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Singh Y, Jaswal S, Singh S, Verma SK, Thareja S. Dual aromatase-steroid sulfatase inhibitors (DASI's) for the treatment of breast cancer: a structure guided ligand based designing approach. J Biomol Struct Dyn 2023; 41:10604-10626. [PMID: 36510679 DOI: 10.1080/07391102.2022.2155702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Dual aromatase-steroid sulfatase inhibitors (DASIs) lead to significant deprivation of estrogen levels as compared to a single target inhibition and thereby exhibited an additive or synergistic effect in the treatment of hormone-dependent breast cancer (HDBC). Triazole-bearing DASI's having structural features of clinically available aromatase inhibitors are identified as lead structures for optimization as DASI's. To identify the spatial fingerprints of target-specific triazole as DASI's, we have performed molecular docking assisted Gaussian field-based comparative 3D-QSAR studies on a dataset with dual aromatase-STS inhibitory activities. Separate contours were generated for both aromatase and steroid sulphates showing respective pharmacophoric structural requirements for optimal activity. These developed 3D-QSAR models also showed good statistical measures with the excellent predictive ability with PLS-generated validation constraints. Comparative steric, electrostatic, hydrophobic, HBA, and HBD features were elucidated using respective contour maps for selective target-specific favourable activity. Furthermore, the molecular docking was used for elucidating the mode of binding as DASI's along with the MD simulation of 100 ns revealed that all the protease-ligand docked complexes are overall stable as compared to reference ligand (inhibitor ASD or Irosustat) complex. Further, the MM-GBSA study revealed that compound 24 binds to aromatase as well as STS active site with relatively lower binding energy than reference complex, respectively. A comparative study of these developed multitargeted QSAR models along with molecular docking and dynamics study can be employed for the optimization of drug candidates as DASI's.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yogesh Singh
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Punjab, India
| | - Shalini Jaswal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Punjab, India
| | - Satwinder Singh
- Department of Computer Science and Technology, School of Engineering and Technology, Central University of Punjab, Punjab, India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Punjab, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Punjab, India
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Verma SK, Kumar N, Thareja S. Gaussian field-based comparative 3D QSAR modelling for the identification of favourable pharmacophoric features of chromene derivatives as selective inhibitors of ALR2 over ALR1. Struct Chem 2021. [DOI: 10.1007/s11224-020-01714-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Verma SK, Ratre P, Jain AK, Liang C, Gupta GD, Thareja S. De novo designing, assessment of target affinity and binding interactions against aromatase: Discovery of novel leads as anti-breast cancer agents. Struct Chem 2020. [DOI: 10.1007/s11224-020-01673-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Banjare L, Verma SK, Jain AK, Thareja S. Design and pharmacophoric identification of flavonoid scaffold‐based aromatase inhibitors. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Laxmi Banjare
- School of Pharmaceutical SciencesGuru Ghasidas Central University Bilaspur Chhattisgarh India
| | - Sant Kumar Verma
- School of Pharmaceutical SciencesGuru Ghasidas Central University Bilaspur Chhattisgarh India
| | - Akhlesh Kumar Jain
- School of Pharmaceutical SciencesGuru Ghasidas Central University Bilaspur Chhattisgarh India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural ProductsCentral University of Punjab Bathinda Punjab India
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Banjare L, Verma SK, Jain AK, Thareja S. Lead Molecules as Novel Aromatase Inhibitors: In Silico De Novo Designing and Binding Affinity Studies. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190703152659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Aromatase inhibitors emerged as a pivotal moiety to selectively block estrogen production, prevention and treatment of tumour growth in breast cancer. De novo drug design is an alternative approach to blind virtual screening for successful designing of the novel molecule against various therapeutic targets.Objective:In the present study, we have explored the de novo approach to design novel aromatase inhibitors.Method:The e-LEA3D, a computational-aided drug design web server was used to design novel drug-like candidates against the target aromatase. For drug-likeness ADME parameters (molecular weight, H-bond acceptors, H-bond donors, LogP and number of rotatable bonds) of designed molecules were calculated in TSAR software package, geometry optimization and energy minimization was accomplished using Chem Office. Further, molecular docking study was performed in Molegro Virtual Docker (MVD).Results:Among 17 generated molecules using the de novo pathway, 13 molecules passed the Lipinski filter pertaining to their bioavailability characteristics. De novo designed molecules with drug-likeness were further docked into the mapped active site of aromatase to scale up their affinity and binding fitness with the target. Among de novo fabricated drug like candidates (1-13), two molecules (5, 6) exhibited higher affinity with aromatase in terms of MolDock score (-150.650, -172.680 Kcal/mol, respectively) while molecule 8 showed lowest target affinity (-85.588 Kcal/mol).Conclusion:The binding patterns of lead molecules (5, 6) could be used as a pharmacophore for medicinal chemists to explore these molecules for their aromatase inhibitory potential.
