Advanced in Protein-Ligand Interaction Studies Optical-Based Spectroscopic Insights and Simulation Perspectives

Amirreza Gholami*; Saman Shirmohammadi

**Amirreza Gholami* and Saman Shirmohammadi**

Volume5-Issue6
Dates: Received: 2024-06-01 | Accepted: 2024-06-15 | Published: 2024-06-18
Pages: 614-629

Abstract

Spectroscopic methods relying on light sources play a crucial role in the identification of protein-ligand interactions. Such experimental techniques open doors for scientists to employ them in disease prevention, treatment, drug synthesis, identification of pathways contributing to different disorders, and unveiling the chemical structure of receptors within the human body. Furthermore, alongside experimental approaches, simulation methods also find utility. The combination of both experimental and theoretical techniques enhances the robustness of researchers' investigations. Conversely, the human body harbors a myriad of distinct proteins, each possessing its own distinct structure and functionality; the disruption of any one of these may lead to a range of ailments. Proteins within the human body have the capacity to engage with diverse ligands, yielding intriguing outcomes. Not only proteins interact with other proteins, but they also engage with pharmaceuticals and other substances within the body. Examination of the bonding types formed between the protein and the specific ligand can be effectively accomplished through optical spectroscopic techniques and simulation inquiries. This paper provides a comprehensive review of recent optical spectroscopy methods, as well as simulation studies, which are currently being employed by researchers in these investigations.

FullText HTML FullText PDF DOI: 10.37871/jbres1934

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How to cite this article

Gholami A, Shirmohammadi S. Advanced in Protein-Ligand Interaction Studies: Optical-Based Spectroscopic Insights and Simulation Perspectives. J Biomed Res Environ Sci. 2024 Jun 18; 5(6): 614-629. doi: 10.37871/jbres1934, Article ID: JBRES1934, Available at: https://www.jelsciences.com/articles/jbres1934.pdf

Subject area(s)

Biochemistry

Biology

References

Maity S, Gundampati RK, Suresh Kumar TK, NMR methods to characterize protein-ligand interactions. Natural Product Communications. 2019;14(5):1934578X19849296. doi: 10.1177/1934578X19849296.
Noor Z, Ahn SB, Baker MS, Ranganathan S, Mohamedali A. Mass spectrometry-based protein identification in proteomics-a review. Brief Bioinform. 2021 Mar 22;22(2):1620-1638. doi: 10.1093/bib/bbz163. PMID: 32047889.
Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics. 2021 Jan 6;230:103990. doi: 10.1016/j.jprot.2020.103990. Epub 2020 Sep 20. PMID: 32961344.
Aletaha N, Gholamreza Dehghan, Leila Sadeghi, Samaneh Rashtbari, Alireza Khataee. Binding mechanism of perphenazine/thioridazine with acetylcholinesterase: Spectroscopic surface plasmon resonance and molecular docking based analysis. Journal of Molecular Liquids. 2023;377:121547. doi: 10.1016/j.molliq.2023.121547.
Dehkordi MF, Farhadian S, Hashemi-Shahraki F, Rahmani B, Darzi S, Dehghan G. The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study. Int J Biol Macromol. 2023 Apr 30;235:123713. doi: 10.1016/j.ijbiomac.2023.123713. Epub 2023 Feb 16. PMID: 36801300.
Barone V, Silvia Alessandrini, Malgorzata Biczysko, James R. Cheeseman, David C Clary, Anne B. McCoy, Ryan J. DiRisio, Frank Neese, Mattia Melosso, Cristina Puzzarini. et al., Computational molecular spectroscopy. Nature Reviews Methods Primers, 2021. 1(1): p. 38. doi: 10.1038/s43586-021-00034-1.
Tiernan H, Byrne B, Kazarian SG. ATR-FTIR spectroscopy and spectroscopic imaging for the analysis of biopharmaceuticals. Spectrochim Acta A Mol Biomol Spectrosc. 2020 Nov 5;241:118636. doi: 10.1016/j.saa.2020.118636. Epub 2020 Jun 22. PMID: 32610215; PMCID: PMC7308041.
