12, Issue 1, Page(s) 26

Language	English
Publishing date	2024-04-07
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2702993-1
ISSN	2193-9616
ISSN	2193-9616
DOI	10.1007/s40203-024-00200-9
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Article ; Online: [No title information]

Lokhande, Kiran Bharat / Shrivastava, Ashish / Singh, Ashutosh

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 23, Page(s) 14259–14274

Abstract: Monkeypox virus (MPXV) outbreak in non-endemic countries is a worldwide public health emergency. An enveloped double-stranded DNA virus belongs to the genus Orth poxvirus. A viral zoonotic infection known as monkeypox has been a serious risk to public ... ...

Abstract	Monkeypox virus (MPXV) outbreak in non-endemic countries is a worldwide public health emergency. An enveloped double-stranded DNA virus belongs to the genus Orth poxvirus. A viral zoonotic infection known as monkeypox has been a serious risk to public health, especially in Africa. However, it has recently spread to other continents, so it might soon become a worldwide problem. There is an increased risk of transmission of the virus because there is a lack of effective treatment that cures the disease. To stop the multi-country outbreak from spreading, it is important to discover effective medications urgently. The objective of the current study is to swiftly find new treatments for the monkeypox virus using advanced computational approaches. By investigating five potential MPXV targets (DNA ligase, Palmytilated Extracellular Enveloped Virus (EEV) membrane protein, Scaffold protein D13, Thymidylate Kinase, and Viral core cysteine proteinase), this research was carried out using cutting-edge computational techniques against human monkeypox virus infection. Here we present the accurate 3D structures and their binding cavities of the selected targets with higher confidence using AlphaFold 2 and SiteMap analysis. Molecular docking and MD simulation analysis revealed the top five potential lead compounds with higher binding affinity and stability toward selected targets. Binding free energy calculations and other essential dynamics analysis supports the finding. The selected lead compounds utilizing virtual screening and drug repurposing approach reported in this study are beneficial for medical scientists and experimental biologists in drug development for the treatment of human MPXV.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Mpox (monkeypox)/drug therapy ; Molecular Docking Simulation ; Membrane Proteins ; Computer Simulation ; DNA Ligases
Chemical Substances	Membrane Proteins ; DNA Ligases (EC 6.5.1.-)
Language	English
Publishing date	2023-02-25
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2183342
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Article ; Online: Docking and simulation studies on cyclin D/CDK4 complex for targeting cell cycle arrest in cancer using flavanone and its congener.

Nagare, Sagar / Lokhande, Kiran Bharat / Swamy, K Venkateswara

Journal of molecular modeling

2023 Volume 29, Issue 4, Page(s) 90

Abstract: Flavanone compounds are naturally occurring phytochemicals present in most of citrus fruits reported to be a potential anticancer moiety as it majorly participates in the inhibition of the cell cycle, apoptosis, and angiogenesis. Because of poor ... ...

Abstract	Flavanone compounds are naturally occurring phytochemicals present in most of citrus fruits reported to be a potential anticancer moiety as it majorly participates in the inhibition of the cell cycle, apoptosis, and angiogenesis. Because of poor bioavailability, natural flavanones were not used as therapeutic targets so flavanone congeners were prepared by modifying at B-functional group using compound libraries such as PubChem Database. Cyclin-dependent kinase is primarily activating the cell cycle and potentiating the M phase, in order to control the cell cycle in cancer cyclin-dependent pathway was targeted and potential cyclin D/CDK4 receptor protein was retrieved from Protein Data Bank (PDBID:2W9Z). The binding site was determined using FlexX docking. Flavanone and its congeners were docked against the 2W9Z receptor protein with the docking software FlexX. For validation of docking results, molecular dynamics simulations of the best-fitting molecule were carried out using Desmond Package. Noncovalent interactions like hydrogen bonds, electrostatic interaction, and Van der walls potentials for stable conformations were calculated. Thus, upon docking and molecular dynamics studies, we discovered the potential flavanone derivatives such as Flavanone 20, Flavanone 25, and Flavanone 29, will become a potential drug target in controlling cell cycle arrest and may become a futuristic candidate in targeting cancer.
MeSH term(s)	Humans ; Cyclins ; Cell Cycle Checkpoints ; Flavanones/pharmacology ; Molecular Dynamics Simulation ; Neoplasms/drug therapy ; Cyclin D ; Cyclin-Dependent Kinase 4
Chemical Substances	Cyclins ; flavanone (WX22P730FB) ; Flavanones ; Cyclin D ; CDK4 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 4 (EC 2.7.11.22)
Language	English
Publishing date	2023-03-07
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05496-6
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Article ; Online: Docking and simulation studies on cyclin D/CDK4 complex for targeting cell cycle arrest in cancer using flavanone and its congener

