INTRODUCTION:

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functionsThe associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore, docking is useful for predicting both the strength and type of signal produced.

Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site. Characterisation of the binding behaviour plays an important role in rational design of drugs as well as to elucidate fundamental biochemical processes [1-3].

REVIEW OF LITERATURE:

Sukanta Kumar Pradhanand et al used the Autodock 4 softwear for conducting several studies and identifing several target sites which influence drug-resistant to M. tb strains. In this case, there is the interaction between the protein Arabinosyl transferase C and two existing drugs (Ethambutol and Isoniazid) and by calculating the binding affinity and mode of binding. Ethambutol formed the five modified molecules (Emb 1, Emb 2, Emb 3, Emb 4 and Emb 5). The Emb 1 and Emb 3 having binding affinity- 5.77Kcal/mol and - 5.13Kcal/mol respectively that are potential inhibitors of Arabinosyl trasferase C in mycobacterium tuberculosis [4].

Mohammed Al bratty used the Autodock Vina softwear for studying the extent and types of binding interaction present in between HAS and Anti Hypertensive drug like telmisartan (TLM). HAS is responsible for binding and transportation of many exogeneous and endogeneous ligand including drug like telmisartan in binding interaction, the TLM significantly interacts with binding site-1 of HAS by forming strong Hydrogen with Glu292 and Lys195 residues that affects concentration of TLM at site of action and also affects on therapeutic effect [5].

Idhayadhulla Akabar and et al used Auto Dock Vina softwear for the molecular interaction study between target protein and ligands. This study more exposed the all inhibitor acquired the negative dock energy against the target protein. In molecular docking investigation it was found that the natural coumarin analogue toddacoumaquinone shows the inhibitory activity with binding energy -7.8Kcal than other compound against main protease of SAR coronavirusin intricate with a-ketomide [6].

Ran Yu and et al used the AutoDockVina softwear in the current spread of noval coronavirus (SAR-CoV-2) situation to discover the Anti Viral drug. This softwear helps to screening the potential drug by molecular docking with structural protein and non-structuralprotein site of new coronavirus. The Ribavirin, remdesivir, chloroquine and luteolin are also studied, the luteoline is bind with high affinity to same site of the main protease of SARS – CoV-2 [7].

Fareeda Athar and et al used the AutoDock. 4.2. for molecular docking studies performed that all derivatives along with the standard inhibitor STX-0119 showed that binding energy released in direct binding with the SH2 domain of STAT3 was the highest for compound 5e (-9.91kcal/mol). In virtual screening, compound 5e was found to exhibit optimum competency in inhibiting STAT3 activity. Compound 5e decreased the activation of STAT3 as observed with Western blot. The compound 5e was identified as a potent antioxidant agent and STAT3 inhibitor and effective agent for cancer treatment [8].

Akinwunmi O. Adeoye and et al used AutoDock softer for Molecular docking and virtual screening to understand the mechanism of ligand binding and to identify potent calcium transporter inhibitors: This study also deals with the evaluation of inhibitory activity of secondary metabolites of ethylacetate partitioned-fraction of Adansoniadigitata stem bark extract on malaria-associated protein using in silico docking studies. Digitata stem bark extract were examined for their antiplasmodial activity. Digitata shows the binding energy ranging between -6.5kcal/mol and -7.1kcal/mol. Among the two chemical constituents, apigenin has the highest docking score along with the highest number of hydrogen bonds formed when compared to quercetin. The analysis results suggest that apigenin and quercetinare acts as an anti-malaria agent [9].

Mohammad Jakir Hosen and et al used the AutoDock Vina softwear for the screening of the drugs against RdRp of SARS-CoV-2. It has been found that RNA dependent RNA polymerase (RdRp) plays a crucial role in SARS-CoV-2 replication, and thus could be a potential drug target. This study revealed that Rifabutin, Rifapentine, Fidaxomicin, 7-methyl-guanosine-5′-triphosphate-5′-guanosine and Ivermectin have a potential inhibitory interaction with RdRp of SARS-CoV-2 and could be effective drugs for COVID-19 [10].