Gholami A, Gholamreza Dehghan, Samaneh Rashtbari, Abolghasem Jouyban. Exploring the interaction of clonazepam and diazepam with tau protein: Multispectral and molecular docking studies. Journal of Molecular Structure. 2022;1258:132669. doi: 10.1016/j.molstruc.2022.132669.
Gholami A, Dehghan G, Rashtbari S, Jouyban A. Probing the Interactions of Lamotrigine and Phenobarbital with Tau Protein: Experimental and Molecular Modeling Studies. Iran J Pharm Res. 2022 Aug 22;21(1):e129599. doi: 10.5812/ijpr-129599. PMID: 36945338; PMCID: PMC10024808.
Yekta R, Leila Sadeghi, Sohrab Ahmadi-Kandjani, Pouriya Naziri. The impact of caffeine on tau-tau interaction: LSPR detection, structural modification and molecular dynamics simulation. Journal of Molecular Liquids. 2021;338:115914. doi: 10.1016/j.molliq.2021.115914.
Prabowo BA, Purwidyantri A, Liu KC. Surface Plasmon Resonance Optical Sensor: A Review on Light Source Technology. Biosensors (Basel). 2018 Aug 26;8(3):80. doi: 10.3390/bios8030080. PMID: 30149679; PMCID: PMC6163427.
Bose A, Thomas I, Abraham E. Fluorescence spectroscopy and its applications: A Review. Int J Adv Pharm Res. 2018;8(1):1-8. doi: 10.7439/ijapa.v8i1.4578.
Wu L , Huang C , Emery BP , Sedgwick AC , Bull SD , He XP , Tian H , Yoon J , Sessler JL , James TD . Förster resonance energy transfer (FRET)-based small-molecule sensors and imaging agents. Chem Soc Rev. 2020 Aug 7;49(15):5110-5139. doi: 10.1039/c9cs00318e. Epub 2020 Jul 22. PMID: 32697225; PMCID: PMC7408345.
Hou X, Songtao L, Zheng C, Feipeng X. Applications of Fourier transform infrared spectroscopy technologies on asphalt materials. Measurement. 2018;121:304-316. doi: 10.1016/j.measurement.2018.03.001.
Miles AJ , Janes RW , Wallace BA . Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review. Chem Soc Rev. 2021 Aug 7;50(15):8400-8413. doi: 10.1039/d0cs00558d. Epub 2021 Jun 15. PMID: 34132259; PMCID: PMC8328188.
Rahdar A, Nooshin , Faezeh A, Abu Bin HS. Dynamic light scattering: A useful technique to characterize nanoparticles. Journal of Nanoanalysis. 2019;6(2):80-89. doi: 10.22034/JNA.2019.667079.
Jakhar R, Mehak DH, Alka K, Chhillar A. Relevance of molecular docking studies in drug designing. Current Bioinformatics. 2020;15(4):270-278. doi: 10.2174/1574893615666191219094216.
Nahaei FS, Rostami A, Mirtagioglu H, Maghoul A, Simonsen I. Switchable Ultra-Wideband All-Optical Quantum Dot Reflective Semiconductor Optical Amplifier. Nanomaterials (Basel). 2023 Feb 10;13(4):685. doi: 10.3390/nano13040685. PMID: 36839053; PMCID: PMC9962858.
Akib TBA, Mou SF, Rahman MM, Rana MM, Islam MR, Mehedi IM, Mahmud MAP, Kouzani AZ. Design and Numerical Analysis of a Graphene-Coated SPR Biosensor for Rapid Detection of the Novel Coronavirus. Sensors (Basel). 2021 May 17;21(10):3491. doi: 10.3390/s21103491. PMID: 34067769; PMCID: PMC8156410.
Fu Y, Zhao J, Chen Z. Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein. Comput Math Methods Med. 2018 Dec 4;2018:3502514. doi: 10.1155/2018/3502514. PMID: 30627209; PMCID: PMC6305025.