Nagare, Sagar / Lokhande, Kiran Bharat / Swamy, K. Venkateswara

J Mol Model. 2023 Apr., v. 29, no. 4 p.90-90

2023

Abstract	Flavanone compounds are naturally occurring phytochemicals present in most of citrus fruits reported to be a potential anticancer moiety as it majorly participates in the inhibition of the cell cycle, apoptosis, and angiogenesis. Because of poor bioavailability, natural flavanones were not used as therapeutic targets so flavanone congeners were prepared by modifying at B-functional group using compound libraries such as PubChem Database. Cyclin-dependent kinase is primarily activating the cell cycle and potentiating the M phase, in order to control the cell cycle in cancer cyclin-dependent pathway was targeted and potential cyclin D/CDK4 receptor protein was retrieved from Protein Data Bank (PDBID:2W9Z). The binding site was determined using FlexX docking. Flavanone and its congeners were docked against the 2W9Z receptor protein with the docking software FlexX. For validation of docking results, molecular dynamics simulations of the best-fitting molecule were carried out using Desmond Package. Noncovalent interactions like hydrogen bonds, electrostatic interaction, and Van der walls potentials for stable conformations were calculated. Thus, upon docking and molecular dynamics studies, we discovered the potential flavanone derivatives such as Flavanone 20, Flavanone 25, and Flavanone 29, will become a potential drug target in controlling cell cycle arrest and may become a futuristic candidate in targeting cancer.
Keywords	Citrus ; angiogenesis ; apoptosis ; bioavailability ; cell cycle checkpoints ; computer software ; cyclin-dependent kinase ; cyclins ; databases ; drugs ; electrostatic interactions ; flavanones ; hydrogen ; models ; moieties ; molecular dynamics ; therapeutics
Language	English
Dates of publication	2023-04
Size	p. 90.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05496-6
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Exploring the role of TLK2 mutation in tropical calcific pancreatitis: an

Shrivastava, Ashish / Magani, Sri Krishna Jayadev / Lokhande, Kiran Bharat / Chintakhindi, Madhusudan / Singh, Ashutosh

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–20

Abstract: Tropical calcific pancreatitis (TCP) is a juvenile form of non-alcoholic chronic pancreatitis seen exclusively in tropical countries. The disease poses a high risk of complications, including pancreatic diabetes and cancer, leading to significant ... ...

Abstract	Tropical calcific pancreatitis (TCP) is a juvenile form of non-alcoholic chronic pancreatitis seen exclusively in tropical countries. The disease poses a high risk of complications, including pancreatic diabetes and cancer, leading to significant mortality due to poor diagnosis and ineffective treatments. This study employed whole exome sequencing (WES) of 5 TCP patient samples to identify genetic variants associated with TCP. Advanced computational techniques were used to gain atomic-level insights into disease progression, including microsecond-scale long MD simulations and essential dynamics.
Language	English
Publishing date	2024-03-18
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2329797
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Article ; Online: Identification and Screening of Novel Anti-Cancer Compounds for Aurora Kinase-A from Chemical Database.

Singh, Ipsa A / Lokhande, Kiran Bharat / Swamy, K Venkateswara

Drug research

2022

Abstract: Aurora kinase is a group of enzymes that belongs to a serine-threonine family and plays a critical role in cellular division. Aurora Kinase A is overexpressed and distributed beyond the nucleus and is involved in tumorigenesis. Flavones are a class of ... ...

