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Ringgit G, Cheong BE, Shah MD, Abdul Kadir NAA, Siddiquee S. Syringic Acid in Canarium odontophyllum for Diabetes and Obesity - A Review. Cell Biochem Biophys 2025:10.1007/s12013-025-01773-8. [PMID: 40377865 DOI: 10.1007/s12013-025-01773-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2025] [Indexed: 05/18/2025]
Abstract
Syringic acid (SA) is a phenolic compound with a significant role in the treatment of diabetes and obesity. Syringic acid possesses anti-obesity and anti-diabetic properties; however, the potential of syringic acid derived from the native Bornean fruit Canarium odontophyllum (C. odontophyllum) for managing diabetes and obesity remains undocumented. This brief discussion explores the possible mechanisms associated with syringic acid's structure and its potential therapeutic effects in managing diabetes and obesity. The relevant information is gathered from previous reports on syringic acid, related to molecular docking studies involving syringic acid-associated enzymes and protein residues. The potential mechanism of syringic acid derived from C. odontophyllum with chemical structure characterized by a benzene ring with hydrogen bonds and its high affinity for enzymes and protein residues targeting diabetes and obesity, including hexokinase 2 (HK2), glycogen synthase kinase (GSK), 2BEL, protein kinase D (PKD), insulin receptor substrate-1 (IRS-1), and insulin receptor beta (IR-β). This review paper provides alternative insights into syringic acid derived from the seasonal fruit of native Bornean fruit associated with molecular docking, structural advantages and mechanism of action in diabetes treatment.
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Affiliation(s)
- Gilbert Ringgit
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia.
| | - Bo Eng Cheong
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Muhammad Dawood Shah
- Higher Institute Centre of Excellence (HICoE), Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Noor Atiqah Aizan Abdul Kadir
- Nutrition in Community Engagement (NICE) Living Laboratory, Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Shafiquzzaman Siddiquee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia.
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Sravanthi R, Mahalakshmi S, Udaya Prakash J, Sakthivel S. Molecular modelling of 6-oxo-5-Sulfanyl-1H-Pyridine-3-Carboxylic acid and its adsorption with the silver complex: Structural, optical, charge transference, dynamics and docking to nipah virus. J Mol Graph Model 2025; 136:108978. [PMID: 39965270 DOI: 10.1016/j.jmgm.2025.108978] [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: 12/21/2024] [Revised: 02/01/2025] [Accepted: 02/11/2025] [Indexed: 02/20/2025]
Abstract
This investigation employs DFT to evaluate the structural, molecular, and electronic feature variations of 6-oxo-5-sulfanyl-1H-pyridine-3-carboxylic acid in gas alongside various solvent media. The complex interactions occurring within the molecule are recognised using the Independent gradient model. The application of various electric fields are used to determine the electrical properties of the compound. The topographical inspection shows extreme electron-dense zones to display a good electron reception character of the molecule. The intense covalence nature is maximal between the aromatic zone's C-C and C-N regions. The compound possesses a maximum interaction with the (LP) → π∗ and π → π∗ transitions. The optical and absorbance property shows an upright enhancement in the addition of the solvents. The significant transference of charges inside the compound is signified using the D and H index values and heat maps. The thermal assessment established that the compound is sustainable at varied temperatures with the pressure at 1 atm. The carboxylate ion of 6O5S1HP3CA interacts with the Ag + clusters and its adsorption characteristics are confirmed by the SERS spectrum. The complex's stability is determined by the MD simulations at various speeds. The physiological scrutiny demonstrates that both the compound and complex are benign and the antiviral activities were studied for Nipah virus for the proteins 7pno and 7skt.
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Affiliation(s)
- R Sravanthi
- Department of Physics, Ethiraj College for Women (Autonomous), Chennai, 600008, Tamil Nadu, India; University of Madras, Chennai, 600005, Tamil Nadu, India
| | - S Mahalakshmi
- Department of Physics, Ethiraj College for Women (Autonomous), Chennai, 600008, Tamil Nadu, India.