Guterres H, Im W. Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. J Chem Inf Model. 2020 Apr 27;60(4):2189-2198. doi: 10.1021/acs.jcim.0c00057. Epub 2020 Apr 10. PMID: 32227880; PMCID: PMC7534544.
Shaghaghi M, Samaneh R, Laleh S, Somaieh S, Gholamreza D. Molecular Interactions of danofloxacin with bovine serum albumin: An experimental and theoretical investigation. Iranian Journal of Analytical Chemistry. 2022;9(2):1-9. doi: 10.30473/ijac.2022.63121.1229.
Rashtbari S, Dehghan G, Sadeghi L, Sareminia L, Iranshahy M, Iranshahi M, Khataee A, Yoon Y. Interaction of bovine serum albumin with ellagic acid and urolithins A and B: Insights from surface plasmon resonance, fluorescence, and molecular docking techniques. Food Chem Toxicol. 2022 Apr;162:112913. doi: 10.1016/j.fct.2022.112913. Epub 2022 Mar 8. PMID: 35276234.
Yekta R, Ahmadi-Kandjani S, Dehghan G, Rashtbari S, Chaghamirzaei P, Allahveisi S. A new optical method to analyze ligand-protein interaction: Affinity-based screening system. Microchemical Journal. 2020;157:104910. doi: 10.1016/j.microc.2020.104910.
Shaghaghi M, Rashtbari S, Vejdani S, Dehghan G, Jouyban A, Yekta R. Exploring the interactions of a Tb(III)-quercetin complex with serum albumins (HSA and BSA): spectroscopic and molecular docking studies. Luminescence. 2020 Jun;35(4):512-524. doi: 10.1002/bio.3757. Epub 2019 Dec 28. PMID: 31883206.
Cheng Y, Li R, Lin Z, Chen F, Dai J, Zhu Z, Chen L, Zhao Y. Structure-activity relationship analysis of dammarane-type natural products as muscle-type creatine kinase activators. Bioorg Med Chem Lett. 2020 Sep 1;30(17):127364. doi: 10.1016/j.bmcl.2020.127364. Epub 2020 Jun 24. PMID: 32738969.
Wallentin L, Eriksson N, Olszowka M, Grammer TB, Hagström E, Held C, Kleber ME, Koenig W, März W, Stewart RAH, White HD, Åberg M, Siegbahn A. Plasma proteins associated with cardiovascular death in patients with chronic coronary heart disease: A retrospective study. PLoS Med. 2021 Jan 13;18(1):e1003513. doi: 10.1371/journal.pmed.1003513. PMID: 33439866; PMCID: PMC7817029.
Gholami A. Alzheimer's disease: The role of proteins in formation, mechanisms, and new therapeutic approaches. Neurosci Lett. 2023 Nov 20;817:137532. doi: 10.1016/j.neulet.2023.137532. Epub 2023 Oct 20. PMID: 37866702.
Gómez-Benito M, Granado N, García-Sanz P, Michel A, Dumoulin M, Moratalla R. Modeling Parkinson's Disease With the Alpha-Synuclein Protein. Front Pharmacol. 2020 Apr 23;11:356. doi: 10.3389/fphar.2020.00356. PMID: 32390826; PMCID: PMC7191035.
Duan L, Zhang XD, Miao WY, Sun YJ, Xiong G, Wu Q, Li G, Yang P, Yu H, Li H, Wang Y, Zhang M, Hu LY, Tong X, Zhou WH, Yu X. PDGFRβ Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2. Neuron. 2018 Oct 10;100(1):183-200.e8. doi: 10.1016/j.neuron.2018.08.030. Epub 2018 Sep 27. PMID: 30269986.
Chakraborty M, Paul S, Mitra I, Bardhan M, Bose M, Saha A, Ganguly T. To reveal the nature of interactions of human hemoglobin with gold nanoparticles having two different morphologies (sphere and star-shaped) by using various spectroscopic techniques. J Photochem Photobiol B. 2018 Jan;178:355-366. doi: 10.1016/j.jphotobiol.2017.11.026. Epub 2017 Nov 22. PMID: 29182925.
