1
|
Yadalam PK, Anegundi RV, Ramadoss R, Shrivastava D, Almufarrij RAS, Srivastava KC. AI-based 3D-QSAR model of FDA-approved repurposed drugs for inhibiting sclerostin. Technol Health Care 2024; 32:3007-3019. [PMID: 39031396 DOI: 10.3233/thc-231358] [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] [Indexed: 07/22/2024]
Abstract
BACKGROUND Wnt activation promotes bone formation and prevents bone loss. The Wnt pathway antagonist sclerostin and additional anti-sclerostin antibodies were discovered as a result of the development of the monoclonal antibody romosozumab. These monoclonal antibodies greatly increase the risk of cardiac arrest. Three-dimensional quantitative structure-activity relationships (3D-QSAR) predicts biological activities of ligands based on their three-dimensional features by employing powerful chemometric investigations such as artificial neural networks (ANNs) and partial least squares (PLS). OBJECTIVE In this study, ligand-receptor interactions were investigated using 3D-QSAR Comparative molecular field analysis (CoMFA). Estimates of steric and electrostatic characteristics in CoMFA are made using Lennard-Jones and Coulomb potentials. METHODS To identify the conditions necessary for the activity of these molecules, fifty Food and Drug Administration (FDA)-approved medications were chosen for 3D-QSAR investigations and done by CoMFA. For QSAR analysis, there are numerous tools available. This study employed Open 3D-QSAR for analysis due to its simplicity of use and capacity to produce trustworthy results. Four tools were used for the analysis on this platform: Py-MolEdit, Py-ConfSearch, and Py-CoMFA. RESULTS Maps that were generated were used to determine the screen's r2 (Coefficient of Multiple Determinations) value and q2 (correlation coefficient). These numbers must be fewer than 1, suggesting a good, trustworthy model. Cross-validated (q2) 0.532 and conventional (r2) correlation values of 0.969 made the CoMFA model statistically significant. The model showed that hydroxamic acid inhibitors are significantly more sensitive to the steric field than the electrostatic field (70%) (30%). This hypothesis states that steric (43.1%), electrostatic (26.4%), and hydrophobic (20.3%) qualities were important in the design of sclerostin inhibitors. CONCLUSION With 3D-QSAR and CoMFA, statistically meaningful models were constructed to predict ligand inhibitory effects. The test set demonstrated the model's robustness. This research may aid in the development of more effective sclerostin inhibitors that are synthesised using FDA-approved medications.
Collapse
Affiliation(s)
- Pradeep Kumar Yadalam
- Department of Periodontics, Saveetha Dental College and Hospitals Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Raghavendra Vamsi Anegundi
- Department of Periodontics, Saveetha Dental College and Hospitals Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ramya Ramadoss
- Department of Oral Biology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Deepti Shrivastava
- Preventive Dentistry Department, Periodontics Division, College of Dentistry, Jouf University, Sakaka, Saudi Arabia
| | | | - Kumar Chandan Srivastava
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Oral Medicine and Maxillofacial Radiology Division, College of Dentistry, Jouf University, Sakaka, Saudi Arabia
- Department of Oral Medicine and Radiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| |
Collapse
|
2
|
Zięba A, Laitinen T, Patel JZ, Poso A, Kaczor AA. Docking-Based 3D-QSAR Studies for 1,3,4-oxadiazol-2-one Derivatives as FAAH Inhibitors. Int J Mol Sci 2021; 22:6108. [PMID: 34204026 PMCID: PMC8201265 DOI: 10.3390/ijms22116108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
