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Singh M, Rajawat J, Kuldeep J, Shukla N, Mishra DP, Siddiqi MI. Integrated support vector machine and pharmacophore based virtual screening driven identification of thiophene carboxamide scaffold containing compound as potential PARP1 inhibitor. J Biomol Struct Dyn 2021; 40:8494-8507. [PMID: 33950778 DOI: 10.1080/07391102.2021.1913229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) inhibition strategy for cancer treatment is gaining advantage particularly in patients having a mutation in BRCA1/BRCA2 gene. To date, four drugs have obtained FDA approval and some inhibitors are in clinical trials. To identify more potent PARP1 inhibitors extensive research is going on to enrich the library of PARP1 inhibitors with compounds belonging to different classes. We employed an integrated virtual screening approach to identify potential PARP1 inhibitors. The sequential support vector machine (SVM) and pharmacophore model based virtual screening was carried out on the Maybridge library. The obtained hits were docked in the binding site of the PARP1 catalytic domain and nine drug-like compounds showing good ADME properties and form critical molecular interactions with the binding site residues were considered for the in vitro PARP1 inhibition assay. MD simulations were performed to decipher the stability of the PARP1-ligand complexes. Hydrogen bond interactions were also probed for their stability during MD simulations. We have identified three compounds (BTB02767, GK01172, and KM09200) showing 50% inhibition of PARP1 enzyme activity at 25 μM. BTB02767 and KM09200 have phthalazinone scaffold, while GK01172 bears a thiophene carboxamide scaffold, which could be a new chemotype of PARP1 inhibitors. In conclusion, GK01172 may serve as an important compound for further development of PARP1 inhibitors containing thiophene carboxamide scaffold.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maninder Singh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
| | - Jyotika Rajawat
- Endocrinology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
| | - Jitendra Kuldeep
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
| | - Nidhi Shukla
- Endocrinology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
| | - Durga Prasad Mishra
- Endocrinology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
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Pant AB. The Implementation of the Three Rs in Regulatory Toxicity and Biosafety Assessment: The Indian Perspective. Altern Lab Anim 2021; 48:234-251. [PMID: 33523713 DOI: 10.1177/0261192920986811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Animal models have long served as a basis for scientific experimentation, biomedical research, drug development and testing, disease modelling and toxicity studies, as they are widely thought to provide meaningful, human-relevant predictions. However, many of these systems are resource intensive and time-consuming, have low predictive value and are associated with great social and ethical dilemmas. Often drugs appear to be effective and safe in these classical animal models, but later prove to be ineffective and/or unsafe in clinical trials. These issues have paved the way for a paradigm shift from the use of in vivo approaches, toward the 'science of alternatives'. This has fuelled several research and regulatory initiatives, including the ban on the testing of cosmetics on animals. The new paradigm has been shifted toward increasing the relevance of the models for human predictivity and translational efficacy, and this has resulted in the recent development of many new methodologies, from 3-D bio-organoids to bioengineered 'human-on-a-chip' models. These improvements have the potential to significantly advance medical research globally. This paper offers a stance on the existing strategies and practices that utilise alternatives to animals, and outlines progress on the incorporation of these models into basic and applied research and education, specifically in India. It also seeks to provide a strategic roadmap to streamline the future directions for the country's policy changes and investments. This strategic roadmap could be a useful resource to guide research institutions, industries, regulatory agencies, contract research organisations and other stakeholders in transitioning toward modern approaches to safety and risk assessment that could replace or reduce the use of animals without compromising the safety of humans or the environment.
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Affiliation(s)
- Aditya B Pant
- System Toxicology and Health Risk Assessment Group, 538266Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, India
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Ahmad S, Bhagwati S, Kumar S, Banerjee D, Siddiqi MI. Molecular modeling assisted identification and biological evaluation of potent cathepsin S inhibitors. J Mol Graph Model 2019; 96:107512. [PMID: 31881466 DOI: 10.1016/j.jmgm.2019.107512] [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: 07/15/2019] [Revised: 11/20/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022]
Abstract
Cathepsin S (CatS) is one of the cysteinyl cathepsins widely studied for its clinical significance and found to be a promising therapeutic target for several diseases; to name a few is arthritis, allergic inflammation, cancer, diabetes, obesity, and cystic fibrosis. Elevated CatS level is a contributing factor for related disorders, and therefore among different strategies to regulate the activity of CatS, one is to design a quality inhibitor. Earlier, we have demonstrated a highly selective CatS inhibitor, RO5444101 interacts primarily with the S2 pocket of the protein which is structurally unique in contrast to other variants of cathepsin. However, the molecular properties of RO5444101 can question its efficacy at the clinical level. In the present study, we have implemented a series of molecular modeling methods to screen the Maybridge library considering the pharmacophoric features of RO5444101 and other relevant inhibitors of CatS. Based on the priority list, eight hits were subjected to biological evaluation. Subsequently, KM07987 was found to be most potent, with the IC50 of <5 μM. Molecular dynamics simulations also relate to our experimental findings and propose the importance of CatS's S2 pocket, which primarily interacts with the inhibitors. Based on the S2 pocket interactions, structural modifications of the promising hits can further be translated into novel scaffolds for improved inhibition of CatS.
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Affiliation(s)
- Sabahuddin Ahmad
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Sudha Bhagwati
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Sushil Kumar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Dibyendu Banerjee
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India.
