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Peng M, Wang Y, Wu C, Cai X, Wu Y, Du E, Zheng L, Fu J. Investigating sulfonamides - Human serum albumin interactions: A comprehensive approach using multi-spectroscopy, DFT calculations, and molecular docking. Biochem Biophys Res Commun 2023; 683:149108. [PMID: 37862782 DOI: 10.1016/j.bbrc.2023.10.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023]
Abstract
The environmental and health risks associated with sulfonamide antibiotics (SAs) are receiving increasing attention. Through multi-spectroscopy, density functional theory (DFT), and molecular docking, this study investigated the interaction features and mechanisms between six representative SAs and human serum albumin (HSA). Multi-spectroscopy analysis showed that the six SAs had significant binding capabilities with HSA. The order of binding constants at 298 K was as follows: sulfadoxine (SDX): 7.18 × 105 L mol-1 > sulfamethizole (SMT): 6.28 × 105 L mol-1 > sulfamerazine (SMR): 2.70 × 104 L mol-1 > sulfamonomethoxine (SMM): 2.54 × 104 L mol-1 > sulfamethazine (SMZ): 3.06 × 104 L mol-1 > sulfadimethoxine (SDM): 2.50 × 104 L mol-1. During the molecular docking process of the six SAs with HSA, the binding affinity range is from -7.4 kcal mol-1 to -8.6 kcal mol-1. Notably, the docking result of HSA-SDX reached the maximum of -8.6 kcal mol-1, indicating that SDX may possess the highest binding capacity to HSA. HSA-SDX binding, identified as a static quenching and exothermic process, is primarily driven by hydrogen bonds (H bonds) or van der Waals (vdW) interactions. The quenching processes of SMR/SMZ/SMM/SDX/SMT to HSA are a combination of dynamic and static quenching, indicating an endothermic reaction. Hydrophobic interactions are primarily accountable for SMR/SMZ/SMM/SDX/SMT and HSA binding. Competition binding results revealed that the primary HSA-SAs binding sites are in the subdomain IB of the HAS structure, consistent with the results of molecule docking. The correlation analysis based on DFT calculations revealed an inherent relationship between the structural chemical features of SAs and the binding performance of HSA-SAs. The dual descriptor (DD) and the electrophilic Fukui function were found to have a significant relationship (0.71 and -0.71, respectively) with the binding constants of HSA-SAs, predicting the binding performance of SAs and HSA. These insights have substantial scientific value for evaluating the environmental risks of SAs as well as understanding their impact on biological life activities.
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Affiliation(s)
- Mingguo Peng
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China; School of Urban Construction, Changzhou University, Changzhou, 213164, China
| | - Yicui Wang
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China
| | - Chunge Wu
- School of Urban Construction, Changzhou University, Changzhou, 213164, China
| | - Xuewen Cai
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China
| | - Yao Wu
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China
| | - Erdeng Du
- School of Urban Construction, Changzhou University, Changzhou, 213164, China.
| | - Lu Zheng
- School of Urban Construction, Changzhou University, Changzhou, 213164, China
| | - Jiajun Fu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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du X, Xinru W, Yao J, Li H, Bao Y, Lan J, Zhao Z, Zong W. Study on the Interaction between Sulfamerazine and Human serum albumin on Molecular Level using Spectral Analysis. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2022.130917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Arora H, Dhiman D, Kumar K, Venkatesu P. Fortification of thermal and structural stability of hemoglobin using choline chloride-based deep eutectic solvents. Phys Chem Chem Phys 2022; 24:29683-29692. [PMID: 36453254 DOI: 10.1039/d2cp03407g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Of late, DESs have occupied the centre stage due to their eco-friendly and resource-efficient nature and their low toxicity. In this work, we have investigated the structural and thermal stability of hemoglobin (Hb) in two choline chloride ([Ch]Cl)-based DESs namely urea [Ch]Cl-urea (DES1) and [Ch]Cl-glycerol (Gly); (DES 2). Different biophysical techniques reveal that the presence of DESs facilitates the stability of Hb in a concentration-dependent manner and the extent of stability is more pronounced in [Ch]Cl-Gly as compared to [Ch]Cl-urea. Additionally, for a better understanding of the role of DESs in modulating the thermal and structural stability of Hb, studies have been performed on Hb in the presence of individual constituents of DESs, i.e., [Ch]Cl, urea, and Gly. Altogether, it was observed that the effect on the stability of Hb was by the presence of the DESs rather than their individual constituents. For instance, urea itself is a destabilizing co-solvent for biomolecules. However, the harmful effects of urea were surpassed when a DES is formed in the presence of [Ch]Cl. Therefore, overall, it can be concluded that both DESs can be described as potential non-harmful, green, and promising solvents for enhancing the structural and thermal stability of Hb.
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Affiliation(s)
- Harshita Arora
- Department of Chemistry, University of Delhi, Delhi, 110 007, India.
| | - Diksha Dhiman
- Department of Chemistry, University of Delhi, Delhi, 110 007, India.
| | - Krishan Kumar
- Department of Chemistry, University of Delhi, Delhi, 110 007, India. .,Department of Biological Engineering, Inha University, Incheon, 22212, Republic of Korea
| | - Pannuru Venkatesu
- Department of Chemistry, University of Delhi, Delhi, 110 007, India.