PrashamsaKoirala, Su HuiSeongand et al used the AutoDock 4.2 softwear for determined the molecular interaction of BACE1 with isolated terpenoids. The AutoDock 4.2 programme revealed that hydroxyl group of lupeol formed two hydrogen bonds with the ASP32 (catalytic aspartic residue) and SER35 residues of BACE1 with the binding energy of (−8.2kcal/mol), while the ketone group of lupenone did not form any hydrogen bonds with BACE1 giving evidence for less binding affinity. It predicted that the dependence of the inhibitory activity in the presence of hydroxyl group which has provided a new basis for BACE1 blockade [11].

A. Lakshmana Rao and et al used the AutoDock 4.2.6softwear. The docking procedure was applied on a set of designed ligands within the region of 2PRG active site using AutoDock 4.2.6 software. Based on the validations and hydrogen bond interactions of various substituents, they were considered for the evaluation. It was done to understand the kind of interactions that occurred between various substituted thiazolidine-2, 4-diones with 2PRG binding site region [12].

Lakshmana Rao ATMAKUR and et al used AutoDock softwear for In vitro anti-inflammatory activity was checked by human red blood cell (HRBC) membrane stabilization and protein denaturation. Using AutoDock, molecular docking studies were carried out to find out the best fit ligands. In molecular docking studies, compounds 4h and 4n exhibited higher binding affinity at PPARγ receptor protein and compound 4k exhibited higher binding affinity at COX-1 and COX-2 actives sites Compounds 4h and 4n exhibited higher binding affinity at PPARγ receptor protein and compound 4k exhibited higher binding affinity at COX isoenzymes’ active sites in molecular docking studies. AutoDock 4.2.6 software was utilized to know the type of interactions of the designed 3D-structured thiazolidinediones with the 2PRG, 1EQG, and 1CX2 active site regions [13].

GanugapatiJayasreeand et al used AutoDock 4.0 for theDocking studies which are essential to understand the interaction between the protein and the ligands. In this case the crucial protein from Insuline receptor and ligands from Cinnamon. Docking studies are essential to understand the interaction between the protein and the ligands. In Autodock studies, the best pose was obtained with least energy value from which it can be hypothesized that these 2 compounds can be considered as potential activators of insulin receptor. After that the lab studies have to be performed to confirm the properties of these 2 compounds. tubulin isotypes. This indicates that select triple-modified 4 –chloro thio colchicines derivatives representhig hlypromising novel cancer chemotherapeutics. All the poses generated by both programs were rescored using the Vina scoring function. The top binding pose of colchicine and the derivatives was predicted by the Vina scoring function for the α-βII. a model which produce the best result sin terms of pIC50 predictions. Active residues involving non-hydrophobic interactions with the ligand are also specified for each compound [14].

Sarfaraz Alamand et al used AutoDockVina software (Scripps Research Chandrajit Dohutia and et al used AutoDock 4.2 to identify the receptor protein PfATP6 was the common target of artemisinin and curcumin. It was initiated to assess the antimalarial activity of six curcumin derivatives based on their binding affinities and correlating the in silico docking outcome with in vitro antimalarial screening. A ligand library of thirty two Knoevenagel condensates of curcumin were designed and docked against PfATP6 protein and six compounds with the best binding scores were synthesized and screened for their antimalarial activity against the sensitive 3D7 strain of Plasmodium falciparum [15].

Adam Huczynski and et al used AutoDock Vina and DOCK 6.5 for In silico studies to predict binding modes of the 4-chloro thiocolchicine derivatives to different β Institute, La Jolla, CA, USA) for molecular docking studies to validate the LibDock score. The designed compounds are optimized and then use for docking experiments. The docking program takes the PDBQT file format of ligands and receptor, a modified PDB file, which has added polar hydrogens and partial charges [16].