| | - Jayavelu Udaya Prakash
- Department of Mechanical Engineering, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Avadi, Chennai, 600062, India
| | - S Sakthivel
- Department of Physics, Panimalar Engineering College, Poonamallee, Chennai, 600123, Tamil Nadu, India
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Khadka M, Sah M, Chaudhary R, Sahani SK, Sahani K, Pandey BK, Pandey D. Spectroscopic, quantum chemical, and topological calculations of the phenylephrine molecule using density functional theory. Sci Rep 2025; 15:208. [PMID: 39747169 PMCID: PMC11697212 DOI: 10.1038/s41598-024-81633-2] [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: 06/13/2024] [Accepted: 11/27/2024] [Indexed: 01/04/2025] Open
Abstract
In this work, Density Functional Theory (DFT) on Gaussian 09 W software was utilized to investigate the phenylephrine (PE) molecule (C9H13NO2). Firstly, the optimized structure of the PE molecule was obtained using B3LYP/6-311 + G (d, p) and CAM-B3LYP/6-311 + G (d, p) basis sets. The electron charge density is shown in Mulliken atomic charge as a bar chart and also as a color-filled map in Molecular Electrostatic Potential (MEP). Using these properties, the possibility of different charge transfers occurring within the molecule was evaluated. The calculated values of the energy gap from HOMO-LUMO mapping, illustrated in Frontier Molecular Orbitals (FMO) and Density of State (DOS), were found to be similar for both the neutral and anion states in the gaseous and water solvent phases. Both the global and local reactivity were studied to understand the reactivity of the PE molecule. Using the thermodynamic parameters, the thermochemical property of the title molecule was understood. Non-covalent interaction was studied to understand the Van der Waals interactions, hydrogen bonds, and steric repulsion in the title molecule. Natural Bond Orbital (NBO) Analysis was performed to understand the strongest stabilization interaction. In the vibrational analysis, Total Electron Density (TED) assignments were done in the intense region where the frequency of the title molecule was shifted distinctly. For vibrational spectroscopy, FT-IR and Raman spectra in the neutral and anion states were plotted and compared. Using the TD-DFT technique, the UV-Vis spectra along with Tauc's plot were studied. Finally, topological analysis, electron localized function (ELF), and localized orbital locator (LOL) were performed in the PE molecule.
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Affiliation(s)
- Mukesh Khadka
- Department of Physics, St.Xavier College, Maitighar, Kathmandu, Nepal
| | - Manoj Sah
- Department of Physics, St.Xavier College, Maitighar, Kathmandu, Nepal
| | - Raju Chaudhary
- Department of Physics, St.Xavier College, Maitighar, Kathmandu, Nepal
| | - Suresh Kumar Sahani
- Department of Science and Technology, Rajarshi Janak University, Janakpurdham, Nepal.
| | - Kameshwar Sahani
- Department of Civil Engineering, Kathmandu University, Kathmandu, Nepal
| | - Binay Kumar Pandey
- Department of Information Technology, College of Technology Govind Ballabh Pant, University of Agriculture and Technology, Pantnagar, Uttrakhand, India
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S Al-Otaibi J, Mary YS, Mary YS, Cristina Gamberini M. SERS analysis, DFT, and solution effects regarding the structural and optical characteristics of folic acid biomolecule adsorbed on a Cu 3 metal cluster. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124161. [PMID: 38493513 DOI: 10.1016/j.saa.2024.124161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
The optical characteristics of folic acid (ABP) and metal clusters of copper (Cu3) at various locations were investigated by means of density functional theory (DFT) computations. Mulliken charge analysis and molecular electrostatic potential (MEP) surface show how charge moves from Cu3 to ABP through the various groups. The peak in the UV-Vis spectra of ABP-Cu3 is caused by bonding and anti-bonding orbitals. In both vacuum and aqueous conditions, the polarizability values of ABP-Cu3 cluster are significantly higher than those of pure ABP, indicating a possible enhancement of the nonlinear optical (NLO) effect. Our research investigates the possibility of using ABP adsorbed metal clusters for NLO materials. Surface enhanced Raman scattering (SERS) in the ABP adsorbed metal clusters enhances the vibrational modes of ABP. Adsorption energies are found to be in the range -17.08 to -58.52 kcal/mol in vacuum and -53.34 to -93.44 kcal/mol in aqueous medium for the different configurations for ABP-Cu3. It indicates that metal clusters adsorbed by ABP are stable in the aqueous media. Experimental IR and UV-Vis of ABP is in agreement with theoretically predicted ones.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Y Sheena Mary
- Department of Physics, FMN College (Autonomous), Kollam, Kerala, University of Kerala, India
| | | | - Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
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Dessai PG, Dessai SP, Dabholkar R, Pednekar P, Naik S, Mamledesai S, Gopal M, Pavadai P, Kumar BK, Murugesan S, Chandavarkar S, Theivendren P, Selvaraj K. Design, synthesis, graph theoretical analysis and molecular modelling studies of novel substituted quinoline analogues as promising anti-breast cancer agents. Mol Divers 2023; 27:1567-1586. [PMID: 35976550 DOI: 10.1007/s11030-022-10512-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/02/2022] [Indexed: 11/26/2022]
Abstract
The most promising class of heterocyclic compounds in medicinal chemistry are those with the quinolin-2-one nucleus. It is a versatile heterocyclic molecule that has been put together with numerous pharmaceutical substances and is crucial in the creation of anticancer medications. In this view, the present research work deals with design, synthesis, and characterization of various analogous of quinolin-2-one nucleus and evaluation of their anticancer activity against MCF-7 cells (adenoma breast cancer cell line). Fourteen new compounds have been synthesised using suitable synthetic route and are characterized by FTIR, 1H NMR, 13C NMR and Mass spectral data. Molecular docking studies of the title compounds were carried out using PyRx 0.8 tool in AutoDock Vina program. All the synthesised compounds were exhibited well conserved hydrogen bonding with one or more amino acid residues in the active pocket of EGFR tyrosine kinase (PDB ID: 1m17). The docking score of the derivatives ranged from - 6.7 to - 9.5 kcal mol-1, standard drug Imatinib with - 9.6 kcal mol-1 and standard active ligand 4-anilinoquinazoline with - 7.7 kcal mol-1. The designed compound IV-A1 showed least binding energy (- 9.5 kcal mol-1) against EGFR tyrosine kinase receptor. Further, top scored compound, IV-A1 found to be most significant against MCF-7 cells with IC50 value of 0.0870 µM mL-1, TGI of 0.0958 µM mL-1, GI50 of 0.00499 µM mL-1, LC50 of 1.670 µM mL-1.
