This is a preview and has not been published.

A Theoretical Study of the Docking of Medicines with some Proteins




Lipophilicity, amino drugs, HOMO, LUMO


A set of ten drug compounds containing an amino group in the structure were determined theoretically. The parameters were entered into a model to forecast the optimal values of practical (log P) medicinal molecules. The drugs were evaluated theoretically using different types of calculations which are AM1, PM3, and Hartree Fock at the basis set (HF/STO-3G). The Physico-chemical data like (entropy, total energy, Gibbs Free Energy,…etc were computed and played an important role in the predictions of the practical lipophilicity values. Besides, Eigenvalues named HOMO and LUMO were determined. Linearity was shown when correlated between the experimental data with the evaluated physical properties. The statistical analysis was used to analyze the descriptors like multiple linear regression analysis performed to derive quantitative structure-activity relationship models which were further evaluated for the values of the prediction. The correlation coefficient gives an excellent relationship of more than (0.980, 0.980, and 0.978) for AM1, PM3, and HF/STO-3G respectively. A docking study was applied for the interaction of medicines with protein. All the drugs were connected with the protein to give the best energy stability for the docking mixtures. Nepafenac (compound No. 8) had the most stable energy with the protein compared with the 4-Aminosalicylic acid (compound No. 2) which had less energy stability.


Download data is not yet available.


Aczkowski K, Biernasiuk A, Baranowskaa C A, Zavyalova O, Redka M, Malm A. Synthesis, lipophilicity determination, DFT calculation, antifungal and DPPH radical scavenging activities of tetrahydrothiophene-3-one based thiazoles, J Mol Struct. 2018; 1171: 717-725.

M.A. Bakht, Alajmi M.F, Alam P, Alam A, Alam P, Aljarba T M. Theoretical and experimental study on lipophilicity and wound healing activity of ginger compounds. Asian Pac J Trop Biomed. 2014; 4: 329-333.

Mc Bride E, Kretsch A, Garibay L, Brigance K, Frey B, Buss B. Rapid experimental and computational determination of phenethylamine drug analog lipophilicity. Forensic Chem. 2016; 1: 58-65.

Roy K, Saha A. Internet Electron. J Mol Des. 2003; 2: 288-305.

Tiziana G, Javier V, Enric G, Enric H, Francisco J L. Lipophilicity in drug design: an overview of lipophilicity descriptors in 3D-QSAR studies. Future Med Chem. 2019; 11(10): 1177-1193.

Moreira J, Ribeiro D, Silva P, Nazareth N, Monteiro M, Palmeira A. New Alkoxy Flavone Derivatives Targeting Caspases: Synthesis and Antitumor Activity Evaluation. Molecules. 2019; 24: 129.

Teodora C, Claudiu N L, Ildiko L. Lipophilicity as a Central Component of Drug-Like Properties of Chalchones and Flavonoid Derivatives. Molecules. 2019; 24: 1505, doi:10.3390/molecules24081505.

Karadzic M, Loncar D, Benedekovic G, Kovacevic I, Popsavin V, Kocacevic S. A comparative study of chromatographic behavior and lipophilicity of selected natural styryl lactones, their derivatives and analogs. Eur J Pharm Sci. 2017; 105: 99-107.

Andrzej C. Determination of the Lipophilicity of Ibuprofen, Naproxen, Ketoprofen, and Flurbiprofen with Thin-Layer Chromatography. J Chem. 2019; Article ID 3407091: 6,

Jadranka V O, Jovana B T, Jasna B Trbojevic-Stankovic, Dejan M N, Ratomir M J. Assessment of the relationship between the molecular properties of calcium channel blockers and plasma protein binding data. Arch Biol Sci. 2017; 69(1): 175-179, doi: 10.2298/ABS160609094O.

Mohammad S A, Lijun L, Yong E L, Dong U L. Synthesis, Antibacterial Activity and Quantum-Chemical Studies of Novel 2-Arylidenehydrazinyl-4-arylthiazole Analogues. Chem Pharm Bull. 2011; 59(5): 568-573.

Tetko I V, Varbanov H P, Galanski M, Talmaciu M, Platts J A, Ravera M. Prediction of LogP for Pt(II) and Pt(IV) Complexes: Comparison of Statistical and Quantum-Chemistry Based Approaches. J Inorg Biochem. 2016; 156: 1–13.

Matthias H M, Klose S T, Hristo P V, Doris H, Verena P, Markus G. Development and Validation of Liquid Chromatography-Based Methods to Assess the Lipophilicity of Cytotoxic Platinum(IV) Complexes. Inorganics. 2018; 6: 130; doi:10.3390/inorganics6040130.