Leena K Pappachen and et al used AutoDock version 4.0 screeing program for doking the Benzothiazole derivatives with the crystallographic structures of the targets. AutoDock screening program also used to know about the hydrogen bonding interactions of all the derived compounds. The number of hydrogen bonding will considerably increase the affinity of ligand target interaction. The AutoDock shows that most of the benzothiazole derivatives show higher hydrogen bonding between the ligand-target interactions. The hydrogen bonding interactions increases the binding energy of ligand-protein interactions. The docking scores obtained for benzothiazole derivatives (BT1, BT2, BT3, BT4) and std. tamoxifen from the preliminary docking program using using AutoDock program were −6.29, −5.25, −7.19, −7.48, −3.86, r. All the four derivatives were synthesized, characterized, and subjected to in vitro anticancer screening by MTT assay in breast cancer (MCF-7) cell lines. Compounds DBT1, DBT2, and DBT3 were the most active compounds against MCF-7 cell lines with inhibitory concentration 50% of 70.0, 64.0 and 65.0, respectively. All the four derivatives show good docking scores when compared to standard drug tamoxifen and can be concluded that all the synthesized benzothiazole ligands show good anticancer property [17].

Gurudeeban Selvaraj and et al used AutoDock 4.0 for the docking analyses, There are different bonding modes of one ligand with multiple active cavities of DPP‐IV. The docking analyses indicate that the bioactive constituents, β‐stigmasterol, barbamide, docosahexaenoic acid, arachidonic acid, and harman shows the best binding energies on DPP‐IV receptor and hydrogen bonding with ASP545, GLY741, TYR754, TYR666, ARG125, TYR547, SER630, and LYS554 residues. This result shows that docosahexaenoic acid, arachidonic acid, β‐stigmasterol, barbamide, harman, ZINC58564986, ZINC56907325, ZINC69432950, ZINC69431828, ZINC73533041, ZINC84287073, ZINC69849395, and ZINC10508406 act as DPP‐IV inhibitors [18].

J. Selvaraj and et al used the AutoDock softwear for validation through structure analysis verification server. For identification, the new potential drugs against GLUT4 protein the molecular docking studies of 20 natural compounds were carried out using AutoDock. The results shows that modeled structure has 87.9% residues at the core region.It was also shows that the good binding interactions of the ligand with both the targets at very low energy level. Based on the docking energy value, H-bond interaction the compounds hesperidin, fisetin, eriodictyol, wogonin, and chrysin was selected as the most potent compounds for GLUT4 protein. Hence, It was conclude that the compound shows the Anti Diabetic activity [19].

Natarajan Kiruthiga and et al used the AutoDock 4.2 for identify the binding modes of titled compounds responsible for the activity on the receptor sites. The compound HFd with 2, 4-dimethoxy group on ring C and 7-hydroxy substitution on ring A showed binding interactions with amino acid residues of alpha amylase as Arg 61, Pro 44, His 299, Gln 41 and Asp 96. Hence the scaffolds were acts as a navigator in the management of diabetic mellitus [20].

Saravanan R.R and et al used the AutoDock program for the docking simulations in the active sites of 2XNU, which shown the successfully reproduce binding modes in terms of lowest docking energy. The target protein structures of 2XNU were docked with MPIPA which shows the excellent results as were seen by the least values of the binding energy with the help of Autodock v4.0, In docking studies of the title derivative it understand that the possibility of these compounds to act as effective inhibitors [21].

Humaira Nadeem and et al used the AutoDock Vina softwear forThe interactions between the compounds and active site residues of H⁺/K⁺ ATPase. SCH28080 was used to validate the docking results. The results clearly indicate that these novel benzimidazole-pyrazole hybrids can present a new class of potential anti ulcer agents and can serve as new anti-ulcer drugs after further investigation [22].

Chandrajit Dohutia and et al used AutoDock 4.2 for receptor molecule for the docking and also study to probe the binding free energy between the ligand library and receptor. Autodock Tools (ADT) also used for optimize the receptor and ligand molecules. For preparation of the receptor molecule, polar hydrogens, Kollman charges and AD4 type of atoms were added, while Gasteiger charges were added on the ligands and maximum numbers of active torsions were given [23].