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Affiliation(s)
- Laxmi Banjare
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495009 (C.G.), India
| | - Sant Kumar Verma
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495009 (C.G.), India
| | - Akhlesh Kumar Jain
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495009 (C.G.), India
| | - Suresh Thareja
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495009 (C.G.), India
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Mandavi S, Verma SK, Banjare L, Dubey A, Bhatt R, Thareja S, Jain AK. A Comprehension into Target Binding and Spatial Fingerprints of Noscapinoid Analogues as Inhibitors of Tubulin. Med Chem 2020; 17:611-622. [PMID: 31951171 DOI: 10.2174/1573406416666200117120348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Owing to its potential to interfere in microtubule dynamics in the mitotic phase of cell cycle and selectively induce apoptosis in cancer cells without affecting normal cells, noscapine and its synthetic analogues have been investigated by other research groups in different cell lines for their capability to be used as anti-cancer agents. OBJECTIVE The present study is focused on the investigation of the mode of binding of noscapinoids with tubulin, prediction of target binding affinities and mapping of their spatial fingerprints (shape and electrostatic). METHODS Molecular docking assisted alignment based 3D-QSAR was used on a dataset (43 molecules) having an inhibitory activity (IC50 = 1.2-250 μM) against human lymphoblast (CEM) cell line. RESULTS AND CONCLUSION Key amino acid residues of target tubulin were mapped for the binding of most potent noscapine analogue (Compound 11) and were compared with noscapine. Spatial fingerprints of noscapinoids for favorable tubulin inhibitory activity were generated and are proposed herewith for further pharmacophoric amendments of noscapine analogues to design and develop novel potent noscapine based anti-cancer agents that may enter into drug development pipeline.
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Affiliation(s)
- Seema Mandavi
- Department of Biotechnology, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
| | - Sant Kumar Verma
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
| | - Laxmi Banjare
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
| | - Amit Dubey
- Chhattisgarh Council of Science and Technology, Raipur-492 014 (C.G.), India
| | - Renu Bhatt
- Department of Biotechnology, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
| | - Suresh Thareja
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
| | - Akhlesh Kumar Jain
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
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Banjare L, Verma SK, Jain AK, Thareja S. Structure Guided Molecular Docking Assisted Alignment Dependent 3DQSAR Study on Steroidal Aromatase Inhibitors (SAIs) as Anti-breast Cancer Agents. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666181010101024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background:
In spite of the availability of various treatment approaches including
surgery, radiotherapy, and hormonal therapy, the steroidal aromatase inhibitors (SAIs) play a
significant role as chemotherapeutic agents for the treatment of estrogen-dependent breast cancer
with the benefit of reduced risk of recurrence. However, due to greater toxicity and side effects
associated with currently available anti-breast cancer agents, there is emergent requirement to
develop target-specific AIs with safer anti-breast cancer profile.
Methods:
It is challenging task to design target-specific and less toxic SAIs, though the molecular
modeling tools viz. molecular docking simulations and QSAR have been continuing for more than
two decades for the fast and efficient designing of novel, selective, potent and safe molecules
against various biological targets to fight the number of dreaded diseases/disorders. In order to
design novel and selective SAIs, structure guided molecular docking assisted alignment dependent
3D-QSAR studies was performed on a data set comprises of 22 molecules bearing steroidal
scaffold with wide range of aromatase inhibitory activity.
Results:
3D-QSAR model developed using molecular weighted (MW) extent alignment approach
showed good statistical quality and predictive ability when compared to model developed using
moments of inertia (MI) alignment approach.
Conclusion:
The explored binding interactions and generated pharmacophoric features (steric and
electrostatic) of steroidal molecules could be exploited for further design, direct synthesis and
development of new potential safer SAIs, that can be effective to reduce the mortality and
morbidity associated with breast cancer.
