1
|
Computational Approaches to the Rational Design of Tubulin-Targeting Agents. Biomolecules 2023; 13:biom13020285. [PMID: 36830654 PMCID: PMC9952983 DOI: 10.3390/biom13020285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microtubules are highly dynamic polymers of α,β-tubulin dimers which play an essential role in numerous cellular processes such as cell proliferation and intracellular transport, making them an attractive target for cancer and neurodegeneration research. To date, a large number of known tubulin binders were derived from natural products, while only one was developed by rational structure-based drug design. Several of these tubulin binders show promising in vitro profiles while presenting unacceptable off-target effects when tested in patients. Therefore, there is a continuing demand for the discovery of safer and more efficient tubulin-targeting agents. Since tubulin structural data is readily available, the employment of computer-aided design techniques can be a key element to focus on the relevant chemical space and guide the design process. Due to the high diversity and quantity of structural data available, we compiled here a guide to the accessible tubulin-ligand structures. Furthermore, we review different ligand and structure-based methods recently used for the successful selection and design of new tubulin-targeting agents.
Collapse
|
2
|
Mondal D, Kalar PL, Kori S, Gayen S, Das K. Recent Developments on Synthesis of Indole Derivatives Through Green Approaches and Their Pharmaceutical Applications. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999201111203812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Indole moiety is often found in different classes of pharmaceutically active molecules
having various biological activities including anticancer, anti-viral, anti-psychotic, antihypertensive,
anti-migraine, anti-arthritis and analgesic activities. Due to enormous applications
of indole derivatives in pharmaceutical chemistry, a number of conventional synthetic
methods as well as green methodology have been developed for their synthesis. Green methodology
has many advantages including high yields, short reaction time, and inexpensive
reagents, highly efficient and environmentally benign over conventional methods. Currently,
the researchers in academia as well as in pharmaceutical industries have been developing
various methods for the chemical synthesis of indole based compounds via green approaches
to overcome the drawbacks of conventional methods. This review reflects the last ten years
developments of the various greener methods for the synthesis of indole derivatives by using microwave, ionic liquids,
water, ultrasound, nanocatalyst, green catalyst, multicomponent reaction and solvent-free reactions etc. (please
see the scheme below). Furthermore, the applications of green chemistry towards developments of indole containing
pharmaceuticals and their biological studies have been represented in this review.
Collapse
Affiliation(s)
- Dipayan Mondal
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh 470003, India
| | - Pankaj Lal Kalar
- Advanced Organic Synthesis Laboratory, Department of Chemistry, Dr. Harisingh Gour University, Sagar, Madhya Pradesh 470003, India
| | - Shivam Kori
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh 470003, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh 470003, India
| | - Kalpataru Das
- Advanced Organic Synthesis Laboratory, Department of Chemistry, Dr. Harisingh Gour University, Sagar, Madhya Pradesh 470003, India
| |
Collapse
|
3
|
Amin SA, Ghosh K, Mondal D, Jha T, Gayen S. Exploring indole derivatives as myeloid cell leukaemia-1 (Mcl-1) inhibitors with multi-QSAR approach: a novel hope in anti-cancer drug discovery. NEW J CHEM 2020. [DOI: 10.1039/d0nj03863f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In humans, the over-expression of Mcl-1 protein causes different cancers and it is also responsible for cancer resistance to different cytotoxic agents.
Collapse
Affiliation(s)
- Sk. Abdul Amin
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata
| | - Kalyan Ghosh
- Laboratory of Drug Design and Discovery
- Department of Pharmaceutical Sciences
- Dr Harisingh Gour University
- Sagar
- India
| | - Dipayan Mondal
- Laboratory of Drug Design and Discovery
- Department of Pharmaceutical Sciences
- Dr Harisingh Gour University
- Sagar
- India
| | - Tarun Jha
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery
- Department of Pharmaceutical Sciences
- Dr Harisingh Gour University
- Sagar
- India
| |
Collapse
|
4
|
Interplay of thermochemistry and Structural Chemistry, the journal (volume 29, 2018, issues 3–4) and the discipline. Struct Chem 2019. [DOI: 10.1007/s11224-019-01359-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
5
|
Bhardwaj B, Baidya ATK, Amin SA, Adhikari N, Jha T, Gayen S. Insight into structural features of phenyltetrazole derivatives as ABCG2 inhibitors for the treatment of multidrug resistance in cancer. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:457-475. [PMID: 31157558 DOI: 10.1080/1062936x.2019.1615545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
ABCG2 is the principal ABC transporter involved in the multidrug resistance of breast cancer. Looking at the current demand in the development of ABCG2 inhibitors for the treatment of multidrug-resistant cancer, we have explored structural requirements of phenyltetrazole derivatives for ABCG2 inhibition by combining classical QSAR, Bayesian classification modelling and molecular docking studies. For classical QSAR, structural descriptors were calculated from the free software tool PaDEL-descriptor. Stepwise multiple linear regression (SMLR) was used for model generation. A statistically significant model was generated and validated with different parameters (For training set: r = 0.825; Q2 = 0.570 and for test set: r = 0.894, r2pred = 0.783). The predicted model was found to satisfy the Golbraikh and Trospha criteria for model acceptability. Bayesian classification modelling was also performed (ROC scores were 0.722 and 0.767 for the training and test sets, respectively). Finally, the binding interactions of phenyltetrazole type inhibitor with the ABCG2 receptor were mapped with the help of molecular docking study. The result of the docking analysis is aligned with the classical QSAR and Bayesian classification studies. The combined modelling study will guide the medicinal chemists to act faster in the drug discovery of ABCG2 inhibitors for the management of resistant breast cancer.