This work aimed to construct 3D-QSAR CoMFA and CoMSIA models for a series of 31 FAAH inhibitors, containing the 1,3,4-oxadiazol-2-one moiety. The obtained models were characterized by good statistical parameters: CoMFA Q2 = 0.61, R2 = 0.98; CoMSIA Q2 = 0.64, R2 = 0.93. The CoMFA model field contributions were 54.1% and 45.9% for steric and electrostatic fields, respectively. In the CoMSIA model, electrostatic, steric, hydrogen bond donor, and hydrogen acceptor properties were equal to 34.6%, 23.9%, 23.4%, and 18.0%, respectively. These models were validated by applying the leave-one-out technique, the seven-element test set (CoMFA r2test-set = 0.91; CoMSIA r2test-set = 0.91), a progressive scrambling test, and external validation criteria developed by Golbraikh and Tropsha (CoMFA r20 = 0.98, k = 0.95; CoMSIA r20 = 0.98, k = 0.89). As the statistical significance of the obtained model was confirmed, the results of the CoMFA and CoMSIA field calculation were mapped onto the enzyme binding site. It gave us the opportunity to discuss the structure-activity relationship based on the ligand-enzyme interactions. In particular, examination of the electrostatic properties of the established CoMFA model revealed fields that correspond to the regions where electropositive substituents are not desired, e.g., in the neighborhood of the 1,3,4-oxadiazol-2-one moiety. This highlights the importance of heterocycle, a highly electronegative moiety in this area of each ligand. Examination of hydrogen bond donor and acceptor properties contour maps revealed several spots where the implementation of another hydrogen-bond-donating moiety will positively impact molecules' binding affinity, e.g., in the neighborhood of the 1,3,4-oxadiazol-2-one ring. On the other hand, there is a large isopleth that refers to the favorable H-bond properties close to the terminal phenoxy group of a ligand, which means that, generally speaking, H-bond acceptors are desired in this area.
Collapse
Affiliation(s)
- Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, PL-20059 Lublin, Poland
| | - Tuomo Laitinen
- School of Pharmacy, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Jayendra Z Patel
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki, FI-00790 Helsinki, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, FI-70211 Kuopio, Finland
- Department of Internal Medicine VIII, University Hospital Tübingen, DE-72076 Tübingen, Germany
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, PL-20059 Lublin, Poland
- School of Pharmacy, University of Eastern Finland, FI-70211 Kuopio, Finland
| |
Collapse
|
3
|
Murumkar PR, Ghuge RB, Chauhan M, Barot RR, Sorathiya S, Choudhary KM, Joshi KD, Yadav MR. Recent developments and strategies for the discovery of TACE inhibitors. Expert Opin Drug Discov 2020; 15:779-801. [PMID: 32281878 DOI: 10.1080/17460441.2020.1744559] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION TNF-α plays a central role in certain autoimmune diseases as well as in inflammation. The current strategy for excluding TNF-α from circulation is to selectively inhibit TNF-α converting enzyme (TACE), an enzyme that cleaves mTNF-α to active TNF-α. Various TACE inhibitors have been discovered by using different strategies to control inflammatory diseases, cancer, and cardiac hypertrophy. AREAS COVERED The present article summarizes the design and discovery of novel TACE inhibitors that have been reported in the literature since 2012 onwards. It also includes some reports concerning the new role that TACE plays in cancer and cardiac hypertrophy. EXPERT OPINION So far, undertaken studies that have looked to design and develop small TACE inhibitors have been discouraging due to the failure of any TACE inhibitors to hit the market. However, some of the latest developments, such as with tartrate-based inhibitors, has given hope to the potentiality of a viable novel selective TACE inhibitor therapeutic in the future. Indeed, some of the novel peptidomimetics and monoclonal antibodies have great potential to pave the way for an effective and safe therapy by selectively inhibiting TACE enzyme.