Abstract	Aurora kinase is a group of enzymes that belongs to a serine-threonine family and plays a critical role in cellular division. Aurora Kinase A is overexpressed and distributed beyond the nucleus and is involved in tumorigenesis. Flavones are a class of flavonoids that are present in plants that show anticancer activity. Similar compounds of 2'Fluoroflavones are retrieved from the PubChem database. Then drug-like filters viz. REOS and PAINS were applied to remove toxic compounds using Canvas software, resulting in 3882 compounds being subjected to Glide docking with Aurora kinase A. The lead compounds were selected on the merit of hydrogen bonding, salt bridge, as well as pi-pi interactions, 4-(6-Fluoro-4-oxychromen-2yl) benzoic acid, has been found one of the best molecules from docking studies. The binding mode of the lead compound with AURKA reveals that the amino acid residues viz, Lys162, Ala213, and His280 are more important for binding with the binding affinity of -11.760 kcal/mol. The molecular dynamics simulations of 100 ns were done, which shows the mean RMSD value of 1.77 Å for all 3 complexes of the protein and Fluoroflavone and its analogs. This shows that Fluoroflavone and its 2 best analogs are tightly attached to the active sites and thus have conformational stability. Our finding suggests that 4-(6-fluoro-4-oxochromen-2-yl)benzoic acid and 4-(4-Oxochromen-2-yl)benzoate can be further used
Language	English
Publishing date	2022-09-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2703847-6
ISSN	2194-9387 ; 2194-9379
ISSN (online)	2194-9387
ISSN	2194-9379
DOI	10.1055/a-1877-4693
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Article ; Online: Molecular Docking and Simulation Studies of Flavanone and its Derived Compounds on PI3K-AKT Pathway Targeting against Cancer.

Nagare, Sagar / Lokhande, Kiran Bharat / Swamy, K Venkateswara

Current drug discovery technologies

2022 Volume 20, Issue 1, Page(s) e260522205302

Abstract: Background: Flavanone compounds and their related derivatives are reported in controlling cell cycle, angiogenesis, and metastasis. Phosphoinositide 3-kinases is a major drug target.: Methods: Crystalize structure of Phosphoinositide 3-kinases-Akt ... ...

Abstract	Background: Flavanone compounds and their related derivatives are reported in controlling cell cycle, angiogenesis, and metastasis. Phosphoinositide 3-kinases is a major drug target. Methods: Crystalize structure of Phosphoinositide 3-kinases-Akt complex obtained from Protein Data Bank (PDBID: 3CQW) was selected as receptor protein and the binding site has been identified with PDBSum Database. Flavanone and its derivatives were retrieved using freely available existing drug databases like Drug Bank, Zinc, and PubChem. New derivatives were modified by altering the flavanone at Beta ring position. This modification would help in maintaining stable structural conformation and retaining better anticancer activity. Retrieved Flavanone derivatives from the drug database were docked against 3CQW Protein with the advanced docking tool FlexX. MD simulations of the best molecule were performed with the Desmond package by calculating nonbonding interactions such as electrostatic interaction and hydrogen bond stable and favorable conformations were calculated. Results: These interaction studies would help identify new potential drug candidates with the help of computer-aided drug designing techniques. Conclusion: Natural chemicals have received a lot of attention because of their vast range of applications in human health and disease prevention without creating any negative side effects. Molecular docking is an essential approach for drug development since it allows for effective screening of potential therapeutics in a short time. We hypothesized in this paper that natural flavanone and its derivatives may be effective as Akt-1 inhibitors.
MeSH term(s)	Humans ; Molecular Docking Simulation ; Phosphatidylinositol 3-Kinases ; Proto-Oncogene Proteins c-akt ; Molecular Dynamics Simulation ; Neoplasms/drug therapy ; Protein Kinase Inhibitors/pharmacology ; Phosphatidylinositols
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Protein Kinase Inhibitors ; Phosphatidylinositols
Language	English
Publishing date	2022-07-13
Publishing country	United Arab Emirates
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1875-6220
ISSN (online)	1875-6220
DOI	10.2174/1570163819666220526150152
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Article ; Online: Identification of potential drug candidates as TGR5 agonist to combat type II diabetes using

Bhimanwar, Rachana S / Lokhande, Kiran Bharat / Shrivastava, Ashish / Singh, Ashutosh / Chitlange, Sohan S / Mittal, Amit

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 22, Page(s) 13314–13331

Abstract: A cell surface bile acid receptor TGR5 being considered as a novel target for Type II diabetes found to be expressed in various tissues. A major role for TGR5 is to maintain blood sugar levels and increase in energy expenditure. These benefits make it a ... ...