Collapse
Affiliation(s)
- B Bhardwaj
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University , Madhya Pradesh , India
| | - A T K Baidya
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University , Madhya Pradesh , India
| | - S A Amin
- b Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal & Pharmaceutical Chemistry , Jadavpur University , Kolkata , India
| | - N Adhikari
- b Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal & Pharmaceutical Chemistry , Jadavpur University , Kolkata , India
| | - T Jha
- b Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal & Pharmaceutical Chemistry , Jadavpur University , Kolkata , India
| | - S Gayen
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University , Madhya Pradesh , India
| |
Collapse
|
6
|
Gaikwad R, Bobde Y, Ganesh R, Patel T, Rathore A, Ghosh B, Das K, Gayen S. 2-Phenylindole derivatives as anticancer agents: synthesis and screening against murine melanoma, human lung and breast cancer cell lines. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2019.1620282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ruchi Gaikwad
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. H. S. Gour University, Sagar, India
| | - Yamini Bobde
- Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Hyderabad, India
| | - Routholla Ganesh
- Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Hyderabad, India
| | - Tarun Patel
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. H. S. Gour University, Sagar, India
| | - Anju Rathore
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. H. S. Gour University, Sagar, India
| | - Balaram Ghosh
- Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Hyderabad, India
| | - Kalpataru Das
- Advance Organic Synthesis Laboratory, Department of Chemistry, Dr. H. S. Gour University, Sagar, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. H. S. Gour University, Sagar, India
| |
Collapse
|
7
|
Banerjee S, Adhikari N, Amin SA, Jha T. Structural exploration of tetrahydroisoquinoline derivatives as HDAC8 inhibitors through multi-QSAR modeling study. J Biomol Struct Dyn 2019; 38:1551-1564. [PMID: 31074329 DOI: 10.1080/07391102.2019.1617782] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Histone deacetylase 8 (HDAC8) is one of the crucial HDACs responsible for influencing the epigenetic functions of the body. Overexpression of HDAC8 is found to be involved in numerous disease conditions such as tumorigenesis, cell proliferation, cancer, viral infections, neuronal disorders and other epigenetic diseases. Therefore, inhibition of HDAC8 is a primary method to combat these diseases. In this article, a multi-QSAR modeling study on tetrahydroisoquinoline derivatives was conducted to identify important contributions of the structural features of these compounds toward HDAC8 inhibition. All these QSAR modeling techniques were individually validated and justified the observations of each other. The results implied that the tetrahydroisoquinoline moiety may be effective as a cap group than as a linker moiety for HDAC8 inhibition. Different substitutions at the tetrahydroisoquinoline scaffold were also found to be crucial in modulating HDAC8 inhibition.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
- School of Pharmaceutical Technology, ADAMAS University, Kolkata, West Bengal, India
| | - Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| |
Collapse
|
8
|
Patel T, Gaikwad R, Jain K, Ganesh R, Bobde Y, Ghosh B, Das K, Gayen S. First Report on 3‐(3‐oxoaryl) Indole Derivatives as Anticancer Agents: Microwave Assisted Synthesis,
In Vitro
Screening and Molecular Docking Studies. ChemistrySelect 2019. [DOI: 10.1002/slct.201900088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tarun Patel
- Laboratory of Drug DesignDiscoveryDepartment of Pharmaceutical SciencesDr. Harisingh Gour University (A Central University) Sagar 470003, (MP) India
- Present address: Faculty of PharmacyKalinga University, Atal nagar Raipur 492101(CG) India
| | - Ruchi Gaikwad
- Laboratory of Drug DesignDiscoveryDepartment of Pharmaceutical SciencesDr. Harisingh Gour University (A Central University) Sagar 470003, (MP) India
| | - Kavita Jain
- Department of ChemistryDr. Harisingh Gour University (A Central University) Sagar 470003, (MP) India
| | - Routholla Ganesh
- Department of Pharmacy, BITS-PilaniHyderabad Campus Hyderabad 500078 India
| | - Yamini Bobde
- Department of Pharmacy, BITS-PilaniHyderabad Campus Hyderabad 500078 India
| | - Balaram Ghosh
- Department of Pharmacy, BITS-PilaniHyderabad Campus Hyderabad 500078 India
| | - Kalpataru Das
- Department of ChemistryDr. Harisingh Gour University (A Central University) Sagar 470003, (MP) India
| | - Shovanlal Gayen
- Laboratory of Drug DesignDiscoveryDepartment of Pharmaceutical SciencesDr. Harisingh Gour University (A Central University) Sagar 470003, (MP) India
| |
Collapse
|
9
|
Gaikwad R, Ghorai S, Amin SA, Adhikari N, Patel T, Das K, Jha T, Gayen S. Monte Carlo based modelling approach for designing and predicting cytotoxicity of 2-phenylindole derivatives against breast cancer cell line MCF7. Toxicol In Vitro 2018; 52:23-32. [DOI: 10.1016/j.tiv.2018.05.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/23/2018] [Accepted: 05/31/2018] [Indexed: 12/20/2022]
|