Collapse
Affiliation(s)
- Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda , Vadodara, India
| | - Rahul B Ghuge
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda , Vadodara, India
| | - Monica Chauhan
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda , Vadodara, India
| | - Rahul R Barot
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda , Vadodara, India
| | - Sharmishtha Sorathiya
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda , Vadodara, India
| | - Kailash M Choudhary
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda , Vadodara, India
| | - Karan D Joshi
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda , Vadodara, India
| | - Mange Ram Yadav
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda , Vadodara, India
| |
Collapse
|
4
|
Murumkar PR, Shinde AC, Sharma MK, Yamaguchi H, Miniyar PB, Yadav MR. Development of a credible 3D-QSAR CoMSIA model and docking studies for a series of triazoles and tetrazoles containing 11β-HSD1 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:265-292. [PMID: 27094303 DOI: 10.1080/1062936x.2016.1167774] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Type 2 diabetes mellitus is described by insulin resistance and high fasting blood glucose. Increased levels of 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) enzyme result in insulin resistance and metabolic syndrome. Inhibition of 11β-HSD1 decreases glucose production and increases hepatic insulin sensitivity. Use of selective 11β-HSD1 inhibitors could prove to be an effective strategy for the treatment of the disease. It was decided to identify the essential structural features required by any compound to possess 11β-HSD1 inhibitory activity. A dataset of 139 triazoles and tetrazoles having 11β-HSD1 inhibitory activity was used for the development of a 3D-QSAR model. The best comparative molecular field analysis (CoMFA) model was generated with databased alignment, which was further used for comparative molecular similarity indices analysis (CoMSIA). The optimal CoMSIA model showed [Formula: see text] = 0.809 with five components, [Formula: see text] = 0.931, SEE = 0.323 and F-value = 249.126. The CoMSIA model offered better prediction than the CoMFA model with [Formula: see text] = 0.522 and 0.439, respectively, indicating that the CoMSIA model appeared to be a better one for the prediction of activity for the newly designed 11β-HSD1 inhibitors. The selectivity aspect of 11β-HSD1 over 11β-HSD2 was studied with the help of docking studies.
Collapse
Affiliation(s)
- P R Murumkar
- a Faculty of Pharmacy , The Maharaja Sayajirao University of Baroda , Vadodara , India
- b Sinhgad Institute of Pharmacy , Narhe , India
| | - A C Shinde
- b Sinhgad Institute of Pharmacy , Narhe , India
| | - M K Sharma
- a Faculty of Pharmacy , The Maharaja Sayajirao University of Baroda , Vadodara , India
- b Sinhgad Institute of Pharmacy , Narhe , India
| | - H Yamaguchi
- c Department of Pharmacy , Meijo University , Nagoya , Japan
| | - P B Miniyar
- b Sinhgad Institute of Pharmacy , Narhe , India
| | - M R Yadav
- a Faculty of Pharmacy , The Maharaja Sayajirao University of Baroda , Vadodara , India
| |
Collapse
|
5
|
Yadav MR, Barmade MA, Tamboli RS, Murumkar PR. Developing steroidal aromatase inhibitors-an effective armament to win the battle against breast cancer. Eur J Med Chem 2015; 105:1-38. [DOI: 10.1016/j.ejmech.2015.09.038] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 01/05/2023]
|
6
|
Sharma MK, Murumkar PR, Giridhar R, Yadav MR. Exploring structural requirements for peripherally acting 1,5-diaryl pyrazole-containing cannabinoid 1 receptor antagonists for the treatment of obesity. Mol Divers 2015; 19:871-93. [DOI: 10.1007/s11030-015-9611-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 07/01/2015] [Indexed: 10/23/2022]
|
7
|
Gupta SP. QSAR Studies on Hydroxamic Acids: A Fascinating Family of Chemicals with a Wide Spectrum of Activities. Chem Rev 2015; 115:6427-90. [DOI: 10.1021/cr500483r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Satya P. Gupta
- Department of Applied Sciences, National Institute of Technical Teachers’ Training and Research, Shamla
Hills, Bhopal-462002, India
| |
Collapse
|
8
|
Zambre VP, Hambarde VA, Petkar NN, Patel CN, Sawant SD. Structural investigations by in silico modeling for designing NR2B subunit selective NMDA receptor antagonists. RSC Adv 2015. [DOI: 10.1039/c5ra01098e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this paper, structural requirements for optimization of NR2B subunit selective NMDA receptor antagonists are discussed.