Drescher DG, Selvakumar D, Drescher MJ. Analysis of Protein Interactions by Surface Plasmon Resonance. Adv Protein Chem Struct Biol. 2018;110:1-30. doi: 10.1016/bs.apcsb.2017.07.003. Epub 2017 Sep 12. PMID: 29412994.
Masson JF. Portable and field-deployed surface plasmon resonance and plasmonic sensors. Analyst. 2020;145(11):3776-3800. doi: 10.1039/D0AN00316F.
Ucak Ozkaya G, Durak MZ, Akyar I, Karatuna O. Antimicrobial Susceptibility Test for the Determination of Resistant and Susceptible S. aureus and Enterococcus spp. Using a Multi-Channel Surface Plasmon Resonance Device. Diagnostics (Basel). 2019 Nov 15;9(4):191. doi: 10.3390/diagnostics9040191. PMID: 31731591; PMCID: PMC6963824.
Hinman SS, McKeating KS, Cheng Q. Surface Plasmon Resonance: Material and Interface Design for Universal Accessibility. Anal Chem. 2018 Jan 2;90(1):19-39. doi: 10.1021/acs.analchem.7b04251. Epub 2017 Nov 7. PMID: 29053253; PMCID: PMC6041476.
Tabasi O, Falamaki C. Recent advancements in the methodologies applied for the sensitivity enhancement of surface plasmon resonance sensors. Analytical methods. 2018;10(32):3906-3925. doi: 10.1039/C8AY00948A.
Nurrohman DT, Chiu NF. Surface plasmon resonance biosensor performance analysis on 2D material based on graphene and transition metal dichalcogenides. ECS Journal of Solid State Science and Technology, 2020;9(11):115023. doi: 10.1149/2162-8777/abb419.
Douzi B. Surface Plasmon Resonance: A Sensitive Tool to Study Protein-Protein Interactions. Methods Mol Biol. 2024;2715:363-382. doi: 10.1007/978-1-0716-3445-5_23. PMID: 37930540..
Taghipour P, Zakariazadeh M, Sharifi M, Ezzati Nazhad Dolatabadi J, Barzegar A. Bovine serum albumin binding study to erlotinib using surface plasmon resonance and molecular docking methods. J Photochem Photobiol B. 2018 Jun;183:11-15. doi: 10.1016/j.jphotobiol.2018.04.008. Epub 2018 Apr 9. PMID: 29679689.
de Paula Rezende J, Hudson EA, Campos de Paula HM, Coelho YL, da Silva LHM, dos Santos Pires AC. Thermodynamic and kinetic study of epigallocatechin-3-gallate-bovine lactoferrin complex formation determined by surface plasmon resonance (SPR): A comparative study with fluorescence spectroscopy. Food Hydrocolloids, 2019. 95: p. 526-532. doi: 10.1016/j.foodhyd.2019.04.065.
Rashtbari S, Khataee S, Iranshahi M, Moosavi-Movahedi AA, Hosseinzadeh G, Dehghan G. Experimental investigation and molecular dynamics simulation of the binding of ellagic acid to bovine liver catalase: Activation study and interaction mechanism. Int J Biol Macromol. 2020 Jan 15;143:850-861. doi: 10.1016/j.ijbiomac.2019.09.146. Epub 2019 Nov 15. PMID: 31739034.
Panigrahi SK, Mishra AK. Inner filter effect in fluorescence spectroscopy: As a problem and as a solution. Journal of Photochemistry and Photobiology C: Photochemistry Reviews, 2019;41:100318. doi: 10.1016/j.jphotochemrev.2019.100318.
Xing P, Hongzhong C, Huijing X, Yanli Z. selective coassembly of aromatic amino acids to fabricate hydrogels with light irradiation‐induced emission for fluorescent imprint. Advanced Materials, 2018;30(5):1705633. doi: 10.1002/adma.201705633.
Sikorska E, Khmelinskii I, Sikorski M. Fluorescence spectroscopy and imaging instruments for food quality evaluation, in Evaluation technologies for food quality. Elsevier. 2019;491-533. doi: 10.1016/B978-0-12-814217-2.00019-6.