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Affiliation(s)
- Laxmi Banjare
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009, C.G., India
| | - Sant Kumar Verma
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009, C.G., India
| | - Akhlesh Kumar Jain
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009, C.G., India
| | - Suresh Thareja
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009, C.G., India
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Verma SK, Yadav YS, Thareja S. 2,4-Thiazolidinediones as PTP 1B Inhibitors: A Mini Review (2012-2018). Mini Rev Med Chem 2019; 19:591-598. [PMID: 30968766 DOI: 10.2174/1389557518666181026092029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/16/2022]
Abstract
2,4-thiazolidinedione (TZD) scaffold is a synthetic versatile scaffold explored by medicinal chemists for the discovery of novel molecules for the target-specific approach to treat or manage number of deadly ailments. PTP 1B is the negative regulator of insulin signaling cascade, and its diminished activity results in abolishment of insulin resistance associated with T2DM. The present review focused on the seven years journey (2012-2018) of TZDs as PTP 1B inhibitors with the insight into the amendments in the structural framework of TZD scaffold in order to optimize/design potential PTP 1B inhibitors. We have investigated the synthesized molecules based on TZD scaffold with potential activity profile against PTP 1B. Based on the SAR studies, the combined essential pharmacophoric features of selective and potent TZDs have been mapped and presented herewith for further design and synthesis of novel inhibitors of PTP 1B. Compound 46 bearing TZD scaffold with N-methyl benzoic acid and 5-(3-methoxy-4-phenethoxy) benzylidene exhibited the most potent activity (IC50 1.1 µM). Imidazolidine-2,4-dione, isosteric analogue of TZD, substituted with 1-(2,4-dichlorobenzyl)-5-(3-(2,4- dichlorobenzyloxy)benzylidene) (Compound 15) also endowed with very good PTP inhibitory activity profile (IC50 0.57 µM). It is noteworthy that Z-configuration is essential in structural framework around the double bond of arylidene for the designing of bi-dentate ligands with optimum activity.
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Affiliation(s)
- Sant Kumar Verma
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
| | - Yatesh Sharad Yadav
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
| | - Suresh Thareja
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur- 495 009 (C.G.), India
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Verma SK, Thareja S. Structure based comprehensive modelling, spatial fingerprints mapping and ADME screening of curcumin analogues as novel ALR2 inhibitors. PLoS One 2017; 12:e0175318. [PMID: 28399135 PMCID: PMC5388491 DOI: 10.1371/journal.pone.0175318] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/23/2017] [Indexed: 12/19/2022] Open
Abstract
Aldose reductase (ALR2) inhibition is the most legitimate approach for the management of diabetic complications. The limited triumph in the drug development against ALR2 is mainly because of its close structural similarity with the other members of aldo-keto reductase (AKR) superfamily viz. ALR1, AKR1B10; and lipophilicity problem i.e. poor diffusion of synthetic aldose reductase inhibitors (ARIs) to target tissues. The literature evidenced that naturally occurring curcumin demonstrates relatively specific and non-competitive inhibition towards human recombinant ALR2 over ALR1 and AKR1B10; however β-diketone moiety of curcumin is a specific substrate for liver AKRs and accountable for it’s rapid in vivo metabolism. In the present study, structure based comprehensive modelling studies were used to map the pharmacophoric features/spatial fingerprints of curcumin analogues responsible for their ALR2 specificity along with potency on a data set of synthetic curcumin analogues and naturally occurring curcuminoids. The data set molecules were also screened for drug-likeness or ADME parameters, and the screening data strongly support that curcumin analogues could be proposed as a good drug candidate for the development of ALR2 inhibitors with improved pharmacokinetic profile compared to curcuminoids due to the absence of β-diketone moiety in their structural framework.
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Affiliation(s)
- Sant Kumar Verma
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur, C.G., India
| | - Suresh Thareja
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur, C.G., India
- * E-mail:
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Payra S, Saha A, Wu CM, Selvaratnam B, Dramstad T, Mahoney L, Verma SK, Thareja S, Koodali R, Banerjee S. Fe–SBA-15 catalyzed synthesis of 2-alkoxyimidazo[1,2-a]pyridines and screening of their in silico selectivity and binding affinity to biological targets. NEW J CHEM 2016. [DOI: 10.1039/c6nj02134d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regioselective synthesis of 2-alkoxyimidazopyridines by Fe-SBA-15 and screening of their in silico binding affinity to biological targets.
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Affiliation(s)
- Soumen Payra
- Department of Chemistry
- Guru Ghasidas Vishwavidyalaya (A Central University)
- Bilaspur-495009
- India
| | - Arijit Saha
- Department of Chemistry
- Guru Ghasidas Vishwavidyalaya (A Central University)
- Bilaspur-495009
- India
| | - Chia-Ming Wu
- Department of Chemistry
- University of South Dakota
- Vermillion
- USA
| | | | - Thorn Dramstad
- Department of Chemistry
- University of South Dakota
- Vermillion
- USA
| | - Luther Mahoney
- Department of Chemistry
- University of South Dakota
- Vermillion
- USA
| | - Sant Kumar Verma
- School of Pharmaceutical Sciences
- Guru Ghasidas Vishwavidyalaya (A Central University)
- Bilaspur-495009
- India
| | - Suresh Thareja
- School of Pharmaceutical Sciences
- Guru Ghasidas Vishwavidyalaya (A Central University)
- Bilaspur-495009
- India
| | - Ranjit Koodali
- Department of Chemistry
- University of South Dakota
- Vermillion
- USA
| | - Subhash Banerjee
- Department of Chemistry
- Guru Ghasidas Vishwavidyalaya (A Central University)
- Bilaspur-495009
- India
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