Collapse
Affiliation(s)
- Vishal P. Zambre
- Pharmaceutical Chemistry Department
- Sinhgad Technical Education Society's Smt. Kashibai Navale College of Pharmacy
- Savitribai Phule Pune University
- Pune
- India
| | - Varsha A. Hambarde
- Pharmaceutical Chemistry Department
- Sinhgad Technical Education Society's Smt. Kashibai Navale College of Pharmacy
- Savitribai Phule Pune University
- Pune
- India
| | - Nilesh N. Petkar
- Pharmaceutical Chemistry Department
- Sinhgad Technical Education Society's Smt. Kashibai Navale College of Pharmacy
- Savitribai Phule Pune University
- Pune
- India
| | - Chinmay N. Patel
- Pharmaceutical Chemistry Department
- Sinhgad Technical Education Society's Smt. Kashibai Navale College of Pharmacy
- Savitribai Phule Pune University
- Pune
- India
| | - Sanjay D. Sawant
- Pharmaceutical Chemistry Department
- Sinhgad Technical Education Society's Smt. Kashibai Navale College of Pharmacy
- Savitribai Phule Pune University
- Pune
- India
| |
Collapse
|
9
|
Sarkate AP, Murumkar PR, Lokwani DK, Kandhare AD, Bodhankar SL, Shinde DB, Bothara KG. Design of selective TACE inhibitors using molecular docking studies: Synthesis and preliminary evaluation of anti-inflammatory and TACE inhibitory activity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:905-923. [PMID: 26588187 DOI: 10.1080/1062936x.2015.1095240] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Tumor necrosis factor-α (TNF-α) converting enzyme (TACE) has been considered one of the principal therapeutic targets for the treatment of TNF-dependent pathologies. Several TACE inhibitors have been reported, but none of them has been successfully passed to phase II clinical trials. In the present work, we attempted to design highly selective new non-hydroxamate sulfonamide TACE inhibitors. The docking study was performed on one of the crystal structures of TACE, selected based on its resolution and R value, to tackle the flexibility issue of the active site. The results allowed us to distinguish the analogues with a higher binding affinity toward the active site of TACE and to identify the substituent of analogues needed for binding with the surrounding site of the enzyme. Finally the analogues were docked on crystal structures of six different matrix metalloproteinases (MMPs) for a selectivity study of TACE over MMPs. Some of these analogues were synthesized and subjected to preliminary testing for in vivo anti-inflammatory activity and TACE inhibitory activity.
Collapse
Affiliation(s)
- A P Sarkate
- a Department of Pharmaceutical Chemistry , Sinhgad Institute of Pharmacy , Pune , Maharashtra , India
| | - P R Murumkar
- a Department of Pharmaceutical Chemistry , Sinhgad Institute of Pharmacy , Pune , Maharashtra , India
| | - D K Lokwani
- b Department of Chemical Technology , Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , Maharashtra , India
| | - A D Kandhare
- c Department of Pharmacology , Poona College of Pharmacy, Bharati Vidyapeeth Deemed University , Pune , Maharashtra , India
| | - S L Bodhankar
- c Department of Pharmacology , Poona College of Pharmacy, Bharati Vidyapeeth Deemed University , Pune , Maharashtra , India
| | - D B Shinde
- b Department of Chemical Technology , Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , Maharashtra , India
| | - K G Bothara
- a Department of Pharmaceutical Chemistry , Sinhgad Institute of Pharmacy , Pune , Maharashtra , India
| |
Collapse
|
10
|
|
11
|
Kanhed AM, Zambre VP, Pawar VA, Sharma MK, Giridhar R, Yadav MR. Structural requirements for imidazo[1,2-a]pyrazine derivatives as Aurora A kinase inhibitors and validation of the model. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1094-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
12
|
Prakash D, Nawani N, Prakash M, Bodas M, Mandal A, Khetmalas M, Kapadnis B. Actinomycetes: a repertory of green catalysts with a potential revenue resource. BIOMED RESEARCH INTERNATIONAL 2013; 2013:264020. [PMID: 23691495 PMCID: PMC3652136 DOI: 10.1155/2013/264020] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 11/18/2022]
Abstract
Biocatalysis, one of the oldest technologies, is becoming a favorable alternative to chemical processes and a vital part of green technology. It is an important revenue generating industry due to a global market projected at $7 billion in 2013 with a growth of 6.7% for enzymes alone. Some microbes are important sources of enzymes and are preferred over sources of plant and animal origin. As a result, more than 50% of the industrial enzymes are obtained from bacteria. The constant search for novel enzymes with robust characteristics has led to improvisations in the industrial processes, which is the key for profit growth. Actinomycetes constitute a significant component of the microbial population in most soils and can produce extracellular enzymes which can decompose various materials. Their enzymes are more attractive than enzymes from other sources because of their high stability and unusual substrate specificity. Actinomycetes found in extreme habitats produce novel enzymes with huge commercial potential. This review attempts to highlight the global importance of enzymes and extends to signify actinomycetes as promising harbingers of green technology.
