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Yu Y, Xia Y, Liang G. Exploring novel lead scaffolds for SGLT2 inhibitors: Insights from machine learning and molecular dynamics simulations. Int J Biol Macromol 2024; 263:130375. [PMID: 38403210 DOI: 10.1016/j.ijbiomac.2024.130375] [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: 11/16/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Sodium-glucose cotransporter 2 (SGLT2) plays a pivotal role in mediating glucose reabsorption within the renal filtrate, representing a well-known target in type 2 diabetes and heart failure. Recent emphasis has been directed toward designing SGLT2 inhibitors, with C-glycoside inhibitors emerging as front-runners. The architecture of SGLT2 has been successfully resolved using cryo-electron microscopy. However, comprehension of the pharmacophores within the binding site of SGLT2 remains unclear. Here, we use machine learning and molecular dynamics simulations on SGLT2 bound with its inhibitors in preclinical or clinical development to shed light on this issue. Our dataset comprises 1240 SGLT2 inhibitors amalgamated from diverse sources, forming the basis for constructing machine learning models. SHapley Additive exPlanation (SHAP) elucidates the crucial fragments that contribute to inhibitor activity, specifically Morgan_3, 162, 310, 325, 366, 470, 597, 714, 926, and 975. Furthermore, the computed binding free energies and per-residue contributions for SGLT2-inhibitor complexes unveil crucial fragments of inhibitors that interact with residues Asn-75, His-80, Val-95, Phe-98, Val-157, Leu-274, and Phe-453 in the binding site of SGLT2. This comprehensive investigation enhances understanding of the binding mechanism for SGLT2 inhibitors, providing a robust framework for evaluating and discovering novel lead scaffolds within this domain.
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Affiliation(s)
- Yuandong Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Yuting Xia
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China.
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Swargiary A, Daimari M, Swargiary A, Biswas A, Brahma D, Singha H. Identification of phytocompounds as potent inhibitors of sodium/glucose cotransporter-2 leading to diabetes treatment. J Biomol Struct Dyn 2024:1-14. [PMID: 38379332 DOI: 10.1080/07391102.2024.2319674] [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: 09/30/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Type-II diabetes, a major metabolic disorder has threatened the very existence of a healthy life since long ago. Commercially available antidiabetic drugs are known for several adverse effects. The present study attempted to identify potential phytocompounds as inhibitors of sodium/glucose cotransporter-2 (SGLT2), a major protein that helps in glucose re-absorption from renal tubules. A total of 28 phytocompounds were collected based on the literature survey. 3D co-ordinates of phytocompounds were collected from PubChem database. Molecular docking was carried out with SGLT2 protein and the best 3 docking complexes were subjected to molecular dynamics simulation for 100 ns. Free energy changes were also analyzed using MM/PBSA analysis. Phytocompounds were also analyzed for their drug-likeness and ADMET properties. Docking study observed a strong binding affinity of phytocompounds (> -7.0 kcal/mol). More than 10 phytocompounds showed better binding affinity compared to reference drugs. Further analysis of three best docking complexes when analyzed by MD simulation showed better stability and compactness of the complexes compared to reference drug, empagliflozin. MM/PBSA analysis also revealed that van der Waals force and electrostatic energy are the major binding energy involved in the complex formation. Like docking energy, free energy analysis also observed stronger binding energies (ΔGGAS) in SGLT2-phytocompound complexes compared to empagliflozin complex. All the phytocompounds showed drug-likeness and considerable ADMET properties. The study, therefore, suggests that Trifolirhizin-6'-monoacetate, Aspalathin, and Quercetin-3-glucoside could be a possible inhibitor of SGLT2 protein. However, further studies need to be carried out to reveal the exact mode of activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ananta Swargiary