Limuddin M, Grant D, Bulloch D, Lee N, Peacock M, Dahl R. Determination of log D via Automated Microfluidic Liquid−Liquid Extraction. J Med Chem. 2008; 51: 5140–5142.

Hawryl A M, Popiołek L P, Hawryl M A, Swieboda R S, Niejedli M A. Chromatographic and calculation methods for analysis of the lipophilicity of newly synthesized thiosemicarbazides and their cyclic analogues 1,2,4-triazol-3-thiones. J Braz Chem Soc. 2015; 26: 1617–1624.

Ammar A Ibrahim, Omer M Yahya, Maher A Ibrahim. Theoretical Prediction of Possible Drug Treatment of COVID-19 using Coumarin Containing Chloroquine Moiety Compounds. Asian J Chem. 2020; 32(12): 3120-3126.

Ammar A Ibrahim. Lipophilicity Determination for Amino-Drugs Compounds Using Theoretical Calculations, Test Eng Manag. July-August 2020: 4636-4645.

Rasha A J, Nafeesa J Kadhim, Ahlam M Farhan. Experimental and Theoretical Study of Neomycin Sulfate as Corrosion Protection for Titanium in Acid Media. Baghdad Sci J. 2021; 18, 2, 2.

Falah A H Mutlak, Ali T Mohi, Tariq J Alwan. Density functional theory study of molecular structure, Electronic properties, UV–Vis spectra on coumarin102. Baghdad Sci J. 2016; 13 , 2.2NCC,2.

Alnajjar R, Mostafa A, Kandeil A, Al-Karmalawy A A. Molecular docking, molecular dynamics, and in vitro studies reveal the potential of angiotensin II receptor blockers to inhibit the COVID-19 main protease. Heliyon . 2020; 6. doi:10.1016/j.heliyon.2020.e05641

Prajapat M, Sarma P, Shekhar N, Avti P, Sinha S, Kaur H. Drug targets for coronavirus: a systematic review. Indian J Pharmacol. 2020; 52: 56–65. DOI: 10.4103/ijp.IJP_115_20

Jairajpuri D S, Hussain A, Nasreen K, Mohammad T, Anjum F, Tabish R M. Identification of natural compounds as potent inhibitors of SARS-CoV-2 main protease using combined docking and molecular dynamics simulations. Saudi J Biol Sci. 2021; 28: 2423–2431. DOI: 10.1016/j.sjbs.2021.01.040

Natalia Sh L, Yury A G, Galina M M, Svetlana V Z, Sergey A Z, Alena S Malyasova. Theoretical and experimental study of interaction of macroheterocyclic compounds with ORF3a of SARS-CoV-2. Scie Rep. 2021; 11:19481 |

Lenin A G, Carla A L, Luis S M, Freddy R, Joan V, Aleivi E Perez. Molecular Docking and Molecular Dynamic Study of two Viral Proteins associated with SARS-CoV-2 with Ivermectin, Preprints (, Posted: 19 April 2020; doi:10.20944/preprints202004.0334.v1.

Ferreira R C, Chaves O A, de Oliveira C H, Ferreira S B, Ferreira V F, Sant’Anna C M. Drug-Protein Interaction: Spectroscopic and Theoretical Analysis on the Association between HSA and 1,4- Naphthoquinone Derivatives. Rev Virtual Quim. 2018; 10, 2: 432-447.

Al-Karmalawy A Ahmed, Dahab A Mohammed, Metwaly M Ahmed, Elhady S Sameh, Eslam B, Elkaeed Ibrahim H Eissa. Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of ACEIs Against SARS-CoV-2 Targeting the hACE2 Receptor. Front Chem. May 2021; 9: Article 661230.

Frisch M J, Trucks G W, Schlegel H B, Scuseria G E, Robb M A, Cheeseman J R, et al. Gaussian 03, revision C. 02; Gaussian, Inc. Wallingford, CT, 2004.

MOE. The Molecular Operating Environment, Version 2005.06, Chemical Computing Group Inc. 2010.

John M Beale, John H Block. Organic medicinal and Pharmaceutical Chemistry, 12th edition, Lippincott Williams & Wilkins, a Wolters Kluwer business, 2011: 976-983.

Edyta R, Barbara D, Justyna S Fiertek, Janusz M. Different Schiff Bases-Structure, Importance and Classification. Molecules, 2022; 27: 787.