Collapse
Affiliation(s)
- Divya Prakash
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | - Neelu Nawani
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | - Mansi Prakash
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | - Manish Bodas
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | - Abul Mandal
- System Biology Research Center, School of Life Sciences, University of Skövde, P.O. Box 408, 541 28 Skövde, Sweden
| | - Madhukar Khetmalas
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | | |
Collapse
|
13
|
Zambre VP, Giridhar R, Yadav MR. Pharmacophore modeling and 3D-QSAR (CoMSIA) studies for structural requirements of some triazine derivatives as G-quadruplex binders for telomerase inhibition. Med Chem Res 2013. [DOI: 10.1007/s00044-012-0447-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
14
|
Murumkar PR, Sharma MK, Shinde AC, Bothara KG. Three-dimensional quantitative structure–activity relationship CoMFA/CoMSIA on pyrrolidine-based tartrate diamides as TACE inhibitors. Med Chem Res 2013. [DOI: 10.1007/s00044-012-0409-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
15
|
Murumkar PR, Giridhar R, Yadav MR. Novel methods and strategies in the discovery of TACE inhibitors. Expert Opin Drug Discov 2012; 8:157-81. [PMID: 23231541 DOI: 10.1517/17460441.2013.744745] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Tumor necrosis factor-α (TNF-α) is a key player in inflammation and joint damage in rheumatoid arthritis (RA). One treatment approach to exclude TNF-α from the biological system is by inhibiting tumor necrosis factor-alpha converting enzyme (TACE), the enzyme responsible for the production of its active form. To date, a number of TACE inhibitors have been reported in the literature from various strategies and methods. AREAS COVERED The following article presents the design and development strategies for the discovery of novel TACE inhibitors which could be of therapeutic utility for the alleviation of inflammatory conditions. The review is based on literature of the subject from 2005 onward. EXPERT OPINION Discovery of a selective TACE inhibitor has remained a major goal for many academic and pharmaceutical industrial research laboratories for quite some time. Identification of selective TACE inhibitors has proved elusive until recently due to structural similarities between TACE and MMPs. The differences in the shape and size of the S1' pocket of TACE and MMPs could be exploited to design selective TACE inhibitors devoid of any MMP inhibitory activity in the near future. It would be a Herculean task to develop a specific TACE inhibitor for clinical treatment of RA because binding subsites of TACE and MMPs are quite similar. However, developments taking place currently in the field as well as in the application of molecular modeling techniques at a wider scale could yet provide clinically useful selective TACE inhibitors in the not too distant future.
Collapse
Affiliation(s)
- Prashant R Murumkar
- The M.S. University of Baroda, Faculty of Technology & Engineering, Pharmacy Department, Kalabhavan, Vadodara-390 001, India
| | | | | |
Collapse
|
16
|
A computational study on thiourea analogs as potent MK-2 inhibitors. Int J Mol Sci 2012; 13:7057-7079. [PMID: 22837679 PMCID: PMC3397511 DOI: 10.3390/ijms13067057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/25/2012] [Accepted: 05/28/2012] [Indexed: 11/17/2022] Open
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MK-2) has been identified as a drug target for the treatment of inflammatory diseases. Currently, a series of thiourea analogs as potent MK-2 inhibitors were studied using comprehensive computational methods by 3D-QSAR, molecular docking and molecular dynamics simulations for a further improvement in activities. The optimal 3D models exhibit high statistical significance of the results, especially for the CoMFA results with r(2) (ncv), q(2) values of 0.974, 0.536 for the internal validation, and r(2) (pred), r(2) (m) values of 0.910, 0.723 for the external validation and Roy's index, respectively. In addition, more rigorous validation criteria suggested by Tropsha were also employed to check the built models. Graphic representation of the results, as contoured 3D coefficient plots, also provides a clue to the reasonable modification of molecules: (i) The substituent with a bulky size and electron-rich group at the C5 position of the pyrazine ring is required to enhance the potency; (ii) The H-bond acceptor group in the C3 position of the pyrazine ring is likely to be helpful to increase MK-2 inhibition; (iii) The small and electropositive substituent as a hydrogen bond donor of the C2 position in the oxazolone ring is favored; In addition, several important amino acid residues were also identified as playing an important role in MK-2 inhibition. The agreement between 3D-QSAR, molecular docking and molecular dynamics simulations also proves the rationality of the developed models. These results, we hope, may be helpful in designing novel and potential MK-2 inhibitors.