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Affiliation(s)
- Prachita Gauns Dessai
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Shivani Prabhu Dessai
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Renuka Dabholkar
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Padmashree Pednekar
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Sahili Naik
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Shivlingrao Mamledesai
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Murugananthan Gopal
- Department of Pharmacognosy, Swamy Vivekananda College of Pharmacy, Elayampalayam, 637205, India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, 560054, India
| | - Banoth Karan Kumar
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani, 333031, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani, 333031, India
| | - Sachin Chandavarkar
- Department of Pharmacognosy, ASPM College of Pharmacy, Sangulwadi, 416 810, India.
| | - Panneerselvam Theivendren
- Department of Pharmaceutical Chemistry, Swamy Vivekanandha College of Pharmacy, Elayampalayam, 637205, India.
| | - Kunjiappan Selvaraj
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India.
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Aguilar-Pineda JA, Febres-Molina C, Cordova-Barrios CC, Campos-Olazával LM, Del-Carpio-Martinez BA, Ayqui-Cueva F, Gamero-Begazo PL, Gómez B. Study of the Rv1417 and Rv2617c Membrane Proteins and Their Interactions with Nicotine Derivatives as Potential Inhibitors of Erp Virulence-Associated Factor in Mycobacterium tuberculosis: An In Silico Approach. Biomolecules 2023; 13:biom13020248. [PMID: 36830617 PMCID: PMC9953637 DOI: 10.3390/biom13020248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/30/2022] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
The increasing emergence of Mycobacterium tuberculosis (Mtb) strains resistant to traditional anti-tuberculosis drugs has alarmed health services worldwide. The search for new therapeutic targets and effective drugs that counteract the virulence and multiplication of Mtb represents a challenge for the scientific community. Several studies have considered the erp gene a possible therapeutic target in the last two decades, since its disruption negatively impacts Mtb multiplication. This gene encodes the exported repetitive protein (Erp), which is located in the cell wall of Mtb. In vitro studies have shown that the Erp protein interacts with two putative membrane proteins, Rv1417 and Rv2617c, and the impairment of their interactions can decrease Mtb replication. In this study, we present five nicotine analogs that can inhibit the formation of heterodimers and trimers between these proteins. Through DFT calculations, molecular dynamics, docking, and other advanced in silico techniques, we have analyzed the molecular complexes, and show the effect these compounds have on protein interactions. The results show that four of these analogs can be possible candidates to counteract the pathogenicity of Mtb. This study aims to combine research on the Erp protein as a therapeutic target in the search for new drugs that serve to create new therapies against tuberculosis disease.
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Affiliation(s)
- Jorge Alberto Aguilar-Pineda
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Camilo Febres-Molina
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago de Chile 8370134, Chile
| | - Cinthia C. Cordova-Barrios
- Departamento de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Lizbeth M. Campos-Olazával
- Facultad de Arquitectura e Ingeniería Civil y del Ambiente, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Bruno A. Del-Carpio-Martinez
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Flor Ayqui-Cueva
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Pamela L. Gamero-Begazo
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago de Chile 8370134, Chile
| | - Badhin Gómez
- Centro de Investigación en Ingeniería Molecular—CIIM, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Departamento de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Correspondence: ; Tel.: +51-982895967
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Afsar N, Jonathan DR, Satheesh D, Manivannan S. Computational description of quantum chemical calculations and pharmacological studies of the synthesized chalcone derivative: A promising NLO material. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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DFT Explorations on the spectral, non-covalent interactions and the invitro analysis of a synthesized anti-bacterial nanocomposite pure hydroxyapatite. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Computational investigation, effects of polar and non-polar solvents on optimized structure with topological parameters (ELF, LOL, AIM, and RDG) of three glycine derivative compounds. Struct Chem 2022. [DOI: 10.1007/s11224-022-01930-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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