1
|
Bahia MS, Kaspi O, Touitou M, Binayev I, Dhail S, Spiegel J, Khazanov N, Yosipof A, Senderowitz H. A comparison between 2D and 3D descriptors in QSAR modeling based on bio-active conformations. Mol Inform 2023; 42:e2200186. [PMID: 36617991 DOI: 10.1002/minf.202200186] [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: 01/03/2023] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/10/2023]
Abstract
QSAR models are widely and successfully used in many research areas. The success of such models highly depends on molecular descriptors typically classified as 1D, 2D, 3D, or 4D. While 3D information is likely important, e. g., for modeling ligand-protein binding, previous comparisons between the performances of 2D and 3D descriptors were inconclusive. Yet in such comparisons the modeled ligands were not necessarily represented by their bioactive conformations. With this in mind, we mined the PDB for sets of protein-ligand complexes sharing the same protein for which uniform activity data were reported. The results, totaling 461 structures spread across six series were compiled into a carefully curated, first of its kind dataset in which each ligand is represented by its bioactive conformation. Next, each set was characterized by 2D, 3D and 2D + 3D descriptors and modeled using three machine learning algorithms, namely, k-Nearest Neighbors, Random Forest and Lasso Regression. Models' performances were evaluated on external test sets derived from the parent datasets either randomly or in a rational manner. We found that many more significant models were obtained when combining 2D and 3D descriptors. We attribute these improvements to the ability of 2D and 3D descriptors to code for different, yet complementary molecular properties.
Collapse
Affiliation(s)
| | - Omer Kaspi
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Meir Touitou
- School of Cancer and Pharmaceutical Sciences, King's College London, London, 150 Stamford Street, SE1 9NH, United Kingdom
| | - Idan Binayev
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Seema Dhail
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Jacob Spiegel
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Netaly Khazanov
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Abraham Yosipof
- Department of Information Systems, College of Law & Business, Ramat-Gan, P.O. Box 852, Bnei Brak, 5110801, Israel
| | - Hanoch Senderowitz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| |
Collapse
|
2
|
Lavanya M, Lin C, Mao J, Thirumalai D, Aabaka SR, Yang X, Mao J, Huang Z, Zhao J. Synthesis and Anticancer Properties of Functionalized 1,6-Naphthyridines. Top Curr Chem (Cham) 2021; 379:13. [PMID: 33624162 DOI: 10.1007/s41061-020-00314-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 11/12/2020] [Indexed: 12/29/2022]
Abstract
The burgeoning interest in synthesis and biological applications of 1,6-naphthyridines reflects the importance of 1,6-naphthyridines in the synthetic as well as medicinal chemistry fields. Specially, 1,6-naphthyridines are pharmacologically active, with variety of applications such as anticancer, anti-human immunodeficiency virus (HIV), anti-microbial, analgesic, anti-inflammatory and anti-oxidant activities. Although collective recent synthetic developments have paved a path to a wide range of functionalized 1,6-naphthyridines, a complete correlation of synthesis with biological activity remains elusive. The current review focuses on recent synthetic developments from the last decade and a thorough study of the anticancer activity of 1,6-naphthyridines on different cancer cell lines. Anticancer activity has been correlated to 1,6-naphthyridines using the literature on the structure-activity relationship (SAR) along with molecular modeling studies. Exceptionally, at the end of this review, the utility of 1,6-naphthyridines displaying activities other than anticancer has also been included as a glimmering extension.