Collapse
|
17
|
Murumkar PR, Le L, Truong TN, Yadav MR. Determination of structural requirements of influenza neuraminidase type A inhibitors and binding interaction analysis with the active site of A/H1N1 by 3D-QSAR CoMFA and CoMSIA modeling. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00050k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
18
|
3D-QSAR and molecular docking studies of azaindole derivatives as Aurora B kinase inhibitors. J Mol Model 2010; 17:1191-205. [PMID: 20697761 DOI: 10.1007/s00894-010-0820-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 07/21/2010] [Indexed: 12/20/2022]
Abstract
The Aurora kinases have been regarded as attractive targets for the development of new anticancer agents. Recently a series of azaindole derivatives with Aurora B inhibitory activities were reported. To explore the relationship between the structures of substituted azaindole derivatives and their inhibition of Aurora B, 3D-QSAR and molecular docking studies were performed on a dataset of 41 compounds. 3D-QSAR, including CoMFA and CoMSIA, were applied to identify the key structures impacting their inhibitory potencies. The CoMSIA model showed better results than CoMFA, with r(2)(cv) value of 0.575 and r(2) value of 0.987. 3D contour maps generated from CoMFA and CoMSIA along with the docking binding structures provided enough information about the structural requirements for better activity. Based on the structure-activity relationship revealed by the present study, we have designed a set of novel Aurora B inhibitors that showed excellent potencies in the developed models. Thus, our results allowed us to design new derivatives with desired activities.
Collapse
|
19
|
Zambre VP, Murumkar PR, Giridhar R, Yadav MR. Development of highly predictive 3D-QSAR CoMSIA models for anthraquinone and acridone derivatives as telomerase inhibitors targeting G-quadruplex DNA telomere. J Mol Graph Model 2010; 29:229-39. [PMID: 20691626 DOI: 10.1016/j.jmgm.2010.07.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 07/07/2010] [Accepted: 07/09/2010] [Indexed: 01/21/2023]
Abstract
G-quadruplex structures of DNA represent a potentially useful target for anticancer drugs. Telomerase enzyme, involved in immortalization of cancer cells is inhibited by stabilization of G-quadruplex at the ends of chromosomes. Anthraquinone and acridone derivatives are promising G-quadruplex ligands as telomerase inhibitors. So far, optimization of these ligands remained hampered due to the lack of creditable quantitative structure-activity relationships. To understand the structural basis of anthraquinone and acridone derivatives, a predictive 3D-QSAR model has been developed for the first time for telomerase inhibitory activity of G4 ligands, employing comparative molecular similarity indices analysis (CoMSIA). Considering the proposition that the basic nitrogens in these compounds should exist in protonated form at physiological pH the protonated forms of the reported compounds were analyzed and investigated. The QSAR model from conformational template Conf1 exhibited best correlative and predictive properties. The actual predictive abilities of the QSAR model were thoroughly validated through an external validation test set of compounds. The statistics indicate a significantly high prediction power of the best model (r(2), 0.721), supporting the proposed molecular mechanism of DNA G-quadruplex ligands.