Cubuk J, Stuchell-Brereton MD, Soranno A. The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy. Essays Biochem. 2022 Dec 16;66(7):875-890. doi: 10.1042/EBC20220065. PMID: 36416865; PMCID: PMC9760427.
Condict L, Kasapis S. Critical issues encountered in the analysis of protein-phenolic binding interactions via fluorescence spectroscopy. Food Hydrocolloids. 2022;124:107219. doi: 10.1016/j.foodhyd.2021.107219.
Kompany-Zareh M, Akbarian S, Najafpour MM. Unsupervised recognition of components from the interaction of BSA with Fe cluster in different conditions utilizing 2D fluorescence spectroscopy. Sci Rep. 2022 Oct 7;12(1):16875. doi: 10.1038/s41598-022-20768-6. PMID: 36207446; PMCID: PMC9547014.
Zacharioudaki DE, Fitilis I, Kotti M. Review of Fluorescence Spectroscopy in Environmental Quality Applications. Molecules. 2022 Jul 27;27(15):4801. doi: 10.3390/molecules27154801. PMID: 35956751; PMCID: PMC9370042.
Wang K, Wu S, Zhao J, Zhou M, Li G, Wang D, Lin L. Quantitative analysis of urea in serum by synchronous modulation and demodulation fluorescence spectroscopy. Spectrochim Acta A Mol Biomol Spectrosc. 2022 Mar 5;268:120645. doi: 10.1016/j.saa.2021.120645. Epub 2021 Nov 18. PMID: 34838422.
Li W, Li X, Han C, Gao L, Wu H, Li M. A new view into three-dimensional excitation-emission matrix fluorescence spectroscopy for dissolved organic matter. Sci Total Environ. 2023 Jan 10;855:158963. doi: 10.1016/j.scitotenv.2022.158963. Epub 2022 Sep 22. PMID: 36155043.
Khalili L. Dehghan G, Moosavi-Movahedi AA, Yoon Y. In vitro and in silico insights into the molecular interaction mechanism of acetylshikonin with bovine serum albumin. Journal of Molecular Liquids, 2022;365:120191. doi: 10.1016/j.molliq.2022.120191.
Heidary Alizadeh B, Dehghan GH, Derakhsh Ahmadi V, Moghimi S, Asadipour A, Foroumadi A. Spectroscopic and molecular docking studies on DNA binding interaction of podophyllotoxin. Journal of Sciences, Islamic Republic of Iran. 2018;29(2):121-127. doi: 10.22059/jsciences.2018.65018.
Mokaberi P, Babayan-Mashhadi F, Amiri Tehrani Zadeh Z, Saberi MR, Chamani J. Analysis of the interaction behavior between Nano-Curcumin and two human serum proteins: combining spectroscopy and molecular stimulation to understand protein-protein interaction. J Biomol Struct Dyn. 2021 Jun;39(9):3358-3377. doi: 10.1080/07391102.2020.1766570. Epub 2020 May 20. PMID: 32397834.
Cheng W, Jinliang M, Sijia W, Ruixin L, Suyue W, Jialiang H, Huaibin K, Lili L, Feng X. Interaction mechanism between resveratrol and ovalbumin based on fluorescence spectroscopy and molecular dynamic simulation. Lwt. 2021;146:111455. doi: 10.1016/j.lwt.2021.111455.
Shaw M, Samanta D, Salam Shaik A, Bhattacharya A, Basu R, Mondal I, Pathak A. Solvent-induced switching between static and dynamic fluorescence quenching of N, S Co-doped carbon dots in sensing of Crotonaldehyde: A detailed systematic study. Optical Materials, 2023. 137: p. 113600. doi: 10.1016/j.optmat.2023.113600.
Koppal VV, Melavanki R, Kusanur R, Patil NR. Analysis of Fluorescence Quenching of Coumarin Derivative under Steady State and Transient State Methods. J Fluoresc. 2021 Mar;31(2):393-400. doi: 10.1007/s10895-020-02663-3. Epub 2021 Jan 6. PMID: 33405018.