CONCLUSION:

This review totally focused on efficiency of AutoDock softwear and its different version such as AutoDock Vina, AutoDock 4.0, AutoDock 4.2.6 for molecular docking study. This information become benchmark for reseachers those uses the AutoDock softwear for study the different therapeutic activities like Antidiabetic activity, AntiMalarial activity, Antiurase activity, Anticancer activity, Antimycobacterial tuberculosis activity, Antioxidant activity, Etc. The AutoDock and its Tools are more efficient to determine the synthesis techniques, spectral analysis, docking simulation, photochemical activities, therapeutic effects, toxicological studies. These observation based on the present review have been becoming a helpful tool to guide researchers for molecular docking study. AutoDock softwear is helpful for researcher as thissoftwear is predicting docking score which is corelate with Invivo or In vitro activity. Sp this is the ultimate tool in drug discovery.

REFERENCE:

1. Rohane S.H., Makwana A.G., 2017. A Review onHydrazone, the fascinating field of investigation in medicinal chemistry. Asian J. Res. Chem. 10, 417-430.

2. Rohane S.H., Makwana A.G., 2019. In silico study for the prediction of multiple pharmacological activities of novel hydrazone derivatives. Ind J. Chem. Sec-B. 58, 387-402.

3. Rohane S.H., Makwana A.G., 2020. Synthesis and in vitro antimycobacterial potential of novel hydrazones of eugenol. Arab J. Chem. 13, 4495–4504.

4. Sukanata Kumar Pradhan, Nisha Das, Pradip, Pradip Kumar Jena, Arabinosyltransferase C enzyme of Mycobacterium tuberculosis, a potential drug target:An insight from molecular docking study, Science direct, (2019) (1-6)

5. Mohammed Al bratty, Spectroscopic and molecular docking studies for characterizing binding mechanism and conformational changes of Human Serum albumin upon interaction with Telmisartan, Saudi Pharmaceutical journal 28(2020), 729-736

6. Idhayadhulla Akbar, Chidambaram satish kumar, Daoud Ali Saud Alarifi, Surendra Kumar Radhkrushnan, In Silico molecular docking: Evaluation of Caumarin based derivatives against SARS-CoV-2,Sep-2020, Journal of Infection and Public Health, (2020) (1-7)

7. Ran Yu, Liangchen, Rong Lan, Rong Shen, Peng Li, computational screening of antagonist against the SARS-CoV-2 (COVID-19) coronavirus by molecular docking, International Journal of Antimicrobial Agents, 562020 (1-26).

8. Fareeda Athar, Rashim Khanam, Iram I. Hejazi, Syed Shahabuddin, Abdul R. Bhat, Pharmacokinetic evaluation, molecular docking and invitro biological evaluation of 1,3,4-oxadiazole derivatives as potent antioxidant and STAT 3 inhibitors, Journal of Pharmaceutical Analysis, Dec-2019 (133-141).

9. Akinwunmi O. Adeoye, John O. Olanlokun, Habib Tijani, Segun. o. Lawal, Cecilia O. Babarinde, Mobolaji T. Akinwole, Clement O. Bewaji, Molecular docking analysis of Apigenin and quercetin from ethylacetate fraction of Adansonia digitata with malaria associated calcium transport protein: An in silico approach, Science direct, Heliyon, Aug 2015(1-8).

10. Mohammad Jakir Hosen, Md. Sorwer Alam Parvez, Mahmudul Hasan, Jomana Janam, Ziaul Karim, Tohura Tahsin, Md. Nazmul Hasan, Prediction for potential inhibitor for RNA polymerase of SARS-CoV-2 using comprehensive drug repurposing and molecular docking approach, International Journal of Biological Macromolecules Sep. 2020(1787-1797).