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Malvacio I, Cuzzolin A, Sturlese M, Vera DMA, Moyano EL, Moro S. Synthesis and preliminary structure-activity relationship study of 2-aryl-2H-pyrazolo[4,3-c]quinolin-3-ones as potential checkpoint kinase 1 (Chk1) inhibitors. J Enzyme Inhib Med Chem 2017; 33:171-183. [PMID: 29210298 PMCID: PMC6010083 DOI: 10.1080/14756366.2017.1404592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The serine-threonine checkpoint kinase 1 (Chk1) plays a critical role in the cell cycle arrest in response to DNA damage. In the last decade, Chk1 inhibitors have emerged as a novel therapeutic strategy to potentiate the anti-tumour efficacy of cytotoxic chemotherapeutic agents. In the search for new Chk1 inhibitors, a congeneric series of 2-aryl-2 H-pyrazolo[4,3-c]quinolin-3-one (PQ) was evaluated by in-vitro and in-silico approaches for the first time. A total of 30 PQ structures were synthesised in good to excellent yields using conventional or microwave heating, highlighting that 14 of them are new chemical entities. Noteworthy, in this preliminary study two compounds 4e2 and 4h2 have shown a modest but significant reduction in the basal activity of the Chk1 kinase. Starting from these preliminary results, we have designed the second generation of analogous in this class and further studies are in progress in our laboratories.
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Affiliation(s)
- Ivana Malvacio
- a Department of Organic Chemistry, INFIQC, School of Chemical Sciences , National University of Cordoba , Cordoba , Argentina.,b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - Alberto Cuzzolin
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - Mattia Sturlese
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - D Mariano A Vera
- c Department of Chemistry, QUIAMM-INBIOTEC, School of Exact and Natural Sciences , National University of Mar del Plata , Mar del Plata , Buenos Aires , Argentina
| | - E Laura Moyano
- a Department of Organic Chemistry, INFIQC, School of Chemical Sciences , National University of Cordoba , Cordoba , Argentina
| | - Stefano Moro
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
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"Hepatocellular carcinoma: A life-threatening disease". Biomed Pharmacother 2016; 84:1679-1688. [PMID: 27823920 DOI: 10.1016/j.biopha.2016.10.078] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 10/13/2016] [Accepted: 10/26/2016] [Indexed: 02/07/2023] Open
Abstract
An estimated rise in liver cancer incidence will increase to 95374 new cases by 2020. Hepatocellular Carcinoma (HCC), the most common primary malignant tumour of the liver, is considered to be the third leading cause of all cancer-related deaths and fifth common cancer worldwide. The reported data shows that the rate of HCC incidence in male population is three to four times higher compared with the female population. In the United States, HCV-induced liver cancer is increasing very fast because of the lack of proper treatment option. There are various treatment strategies available for HCC like liver transplantation, resection, ablation, embolization and chemotherapy still the prognosis is destitute. If the patient is eligible, liver transplantation is the only therapeutic option that may give around 90% survival rate, but the scarcity of liver donor limits its broad applicability. A sudden address is necessary to develop specific drugs, personalized medicine, for HCC.
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Wang J, Shu M, Wang Y, Hu Y, Wang Y, Luo Y, Lin Z. Identification of potential CCR5 inhibitors through pharmacophore-based virtual screening, molecular dynamics simulation and binding free energy analysis. MOLECULAR BIOSYSTEMS 2016; 12:3396-3406. [DOI: 10.1039/c6mb00577b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Employing the combined strategy to identify novel CCR5 inhibitors and provide a basis for rational drug design.
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Affiliation(s)
- Juan Wang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Mao Shu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yong Hu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yuanliang Wang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Yanfeng Luo
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Zhihua Lin
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- College of Chemistry and Chemical Engineering
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Singh N, Tiwari S, Srivastava KK, Siddiqi MI. Identification of Novel Inhibitors of Mycobacterium tuberculosis PknG Using Pharmacophore Based Virtual Screening, Docking, Molecular Dynamics Simulation, and Their Biological Evaluation. J Chem Inf Model 2015; 55:1120-9. [PMID: 25965448 DOI: 10.1021/acs.jcim.5b00150] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PknG is a Ser/thr protein kinase that plays a crucial role in regulatory processes within the mycobacterial cell and signaling cascade of the infected host cell. The essentiality of PknG in mycobacterial virulence by blocking phagosome-lysosome fusion as well as its role in intrinsic antibiotic resistance makes it an attractive drug target. However, only very few compounds have been reported as Mycobacterium tuberculosis PknG (MtPknG) inhibitors so far. Therefore, in an effort to find potential inhibitors against MtPknG, we report here a sequential pharmacophore-based virtual screening workflow, 3-fold docking with different search algorithms, and molecular dynamic simulations for better insight into the predicted binding mode of identified hits. After detailed analysis of the results, six ligands were selected for in vitro analysis. Three of these molecules showed significant inhibitory activity against MtPknG. In addition, inhibitory studies of mycobacterial growth in infected THP-1 macrophages demonstrated considerable growth inhibition of M. bovis BCG induced through compound NRB04248 without any cytotoxic effect against host macrophages. Our results suggest that the compound NRB04248 can be explored for further design and optimization of MtPknG inhibitors.
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