Asemi-Esfahani Z, Behzad S, Sadegh F, Lida M.Food additive dye-lysozyme complexation: Determination of binding constants and binding sites by fluorescence spectroscopy and modeling methods. Journal of Molecular Liquids. 2022;363:119749. doi: 10.1016/j.molliq.2022.119749.
Sistani P, Dehghan G, Sadeghi L. Structural and kinetic insights into HIV-1 reverse transcriptase inhibition by farnesiferol C. Int J Biol Macromol. 2021 Mar 31;174:309-318. doi: 10.1016/j.ijbiomac.2021.01.173. Epub 2021 Jan 29. PMID: 33524481.
Liao J, Madahar V, Dang R, Jiang L. Quantitative FRET (qFRET) Technology for the Determination of Protein-Protein Interaction Affinity in Solution. Molecules. 2021 Oct 20;26(21):6339. doi: 10.3390/molecules26216339. PMID: 34770748; PMCID: PMC8588070.
Magalhães S, Goodfellow BJ, Nunes A. FTIR spectroscopy in biomedical research: How to get the most out of its potential. Applied Spectroscopy Reviews. 2021;56(8-10):869-907. doi: 10.1080/05704928.2021.1946822.
Jozanikohan G, Abarghooei MN. The Fourier transform infrared spectroscopy (FTIR) analysis for the clay mineralogy studies in a clastic reservoir. Journal of Petroleum Exploration and Production Technology. 2022:1-14. doi: 10.1007/s13202-021-01449-y.
Guerrero‐Pérez MO, Patience GS. Experimental methods in chemical engineering: Fourier transform infrared spectroscopy- FTIR. The Canadian Journal of Chemical Engineering. 2020;98(1):25-33. doi: 10.1002/cjce.23664.
Fakayode SO, Baker G, Bwambok DK, Bhawawet N, Elzey B, Siraj N, Macchi S, Pollard D, Pérez, A'ja V Duncan RL, Warner I. Molecular (Raman, NIR, and FTIR) spectroscopy and multivariate analysis in consumable products analysis1. Applied Spectroscopy Reviews. 2020;55(8):647-723.
Miller LM, Bourassa MW, Smith RJ. FTIR spectroscopic imaging of protein aggregation in living cells. Biochim Biophys Acta. 2013 Oct;1828(10):2339-46. doi: 10.1016/j.bbamem.2013.01.014. Epub 2013 Jan 25. PMID: 23357359; PMCID: PMC3722250.
Zhao X, Wang Y, Zhao D. Structural analysis of biomacromolecules using circular dichroism spectroscopy. Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics. 2023:77-103. doi: 10.1016/B978-0-323-99127-8.00013-1.
Ojaghi S, Soheila M, Mojtaba A, Sirous G, Nooshin B, Sajjad E, Reza K. Sunset yellow degradation product, as an efficient water-soluble inducer, accelerates 1N4R Tau amyloid oligomerization: In vitro preliminary evidence against the food colorant safety in terms of “Triggered Amyloid Aggregation”. Bioorganic chemistry. 2020;103:104123. doi: 10.1016/j.bioorg.2020.104123.
Keiderling TA, Lakhani A. Mini review: Instrumentation for vibrational circular dichroism spectroscopy, still a role for dispersive instruments. Chirality. 2018 Mar;30(3):238-253. doi: 10.1002/chir.22799. Epub 2018 Jan 2. PMID: 29293282.
Mitri F. Optical radiation force circular dichroism spectroscopy. Journal of Quantitative Spectroscopy and Radiative Transfer. 2020;244:106850.
Sonawane SK, Chidambaram H, Boral D, Gorantla NV, Balmik AA, Dangi A, Ramasamy S, Marelli UK, Chinnathambi S. EGCG impedes human Tau aggregation and interacts with Tau. Sci Rep. 2020 Jul 28;10(1):12579. doi: 10.1038/s41598-020-69429-6. PMID: 32724104; PMCID: PMC7387440.