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Rupreo V, Luikham S, Bhattacharyya J. PROTEIN BINDING CHARACTERISTICS OF YOHIMBINE, A NATURAL INDOLE ALKALOID BASED DRUG FOR ERECTILE DYSFUNCTION. LUMINESCENCE 2022; 37:1532-1540. [PMID: 35816091 DOI: 10.1002/bio.4327] [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: 04/06/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/08/2022]
Abstract
Even to this day, talking about sexual-dysfunctions largely remains a taboo. Hence less studies were recorded and fewer remedies given. Erectile dysfunction (ED) is one of the most commonly treated psychological disorders which leads to major distress, interpersonal limitation and reduces the quality of life & marriage. This study aimed to assess a plant-derived molecule, Yohimbine (Yoh, a β-carboline indole-alkaloid; often used for ED treatment) and its potential binding phenomenon with hemoglobin (Hb). Successful binding of the Yoh with Hb is evident from spectroscopic and molecular-docking results. Yoh quenched the fluorescence of Hb efficiently through static mode. The binding affinity was in the order of 105 M-1 with 1:1 stoichiometry. Thermodynamic analyses concluded that the protein-ligand association to be spontaneous and attributed by entropy-driven exothermic-binding. Non-polyelectrolytic factor was the core, dominating factor. The structural aspects have been deciphered through infra-red spectroscopy and computational-methods. The giant 3D-protein moiety was significantly perturbed through drug-binding. Hydrophobic forces and hydrogen bonding participation were stipulated by molecular modeling data. This study reveals the detailed interaction pattern and molecular mechanism of Hb-Yoh binding; correlating the structure-function relationship for the first time; therefore, holds enormous importance from the standpoint of rational and efficient drug-designing & development.
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Affiliation(s)
- Vibeizonuo Rupreo
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, India
| | - Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, India
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Mavani A, Ovung A, Luikham S, Suresh Kumar G, Das A, Ray D, Aswal VK, Bhattacharyya J. Biophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin. J Biomol Struct Dyn 2022; 41:3779-3790. [PMID: 35380096 DOI: 10.1080/07391102.2022.2057358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The molecular mechanism of the heme protein, hemoglobin (Hb) interaction with sulfa molecule, sulfadiazine (SDZ) has been investigated through spectroscopic, neutron scattering and molecular modeling techniques. Absorption and emission spectroscopic studies showed that SDZ molecules were bound to Hb protein, non-cooperatively. The binding affinityof SDZ-Hb complex at standard experimental condition was evaluated to be around (4.2 ± 0.07) ×104, M-1with 1:1 stoichiometry. Drug induced structural perturbation of the 3 D protein moiety was confirmed through circular dichroism (CD), synchronous fluorescence and small angle neutron scattering methods. From the temperature dependent spectrofluorometric studies, the negative standard molar Gibbs energy change suggested the spontaneity of the reaction. The negative enthalpy and positive entropy change(s) indicated towards the involvement of both electrostatic and hydrophobic forces during the association process. Salt dependent fluorescence study revealed major contributions from non-poly-electrolytic forces. Molecular modeling studies determined the probable binding sites, types of interaction involved and the conformational alteration of the compactness of the Hb structure upon interaction with SDZ molecule. Overall, the study provides detailed insights into the binding mechanism of SDZ antibiotics to Hb protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A. Mavani
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Aben Ovung
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Abhi Das
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Debes Ray
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Vinod K. Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
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Ovung A, Mavani A, Ghosh A, Chatterjee S, Das A, Suresh Kumar G, Ray D, Aswal VK, Bhattacharyya J. Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods. ACS OMEGA 2022; 7:4932-4944. [PMID: 35187312 PMCID: PMC8851458 DOI: 10.1021/acsomega.1c05554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/24/2022] [Indexed: 05/16/2023]
Abstract
Protein-ligand interaction studies are useful to determine the molecular mechanism of the binding phenomenon, leading to the establishment of the structure-function relationship. Here, we report the binding of well-known antibiotic sulfonamide drugs (sulfamethazine, SMZ; and sulfadiazine, SDZ) with heme protein myoglobin (Mb) using spectroscopic, calorimetric, ζ potential, and computational methods. Formation of a 1:1 complex between the ligand and Mb through well-defined equilibrium was observed. The binding constants obtained between Mb and SMZ/SDZ drugs were on the order of 104 M-1. SMZ with two additional methyl (-CH3) substitutions has higher affinity than SDZ. Upon drug binding, a notable loss in the helicity (via circular dichroism) and perturbation of the three-dimensional (3D) protein structure (via infrared and synchronous fluorescence experiments) were observed. The binding also indicated the dominance of non-polyelectrolytic forces between the amino acid residues of the protein and the drugs. The ligand-protein binding distance signified high probability of energy transfer between them. Destabilization of the protein structure upon binding was evident from differential scanning calorimetry results and ζ potential analyses. Molecular docking presented the best probable binding sites of the drugs inside protein pockets. Thus, the present study explores the potential binding characteristics of two sulfonamide drugs (with different substitutions) with myoglobin, correlating the structural and energetic aspects.
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Affiliation(s)
- Aben Ovung
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
| | - A. Mavani
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
| | - Ambarnil Ghosh
- UCD
Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sabyasachi Chatterjee
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Abhi Das
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Debes Ray
- Solid
State Physics Division, Bhabha Atomic Research
Centre, Mumbai 400085, India
| | - Vinod K. Aswal
- Solid
State Physics Division, Bhabha Atomic Research
Centre, Mumbai 400085, India
| | - Jhimli Bhattacharyya
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
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