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Manita Daimari
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Arup Swargiary
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Arup Biswas
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Dulur Brahma
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Hiloljyoti Singha
- Pharmacology and Bioinformatics Laboratory, Department of Zoology, Bodoland University, Kokrajhar, Assam, India
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Phytochemicals as Regulators of Tumor Glycolysis and Hypoxia Signaling Pathways: Evidence from In Vitro Studies. Pharmaceuticals (Basel) 2022; 15:ph15070808. [PMID: 35890106 PMCID: PMC9315613 DOI: 10.3390/ph15070808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
The full understanding of the complex nature of cancer still faces many challenges, as cancers arise not as a result of a single target disruption but rather involving successive genetic and epigenetic alterations leading to multiple altered metabolic pathways. In this light, the need for a multitargeted, safe and effective therapy becomes essential. Substantial experimental evidence upholds the potential of plant-derived compounds to interfere in several important pathways, such as tumor glycolysis and the upstream regulating mechanisms of hypoxia. Herein, we present a comprehensive overview of the natural compounds which demonstrated, in vitro studies, an effective anticancer activity by affecting key regulators of the glycolytic pathway such as glucose transporters, hexokinases, phosphofructokinase, pyruvate kinase or lactate dehydrogenase. Moreover, we assessed how phytochemicals could interfere in HIF-1 synthesis, stabilization, accumulation, and transactivation, emphasizing PI3K/Akt/mTOR and MAPK/ERK pathways as important signaling cascades in HIF-1 activation. Special consideration was given to cell culture-based metabolomics as one of the most sensitive, accurate, and comprising approaches for understanding the response of cancer cell metabolome to phytochemicals.
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Badiger AS, Jayadev K, Manu G, Raj R, Ammanagi A, Bajpe SN, Ramu R. Molecular docking and simulation analysis of the FimH protein with secondary metabolites from the Garcinia species. Bioinformation 2022; 18:76-81. [PMID: 36420433 PMCID: PMC9649499 DOI: 10.6026/97320630018076] [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: 11/14/2021] [Revised: 12/31/2021] [Accepted: 12/31/2021] [Indexed: 09/19/2023] Open
Abstract
It is of interest to document the molecular docking and simulation analysis of the FimH protein with 10 secondary metabolites from Garcinia species in the context of drug discovery for Urinary tract infections (UTIs). We report the optimal binding features of flavonoids with the FimH protein for further consideration in drug discovery.
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Affiliation(s)
- Abhijeeth S Badiger
- Department of Biotechnology, Sri Dharmasthala Manjunatheshwara College, Ujire - 574240, Karnataka, India
- Department of PG studies in Biotechnology, Alva's College, Moodbidri - 574227, Karnataka, India
| | - K Jayadev
- Department of PG studies in Biotechnology, Alva's College, Moodbidri - 574227, Karnataka, India
| | - G Manu
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru - 570015, Karnataka, India
| | - Ranjith Raj
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru - 570015, Karnataka, India
| | - Avinash Ammanagi
- Department of PG studies in Microbiology and Biotechnology, Karnataka University, Dharwad - 580003, Karnataka, India
| | - Shrisha Naik Bajpe
- Department of Biotechnology, Sri Dharmasthala Manjunatheshwara College, Ujire - 574240, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India
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Tutone M, Almerico AM. Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics. Molecules 2021; 26:molecules26247500. [PMID: 34946582 PMCID: PMC8707150 DOI: 10.3390/molecules26247500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
To date, computational approaches have been recognized as a key component in drug design and discovery workflows [...].