Kumar P, Bhardwaj T, Garg N, Giri R. Microsecond simulations and CD spectroscopy reveals the intrinsically disordered nature of SARS-CoV-2 spike-C-terminal cytoplasmic tail (residues 1242-1273) in isolation. Virology. 2022 Jan;566:42-55. doi: 10.1016/j.virol.2021.11.005. Epub 2021 Nov 27. PMID: 34864296; PMCID: PMC8626822.
Zhang C, Jin Z, Zeng B, Wang W, Palui G, Mattoussi H. Characterizing the Brownian Diffusion of Nanocolloids and Molecular Solutions: Diffusion-Ordered NMR Spectroscopy vs Dynamic Light Scattering. J Phys Chem B. 2020 Jun 4;124(22):4631-4650. doi: 10.1021/acs.jpcb.0c02177. Epub 2020 May 21. PMID: 32356987.
Waghmare M, Bipin SK, Chaudhari P, Dongre PM. Multiple layer formation of bovine serum albumin on silver nanoparticles revealed by dynamic light scattering and spectroscopic techniques. Journal of Nanoparticle Research. 2018;20:1-21. doi: 10.1007/s11051-018-4286-3.
Morozova OV, Pavlova ER, Bagrov DV, Barinov NA, Prusakov KA, Isaeva EI, Podgorsky VV, Basmanov DV, Klinov DV. Protein nanoparticles with ligand-binding and enzymatic activities. Int J Nanomedicine. 2018 Oct 18;13:6637-6646. doi: 10.2147/IJN.S177627. PMID: 30425479; PMCID: PMC6202000.
Carvalho PM, Felício MR, Santos NC, Gonçalves S, Domingues MM. Application of Light Scattering Techniques to Nanoparticle Characterization and Development. Front Chem. 2018 Jun 25;6:237. doi: 10.3389/fchem.2018.00237. PMID: 29988578; PMCID: PMC6026678.
Guo XJ, Hao AJ, Han XW, Kang PL, Jiang YC, Zhang XJ. The investigation of the interaction between ribavirin and bovine serum albumin by spectroscopic methods. Mol Biol Rep. 2011 Aug;38(6):4185-92. doi: 10.1007/s11033-010-0539-7. Epub 2010 Dec 3. PMID: 21127994.
Fan J, Fu A, Zhang L. Progress in molecular docking. Quantitative Biology, 2019;7:83-89. doi: 10.1007/s40484-019-0172-y.
Prieto-Martínez FD, Arciniega M, Medina-Franco JL. Molecular docking: current advances and challenges. TIP. Revista especializada en ciencias químico-biológicas. 2018;21. doi: 10.22201/fesz.23958723e.2018.0.143.
Sethi A, Khusbhoo J, Sasikala K, Mallika A. Molecular docking in modern drug discovery: Principles and recent applications. Drug discovery and development-new advances, 2019. 2: p. 1-21. doi: 10.5772/intechopen.85991.
Butt SS, Yasmin B, Maria S, Mehak R.Molecular docking using chimera and autodock vina software for nonbioinformaticians. JMIR Bioinformatics and Biotechnology. 2020;1(1):e14232. doi: 10.2196/14232.
Dong D, Xu Z, Zhong W, Peng S. Parallelization of Molecular Docking: A Review. Curr Top Med Chem. 2018;18(12):1015-1028. doi: 10.2174/1568026618666180821145215. PMID: 30129415.
Solis-Vasquez L, Tillack AF, Santos-Martins D, Koch A, LeGrand S, Forli S. Benchmarking the Performance of Irregular Computations in AutoDock-GPU Molecular Docking. Parallel Comput. 2022 Mar;109:102861. doi: 10.1016/j.parco.2021.102861. Epub 2021 Nov 11. PMID: 34898769; PMCID: PMC8654209.
Reddy KK, Rathore RS, Srujana P, Burri RR, Reddy CR, Sumakanth M, Reddanna P, Reddy MR. Performance Evaluation of Docking Programs- Glide, GOLD, AutoDock & SurflexDock, Using Free Energy Perturbation Reference Data: A Case Study of Fructose-1, 6-bisphosphatase-AMP Analogs. Mini Rev Med Chem. 2020;20(12):1179-1187. doi: 10.2174/1389557520666200526183353. PMID: 32459606.
