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Yang Z, Zhao J. Molecular Insights into Macromolecules Structure, Function, and Regulation. Int J Mol Sci 2024; 25:5296. [PMID: 38791335 PMCID: PMC11121550 DOI: 10.3390/ijms25105296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Macromolecules exhibit ordered structures and complex functions in an aqueous environment with strong thermodynamic fluctuations [...].
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China;
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Shafiq N, Shakoor B, Yaqoob N, Parveen S, Brogi S, Mohammad Salamatullah A, Rashid M, Bourhia M. A virtual insight into mushroom secondary metabolites: 3D-QSAR, docking, pharmacophore-based analysis and molecular modeling to analyze their anti-breast cancer potential. J Biomol Struct Dyn 2024:1-22. [PMID: 38299565 DOI: 10.1080/07391102.2024.2304137] [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: 08/04/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024]
Abstract
Breast cancer is a major issue of investigation in drug discovery due to its rising frequency and global dominance. Plants are significant natural sources for the development of novel medications and therapies. Medicinal mushrooms have many biological response modifiers and are used for the treatment of many physical illnesses. In this research, a database of 89 macro-molecules with anti-breast cancer activity, which were previously isolated from the mushrooms in literature, has been selected for the three-dimensional quantitative structure-activity relationships (3D-QSAR) studies. The 3D-QSAR model was necessarily used in Pharmacopoeia virtual evaluation of the database to develop novel MCF-7 inhibitors. With the known potential targets of breast cancer, the docking studies were achieved. Using molecular dynamics simulations, the targets' stability with the best-chosen natural product molecule was found. Furthermore, the absorption, distribution, metabolism, excretion, and toxicity of three compounds, resulting after the docking study, were predicted. The compound C1 (Pseudonocardian A) showed the features of effective compounds because it has bioavailability from different coral species and is toxicity-free for the prevention of many dermatological illnesses. C1 is chemically active and possesses charge transfer inside the monomer, as seen by the band gaps of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) electrons. The reactivity descriptors ionization potential, electron affinity, chemical potential (μ), hardness (η), softness (S), electronegativity (χ), and electrophilicity index (ω) have been estimated using the energies of frontier molecular orbitals (HOMO-LUMO). Additionally, molecular electrostatic potential maps were created to show that the C1 is reactive.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Bushra Shakoor
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Nazia Yaqoob
- Green Chemistry Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Simone Brogi
- Department of Pharmacy, Pisa University, Pisa, Italy
| | - Ahmad Mohammad Salamatullah
- Department of Food Science & Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Maryam Rashid
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
- Laboratory of Chemistry-Biochemistry, Environment, Nutrition, and Health, Faculty of Medicine and Pharmacy, University Hassan II, Casablanca, Morocco
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Roney M, Dubey A, Issahaku AR, Uddin MN, Tufail A, Wilhelm A, Zamri NB, Aluwi MFFM. Insights from in silico exploration of major curcumin analogs targeting human dipeptidyl peptidase IV. J Biomol Struct Dyn 2024:1-14. [PMID: 38260948 DOI: 10.1080/07391102.2024.2306197] [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: 10/21/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
The goal of this work is to use a variety of in-silico techniques to identify anti-diabetic agents against DPP-IV enzyme from five main curcumin analogues. To produce the successful molecules, five main curcumin analogues were docked into the active site of DPP-IV enzyme. In comparison to the control molecule (Saxagliptin, -6.9 kcal/mol), all the compounds have the highest binding affinity (-7.6 to -7.7 kcal/mol) for the DPP-IV enzyme. These compounds underwent further testing for studies on drug-likeness, pharmacokinetics, and acute toxicity to see the efficacy and safety of compounds. To assess the stability of the docking complex and the binding posture identified during the docking experiment, our study got THC as the lead compound, which was then exposed to 200 ns of molecular dynamic simulation and PCA analysis. Additionally, DFT calculations were conducted to determine the thermodynamic, molecular orbital, and electrostatic potential characteristics of lead compound. Overall, the lead chemical has shown strong drug-like properties, is non-toxic, and has a sizable affinity for the DPP-IV enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Amit Dubey
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | | | - Md Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Aisha Tufail
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | - Anke Wilhelm
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
| | - Normaiza Binti Zamri
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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Roney M, Issahaku AR, Govinden U, Gazali AM, Aluwi MFFM, Zamri NB. Diabetic wound healing of aloe vera major phytoconstituents through TGF-β1 suppression via in-silico docking, molecular dynamic simulation and pharmacokinetic studies. J Biomol Struct Dyn 2023:1-14. [PMID: 37942697 DOI: 10.1080/07391102.2023.2279280] [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: 09/06/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
To restore the integrity of the skin and subcutaneous tissue, the wound healing process involves a complex series of well-orchestrated biochemical and cellular events. Due to the existence of various active components, accessibility and few side effects, some plant extracts and their phytoconstituents are recognised as viable options for wound healing agents. To find possible inhibitors of diabetic wound healing, four main constituents of aloe vera were identified from the literature. TGF-β1 and the compounds were studied using molecular docking to see how they interacted with the active site of target protein (PDB ID: 6B8Y). The pharmacokinetics investigation of the aloe emodin with the highest dock score complied with all the Lipinski's rule of five and pharmacokinetics criteria. Conformational change in the docked complex of Aloe emodin was investigated with the Amber simulation software, via a molecular dynamic (MD) simulation. The MD simulations of aloe emodin bound to TGF-β1 showed the significant structural rotations and twists occurring from 0 to 200 ns. The estimate of the aloe emodin-TGF-β1 complex's binding free energy has also been done using MM-PBSA/GBSA techniques. Additionally, aloe emodin has a wide range of enzymatic activities since their probability active (Pa) values is >0.700. 'Aloe emodin', an active extract of aloe vera, has been identified as the key chemical in the current investigation that can inhibit diabetic wound healing. Both in-vitro and in-vivo experiments will be used in a wet lab to confirm the current computational findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Abdul Razak, Gambang, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Gambang, Malaysia
| | - Abdul Rashid Issahaku
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
- West African Centre for Computational Research and Innovation, Ghana, West Africa
| | - Usha Govinden
- Discipline of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, School of Health Sciences, University of Kwazulu Natal, Westville, South Africa
| | - Ahmad Mahfuz Gazali
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Abdul Razak, Gambang, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Abdul Razak, Gambang, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Gambang, Malaysia
| | - Normaiza Binti Zamri
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Abdul Razak, Gambang, Malaysia
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