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Kumar S, Prajapati KS, Shuaib M, Kushwaha PP, Tuli HS, Singh AK. Five-Decade Update on Chemopreventive and Other Pharmacological Potential of Kurarinone: a Natural Flavanone. Front Pharmacol 2021; 12:737137. [PMID: 34646138 PMCID: PMC8502857 DOI: 10.3389/fphar.2021.737137] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/24/2021] [Indexed: 02/05/2023] Open
Abstract
In the present article we present an update on the role of chemoprevention and other pharmacological activities reported on kurarinone, a natural flavanone (from 1970 to 2021). To the best of our knowledge this is the first and exhaustive review of kurarinone. The literature was obtained from different search engine platforms including PubMed. Kurarinone possesses anticancer potential against cervical, lung (non-small and small), hepatic, esophageal, breast, gastric, cervical, and prostate cancer cells. In vivo anticancer potential of kurarinone has been extensively studied in lungs (non-small and small) using experimental xenograft models. In in vitro anticancer studies, kurarinone showed IC50 in the range of 2–62 µM while in vivo efficacy was studied in the range of 20–500 mg/kg body weight of the experimental organism. The phytochemical showed higher selectivity toward cancer cells in comparison to respective normal cells. kurarinone inhibits cell cycle progression in G2/M and Sub-G1 phase in a cancer-specific context. It induces apoptosis in cancer cells by modulating molecular players involved in apoptosis/anti-apoptotic processes such as NF-κB, caspase 3/8/9/12, Bcl2, Bcl-XL, etc. The phytochemical inhibits metastasis in cancer cells by modulating the protein expression of Vimentin, N-cadherin, E-cadherin, MMP2, MMP3, and MMP9. It produces a cytostatic effect by modulating p21, p27, Cyclin D1, and Cyclin A proteins in cancer cells. Kurarinone possesses stress-mediated anticancer activity and modulates STAT3 and Akt pathways. Besides, the literature showed that kurarinone possesses anti-inflammatory, anti-drug resistance, anti-microbial (fungal, yeast, bacteria, and Coronavirus), channel and transporter modulation, neuroprotection, and estrogenic activities as well as tyrosinase/diacylglycerol acyltransferase/glucosidase/aldose reductase/human carboxylesterases 2 inhibitory potential. Kurarinone also showed therapeutic potential in the clinical study. Further, we also discussed the isolation, bioavailability, metabolism, and toxicity of Kurarinone in experimental models.
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Affiliation(s)
- Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Prem Prakash Kushwaha
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Ambala, India
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
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Montes-Robledo A, Baldiris-Avila R, Galindo JF. D-Mannoside FimH Inhibitors as Non-Antibiotic Alternatives for Uropathogenic Escherichia coli. Antibiotics (Basel) 2021; 10:antibiotics10091072. [PMID: 34572654 PMCID: PMC8465801 DOI: 10.3390/antibiotics10091072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, mannosides, and molecules that inhibit their assembly. This work has focused on the ability of a set of monosubstituted and disubstituted phenyl mannosides to inhibit FimH. To determine the 3D structure of FimH for our in silico studies, we obtained fifteen sequences by PCR amplification of the fimH gene from 102 UPEC isolates. The fimH sequences in BLAST had a high homology (97–100%) to our UPEC fimH sequences. A search for the three-dimensional crystallographic structure of FimH proteins in the PDB server showed that proteins 4X5P and 4XO9 were found in 10 of the 15 isolates, presenting a 67% influx among our UPEC isolates. We focused on these two proteins to study the stability, free energy, and the interactions with different mannoside ligands. We found that the interactions with the residues of aspartic acid (ASP 54) and glutamine (GLN 133) were significant to the binding stability. The ligands assessed demonstrated high binding affinity and stability with the lectin domain of FimH proteins during the molecular dynamic simulations, based on MM-PBSA analysis. Therefore, our results suggest the potential utility of phenyl mannoside derivatives as FimH inhibitors to mitigate urinary tract infections produced by UPEC; thus, decreasing colonization, disease burden, and the costs of medical care.
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Affiliation(s)
- Alfredo Montes-Robledo
- Grupo de Investigación Microbiología Clínica y Ambiental, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena de Indias 13001, Colombia;
- Maestría en Microbiología, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias 13001, Colombia
| | - Rosa Baldiris-Avila
- Grupo de Investigación Microbiología Clínica y Ambiental, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena de Indias 13001, Colombia;
- Maestría en Microbiología, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias 13001, Colombia
- Grupo de Investigación CIPTEC, Facultad de Ingeniería, Fundacion Universitaria Tecnologico Comfenalco—Cartagena, Cartagena de Indias 13001, Colombia
- Correspondence: (R.B.-A.); (J.F.G.)
| | - Johan Fabian Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 11321, Colombia
- Correspondence: (R.B.-A.); (J.F.G.)
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