Banchi L, Fingerhuth M, Babej T, Ing C, Arrazola JM. Molecular docking with Gaussian Boson Sampling. Sci Adv. 2020 Jun 5;6(23):eaax1950. doi: 10.1126/sciadv.aax1950. PMID: 32548251; PMCID: PMC7274809.
Afef G, Hitler L, Thierry R, Isangb BB, Innocent B, Riadh K. X-ray crystallography, spectral analysis, DFT studies, and molecular docking of (C9H15N3)[CdCl4] hybrid material against methicillin-resistant Staphylococcus aureus (MRSA). Polycyclic Aromatic Compounds. 2023:1-23.
Nahaei FS, Rostami A, Mirtagioglu H, Maghoul A, Simonsen I. Switchable Ultra-Wideband All-Optical Quantum Dot Reflective Semiconductor Optical Amplifier. Nanomaterials (Basel). 2023 Feb 10;13(4):685. doi: 10.3390/nano13040685. PMID: 36839053; PMCID: PMC9962858.
Serat Nahaei F, Rostami A, Matloub S. Ultrabroadband reflective semiconductor optical amplifier using superimposed quantum dots. Journal of Nanophotonics. 2021;15(3):036009-036009. doi: 10.1117/1.JNP.15.036009.
87Nahaei FS, Rostami A, Mirtaheri P. Quantum Dot Reflective Semiconductor Optical Amplifiers: Optical Pumping Compared with Electrical Pumping. Nanomaterials (Basel). 2022 Jun 22;12(13):2143. doi: 10.3390/nano12132143. PMID: 35807979; PMCID: PMC9267988.
Nahaei FS, Rostami A, Matloub S. Selective band amplification in ultra-broadband superimposed quantum dot reflective semiconductor optical amplifiers. Appl Opt. 2022 May 20;61(15):4509-4517. doi: 10.1364/AO.427496. PMID: 36256292.
Viscomi F. Light Matter interaction in hybrid plasmonic/photonic nanogaps. 2020.
Luo Z, Yajuan W, Lihui L, Ziyu L, Chenguang Z, Xin Y, Ming H, Jianhua H, Delang L, Xiaoli Z, Dong L, Anlian P. Plasmonically engineered light-matter interactions in Au-nanoparticle/MoS 2 heterostructures for artificial optoelectronic synapse. Nano Research. 2022;1-9. doi: 10.1007/s12274-021-3875-0.
Khan SA, Khan Nz, Xie Y, Abbas MT, Rauf M, Mehmood I, Runowski M, Agathopoulos S, Zhu J. Optical sensing by metamaterials and metasurfaces: from physics to biomolecule detection. Advanced Optical Materials. 2022;10(18):2200500. doi: 1002/adom.202200500.
Adak S, Tripathi LN. Nanoantenna enhanced terahertz interaction of biomolecules. Analyst, 2019;144(21):6172-6192. doi: 10.1039/C9AN00798A.
Bensalah H, Hocini A, Bahri H, Khedrouche D, Ingebrandt S, Pachauri V. A plasmonic refractive index sensor with high sensitivity and its application for temperature and detection of biomolecules. Journal of Optics. 2023;52(3):1035-1046. doi: 10.1007/s12596-022-00922-z
Pant U, Mohapatra S, Moirangthem RS. Total internal reflection ellipsometry based SPR sensor for studying biomolecular interaction. Materials Today: Proceedings. 2020;28:254-257. 10.1016/j.matpr.2020.01.602.
Ambika S, Manojkumar Y, Arunachalam S, Gowdhami B, Meenakshi Sundaram KK, Solomon RV, Venuvanalingam P, Akbarsha MA, Sundararaman M. Biomolecular Interaction, Anti-Cancer and Anti-Angiogenic Properties of Cobalt(III) Schiff Base Complexes. Sci Rep. 2019 Feb 25;9(1):2721. doi: 10.1038/s41598-019-39179-1. PMID: 30804454; PMCID: PMC6389928.