Collapse
Affiliation(s)
- Mallu Lavanya
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu, 610500, Xindu, People's Republic of China.,School of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, People's Republic of China
| | - Chong Lin
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu, 610500, Xindu, People's Republic of China.
| | - Jincheng Mao
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu, 610500, Xindu, People's Republic of China.
| | | | - Sreenath Reddy Aabaka
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu, 610500, Xindu, People's Republic of China
| | - Xiaojiang Yang
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu, 610500, Xindu, People's Republic of China
| | - Jinhua Mao
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu, 610500, Xindu, People's Republic of China
| | - Zhiyu Huang
- School of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, People's Republic of China
| | - Jinzhou Zhao
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu, 610500, Xindu, People's Republic of China
| |
Collapse
|
3
|
Arora M, Choudhary S, Silakari O. In silico guided designing of 4-(1H-benzo[d]imidazol-2-yl)phenol-based mutual-prodrugs of NSAIDs: synthesis and biological evaluation. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:761-784. [PMID: 32867537 DOI: 10.1080/1062936x.2020.1810117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The free COOH group of conventional NSAIDs is a structural feature for non-selective cyclooxygenase (COX) inhibition and the molecular cause of their gastrointestinal (GI) toxicity. In this context, an in house database of synthesizable ester prodrugs of some well-known NSAIDs was developed by combining their -COOH group with -OH of a newly identified antioxidant 4-(1H-benzo[d]imidazol-2-yl)phenol (BZ). The antioxidant potential of BZ was unveiled through in silico PASS prediction and in vitro/in vivo evaluation. The in house database of NSAIDs-BZ prodrugs was first subjected to screening with our previously reported pharmacophore models of hCES1 (AAHRR.430) and hCES2 (AHHR.21) for determining hydrolytic susceptibility. Biotransformation behaviour of screened prodrugs was then assessed by using QM/MM and sterimol parameterization, followed by ADMET calculations to predict the drug likeness. On the basis of in silico results, five prodrugs were duly synthesized and the best three were subject to the in vivo evaluation for their anti-inflammatory, analgesic, antioxidant activities, and ulcerogenic index. Among these prodrugs, BN2 and BN5 displayed better anti-inflammatory and analgesics potential in comparison to their parent drugs. All the prodrugs were found to be gastro sparing in the rat model and significantly improved the levels of oxidative stress biomarkers in both blood plasma as well as gastric homogenate.
Collapse
Affiliation(s)
- M Arora
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University , Patiala, India
| | - S Choudhary
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University , Patiala, India
| | - O Silakari
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University , Patiala, India
| |
Collapse
|
4
|
Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles. Microorganisms 2019; 8:microorganisms8010059. [PMID: 31905784 PMCID: PMC7023208 DOI: 10.3390/microorganisms8010059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 11/25/2022] Open
Abstract
SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria.
Collapse
|
5
|
hCES1 and hCES2 mediated activation of epalrestat-antioxidant mutual prodrugs: Unwinding the hydrolytic mechanism using in silico approaches. J Mol Graph Model 2019; 91:148-163. [DOI: 10.1016/j.jmgm.2019.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 01/07/2023]
|
6
|
Xu G, Gao Y, Sun B, Peng L, Mao L, Jiang Y, Ding Q. A Convenient Synthesis and Biological Research of Novel 5,6,7,8-Tetrahydro-1,6-naphthyridin-2(1 H)-one Derivatives Hydrochloride as Cytotoxic Agents. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Guiqing Xu
- Henan Engineering Research Center of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453002 Henan People's Republic of China
| | - Yuan Gao
- Henan Engineering Research Center of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453002 Henan People's Republic of China
| | - Bin Sun
- College of Chemistry, Chemical Engineering and Materials Science; Shandong Normal University; Jinan 250014 Shandong People's Republic of China
| | - Lizeng Peng
- Jinan Asia Pharma Tech Co., Ltd. Shandong; Jinan 250101 Shandong People's Republic of China
| | - Longfei Mao
- Henan Engineering Research Center of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453002 Henan People's Republic of China
| | - Yuqin Jiang
- Henan Engineering Research Center of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453002 Henan People's Republic of China