11. Prashama Koirala, Su Hui Seog, Hyun Ah Jung, Jae Sue Choi, Comparative molecular docking study of lupeol and lupenone isolated from Pueraria lobata that inhibit BASE1: Probable remedies for Alzheimer’s disease, AsianPasific Journal of Tropical Medicine, (2017) (1117-1122)

12. A. Lakshmana Roa, Srikanthkumar Karumanchi, Srikala Rajala, V Basaveswara Mandava, Synthesis and Hypoglycemic Anti inflementory Activity Screening of Novel substituted 5-[Morpholino (pheny)-Thiazolidine-2, 4-Diones and their molecular docking studies, Turkish Journal of Pharmaceutical Science 2019;16(4): (380-391).

13. A. Lakshmana Roa, K. Srikant Kumar, M.V. Basaveswara Roa, Design, synthesis, biological, evaluation and molecular docking studies of novel 3-substituted-5-[(indole-3-yl) methylene-thiazolidine -2.4-dione derivatives, Heliyon, 2018(1-27).

14. Ganugapati Jayasree, Molecular docking studies of Antidiabetic activity of cinnamon compounds, Asian Journal of Pharmaceutical and Clinical Research, vol 7(suppl2): 31-37

15. Sarfaraj Alam, Firoj Khan, QSAR and docking studies on Xanthone derivatives for anticancer activity targeting DNA topoisomerase IIa.(183-195).

16. Adam Huczynski, Greta Klejborowska, Alicja Urbaniak. Ewa Maj Jordane Pretto, Mahshad Moshari, Joanna Wietrzyk, Jacj A. Tusznski’ Timothy C. Chambers, synthesis and biological evaluation and molecular docking studies of new amides of 4-Chlorothiocolchine as anticancer drug, Bioorganic Chemistry (2020)(1-11).

17. Leena K Pappachen, Subin Mary Zachariah, Deepthy Chandran In silicodesign, synthesis and characterization of some novel Benzothiazole Derivatives ac Anticancer Drug, Asian Journal of Pharmaceutical and Clinical Research vol.10 Issue 4, 2017 (150-155).

18. Gurub deeban selvaraj, Styavani Kalimurti, Zeynep E. Cakmak, Turgay Cakmak, Phycological research, http:/doi.org/10.1111/ pre.12141(291-299).

19. J. Selvaraj, R. Ponnulakshmi, V. Vishnupriya, B. shyamaladevi, Identification of new antidiabetic agents targeting GLUT4 protien using Insilico Analysis, International Journal of Green Pharmacy, Oct-Dec 2018(Suppl).12(4)/S(876-882).

20. Natarajan Kiruthiga, Thangavelu Prabha, Chellappa Selvinthanuja, Kulandevi Srinivasan, Thangavel Sivakumar, Multi docking studing Studies on 2-Phenyl-4h-Chromen-4-One Hybried and Evaluation of antidiabetic activity, Journal of Pharmaceutical Science and Research vol.10(12)2018, (3018-3024)

21. Saravanan R.R, Saravanan B., Manivannan, Synthesis and molecular docking studies of Indole based compound (2-methyl-1-phenylsulfonyl-1h-Indole-3-yl) Phenylmethyl Acetate to nicotinic acetylcholine receptor, Journal of Chemical and Pharmaceutical Research, 2012, 4(6): (3057-3062).

22. Humaira Nadeem, Abida Noor, Neelam Gul Qazi, Arifullah Khan, Rehan Zafar Paracha, fawad Ali, Adil Saeed, Synthesis, Characterization, antiulcer action and molecular docking evaluation of novel benzimide pyrazole hybrids, Chemistry Central Journal v,11, 2017(134-144).

23. Chandrajit Dohutia, Dipak Chetia, Kabita Gogoi, Dibya Rajan Bhattacharyya, Kishoresarma, Molecular Docking, synthesis and in vitro antimalarial evaluation of certain novel curcumin analogues, Braz. J. Pharm. Sci. 2017; 53(4): (1-14).

Received on 07.11.2020 Modified on 19.11.2020

Asian J. Research Chem. 2021; 14(1):92-96.

DOI: 10.5958/0974-4150.2021.00016.X