Collapse
Affiliation(s)
- Vishal P Zambre
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara 390001, Gujarat, India
| | | | | | | |
Collapse
|
20
|
Murumkar PR, DasGupta S, Chandani SR, Giridhar R, Yadav MR. Novel TACE inhibitors in drug discovery: a review of patented compounds. Expert Opin Ther Pat 2010; 20:31-57. [PMID: 20021284 DOI: 10.1517/13543770903465157] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
TNF-alpha converting enzyme (TACE), a pro-inflammatory cytokine, catalyzes the formation of TNF-alpha from membrane bound TNF-alpha precursor protein. TNF-alpha is believed to play pathophysiological roles in inflammation, anorexia, cachexia, septic shock, viral replication and so on. TNF-alpha is a key player in inflammation and joint damage in rheumatoid arthritis. While a variety of TACE inhibitors have been reported in the literature, a vast majority of these compounds are peptidic and peptide-like compounds that are expected to have bioavailability and pharmacokinetic problems, common to such compounds, limiting their clinical effectiveness. Low molecular mass, long acting, orally bioavailable inhibitors of TACE are, therefore, highly desirable for the treatment of potential chronic diseases mentioned above. A review of patented compounds as TACE inhibitors in drug discovery is given. A selection of interesting patents recorded from 2001 to 2009 is presented. Various novel TACE inhibitors developed by different companies have been discussed.
Collapse
Affiliation(s)
- Prashant R Murumkar
- The M.S. University of Baroda, Faculty of Technology & Engineering, Department of Pharmacy, Kalabhavan, Vadodara, 390 001, India
| | | | | | | | | |
Collapse
|
21
|
Murumkar PR, Zambre VP, Yadav MR. Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors. J Comput Aided Mol Des 2010; 24:143-56. [DOI: 10.1007/s10822-010-9322-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 02/09/2010] [Indexed: 11/25/2022]
|
22
|
Cong Y, Yang XG, Lv W, Xue Y. Prediction of novel and selective TNF-alpha converting enzyme (TACE) inhibitors and characterization of correlative molecular descriptors by machine learning approaches. J Mol Graph Model 2009; 28:236-44. [DOI: 10.1016/j.jmgm.2009.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/17/2009] [Accepted: 08/03/2009] [Indexed: 11/26/2022]
|
23
|
Zambre VP, Murumkar PR, Giridhar R, Yadav MR. Structural Investigations of Acridine Derivatives by CoMFA and CoMSIA Reveal Novel Insight into Their Structures toward DNA G-Quadruplex Mediated Telomerase Inhibition and Offer a Highly Predictive 3D-Model for Substituted Acridines. J Chem Inf Model 2009; 49:1298-311. [DOI: 10.1021/ci900036w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vishal P. Zambre
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara - 390001, Gujarat, India
| | - Prashant R. Murumkar
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara - 390001, Gujarat, India
| | - Rajani Giridhar
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara - 390001, Gujarat, India
| | - Mange Ram Yadav
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara - 390001, Gujarat, India
| |
Collapse
|
24
|
DasGupta S, Murumkar PR, Giridhar R, Yadav MR. Studies on novel 2-imidazolidinones and tetrahydropyrimidin-2(1H)-ones as potential TACE inhibitors: design, synthesis, molecular modeling, and preliminary biological evaluation. Bioorg Med Chem 2009; 17:3604-17. [PMID: 19394232 DOI: 10.1016/j.bmc.2009.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/31/2009] [Accepted: 04/01/2009] [Indexed: 12/18/2022]
Abstract
Compounds belonging to the class of 2-imidazolidinones and tetrahydropyrimidin-2(1H)-ones were synthesized and evaluated for their TACE inhibitory activity. Most of the compounds showed very good TACE inhibitory activity. Docking study clearly indicates importance of the P1' group of the inhibitor for the TACE inhibitory activity. This work proves that these two classes of molecules could be used as potential leads for the development of TACE inhibitors.
Collapse
Affiliation(s)
- Shirshendu DasGupta
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M. S. University of Baroda, Vadodara 390 001, Gujarat, India
| | | | | | | |
Collapse
|
25
|
Current perspective of TACE inhibitors: A review. Bioorg Med Chem 2009; 17:444-59. [DOI: 10.1016/j.bmc.2008.11.067] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2008] [Revised: 11/12/2008] [Accepted: 11/24/2008] [Indexed: 12/20/2022]
|