| | - Qingjie Ding
- Henan Engineering Research Center of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang 453002 Henan People's Republic of China
| |
Collapse
|
7
|
Jukič M, Konc J, Gobec S, Janežič D. Identification of Conserved Water Sites in Protein Structures for Drug Design. J Chem Inf Model 2017; 57:3094-3103. [DOI: 10.1021/acs.jcim.7b00443] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, SI−1000, Ljubljana, Slovenia
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
| |
Collapse
|
8
|
Pharmacophore and docking-based hierarchical virtual screening for the designing of aldose reductase inhibitors: synthesis and biological evaluation. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1510-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
9
|
Aldose reductase inhibitors for diabetic complications: Receptor induced atom-based 3D-QSAR analysis, synthesis and biological evaluation. J Mol Graph Model 2015; 59:59-71. [DOI: 10.1016/j.jmgm.2015.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 03/23/2015] [Accepted: 03/26/2015] [Indexed: 01/26/2023]
|
10
|
In silico design: extended molecular dynamic simulations of a new series of dually acting inhibitors against EGFR and HER2. J Mol Graph Model 2013; 44:220-31. [PMID: 23911931 DOI: 10.1016/j.jmgm.2013.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/13/2013] [Accepted: 06/17/2013] [Indexed: 01/23/2023]
Abstract
Based on the hit structures that have been identified in our previous studies against EGFR and HER2, new potential inhibitors that share the same scaffold of the hit structures are designed and screened in silico. Insights into understanding the potential inhibitory effect of the new inhibitors against both EGFR and HER2 receptors is obtained using extended molecular dynamics (MD) simulations and different scoring techniques. The binding mechanisms and dynamics are detailed with respect to two approved inhibitors against EGFR (lapatinib) and HER2 (SYR127063). The best scoring inhibitor (T9) is chosen for additional in silico investigation against both the wild-type and T790M mutant strain of EGFR and the wild-type HER2. The results reveal that certain substitution patterns increase the stability and assure stronger binding and higher H-bond occupancy of the conserved water molecule that is commonly observed with kinase crystal structures. Furthermore, the new inhibitor (T9) forms stable interactions with the mutant strain as a direct consequence of the enhanced ability to form additional hydrogen bonding interactions with binding site residues.
Collapse
|
11
|
Vyas B, Silakari O, Bahia MS, Singh B. Glutamine: fructose-6-phosphate amidotransferase (GFAT): homology modelling and designing of new inhibitors using pharmacophore and docking based hierarchical virtual screening protocol. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:733-752. [PMID: 23767808 DOI: 10.1080/1062936x.2013.797493] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Glutamine: fructose-6-phosphate amidotransferase (GFAT), also termed GFPT1 and GFAT1, catalyzes the first committed step of the hexosamine biosynthesis pathway in mammals and consequently plays an important role in type 2 diabetes. In the present study, a combination of pharmacophore modelling, homology modelling, and molecular docking analysis was performed to design new glutamine competitive inhibitors of human GFAT, and to investigate important interaction details of inhibitor molecules. A pharmacophore model of GFAT inhibitors was developed, subsequently validated, and utilized for the screening by the PHASE database to identify new molecules. Afterwards, homology modelling was performed to construct the glutamine-binding site of the GFAT protein. The modelled active site was utilized to dock the studied molecules to investigate important receptor-ligand interactions and to scrutinize database-screened molecules on the basis of essential interactions. This systematic in silico protocol helped us to identify new molecules that would be explored for the treatment of type 2 diabetes and its complications.
Collapse
Affiliation(s)
- B Vyas
- Department of Chemistry, Punjabi University, Patiala, India
| | | | | | | |
Collapse
|
12
|
3D-QSAR analysis of benzimidazole inhibitors of interleukin-2 inducible T cell kinase (ITK) considering receptor flexibility and water importance for molecular alignment. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0548-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
13
|
Kumari A, Kaur M, Bahia MS, Silakari O. 3D-QSAR analysis of anilinoquinoline inhibitors of colony stimulating factor-1 kinase (cFMS): implementation of field-based molecular alignment. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0513-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|