Abstract	A cell surface bile acid receptor TGR5 being considered as a novel target for Type II diabetes found to be expressed in various tissues. A major role for TGR5 is to maintain blood sugar levels and increase in energy expenditure. These benefits make it a potential candidate for the treatment of type 2 diabetes, obesity and other metabolic disorder. To date, many novel TGR5 agonists have been synthesized and evaluated in the literature, but very few
MeSH term(s)	Humans ; Molecular Dynamics Simulation ; Molecular Docking Simulation ; Diabetes Mellitus, Type 2/drug therapy ; Coumarins
Chemical Substances	Coumarins
Language	English
Publishing date	2023-02-01
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2173654
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Article: [No title information]

Singh, Ipsa A. / Lokhande, Kiran Bharat / Swamy, K. Venkateswara

Drug Research

2022 Volume 73, Issue 01, Page(s) 30–39

Abstract	Aurora kinase is a group of enzymes that belongs to a serine-threonine family and plays a critical role in cellular division. Aurora Kinase A is overexpressed and distributed beyond the nucleus and is involved in tumorigenesis. Flavones are a class of flavonoids that are present in plants that show anticancer activity. Similar compounds of 2’Fluoroflavones are retrieved from the PubChem database. Then drug-like filters viz. REOS and PAINS were applied to remove toxic compounds using Canvas software, resulting in 3882 compounds being subjected to Glide docking with Aurora kinase A. The lead compounds were selected on the merit of hydrogen bonding, salt bridge, as well as pi-pi interactions, 4-(6-Fluoro-4-oxychromen-2yl) benzoic acid, has been found one of the best molecules from docking studies. The binding mode of the lead compound with AURKA reveals that the amino acid residues viz, Lys162, Ala213, and His280 are more important for binding with the binding affinity of -11.760 kcal/mol. The molecular dynamics simulations of 100 ns were done, which shows the mean RMSD value of 1.77 Å for all 3 complexes of the protein and Fluoroflavone and its analogs. This shows that Fluoroflavone and its 2 best analogs are tightly attached to the active sites and thus have conformational stability. Our finding suggests that 4-(6-fluoro-4-oxochromen-2-yl)benzoic acid and 4-(4-Oxochromen-2-yl)benzoate can be further used in vitro and in vivo experiments and can probably serve as a novel drug for cancer treatment.
Keywords	Aurora kinase A ; Fluoroflavones ; chemoinformatics ; Glide docking ; MD simulation ; Enrichment calculations
Language	English
Publishing date	2022-09-22
Publisher	Georg Thieme Verlag
Publishing place	Stuttgart ; New York
Document type	Article
ZDB-ID	2703847-6
ISSN	2194-9387 ; 2194-9379
ISSN (online)	2194-9387
ISSN	2194-9379
DOI	10.1055/a-1877-4693
Database	Thieme publisher's database

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Article ; Online: Novel B, C-ring truncated deguelin derivatives reveals as potential inhibitors of cyclin D1 and cyclin E using molecular docking and molecular dynamic simulation.

Lokhande, Kiran Bharat / Ghosh, Payel / Nagar, Shuchi / Venkateswara Swamy, K

Molecular diversity

2021 Volume 26, Issue 4, Page(s) 2295–2309

Abstract: The overexpression of cyclin D1 and cyclin E due to their oncogenic potential and amplification has been associated with a higher mortality rate in many cancers. The deguelin is a natural compound, has shown promising anti-cancer activity by directly ... ...

Abstract	The overexpression of cyclin D1 and cyclin E due to their oncogenic potential and amplification has been associated with a higher mortality rate in many cancers. The deguelin is a natural compound, has shown promising anti-cancer activity by directly binding cyclin D1 and cyclin E and thus suppressing its function. The C7a atomic position of deguelin structure contains a proton that generates stabilized radical, as a result, decomposed deguelin reduces its structural stability and significantly decreases its biological activity. To design deguelin derivatives with the reduced potential side effect, series of B, C-ring truncated derivatives were investigated as cyclin D1 and cyclin E inhibitors. R-group-based enumeration was implemented in the deguelin scaffold using the R-group enumeration module of Schrödinger. Drug-Like filters like, REOS and PAINs series were applied to the enumerated compound library to remove compounds containing reactive functional groups. Further, screened compounds were docked within the ligand-binding cavity of cyclin D1 and cyclin E crystal structure, using Glide SP and XP protocol to obtain docking poses. Enrichment calculations were done using SchrÖdinger software, with 1000 decoy compounds (from DUD.E database) and 60 compounds (XP best poses) along with deguelin, to validate the docking protocol. The receiver operating characteristic (ROC) curve indicates R
MeSH term(s)	Cyclin D1/metabolism ; Cyclin E/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Rotenone/analogs & derivatives
Chemical Substances	Cyclin E ; Rotenone (03L9OT429T) ; Cyclin D1 (136601-57-5) ; deguelin (K5Z93K66IE)
Language	English
Publishing date	2021-10-09
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/s11030-021-10334-z
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