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Applied Sciences
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Latest Advances in Computational Chemistry and Molecular Docking for Biological...
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Latest Advances in Computational Chemistry and Molecular Docking for Biological Macromolecules

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Biomedical Engineering".

Deadline for manuscript submissions: closed (20 December 2023) | Viewed by 5667

Special Issue Editors

Dr. Antonija Tomić

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Guest Editor
Division of Organic Chemistry and Biochemistry, Laboratory for Protein Biochemistry and Molecular Modelling, Ruđer Bošković Institute, 10 000 Zagreb, Croatia
Interests: molecular modelling; molecular dynamics simulations; quantum mechanics – molecular mechanics calculations; ligand binding; protein dynamics; reaction mechanisms
Prof. Dr. Snezana Agatonovic-Kustrin

E-Mail Website
Guest Editor
School of Pharmacy and Applied Science, La Trobe Institute for Molecular Sciences, La Trobe University, Edwards Rd, Bendigo 3550, Australia
Interests: medicinal chemistry; analytical chemistry; pharmaceutical analysis; chromatography; HPTLC; natural product chemistry; computational chemistry; chemometrics; QSAR
Special Issues, Collections and Topics in MDPI journals
Dr. Dejan Agić

E-Mail Website
Guest Editor
Faculty Of Agrobiotechnical Sciences Osijek, J. J. Strossmayer University in Osijek, 31000 Osijek, Croatia
Interests: natural sciences; biochemistry and molecular biology

Special Issue Information

Dear Colleagues,

In recent decades, the application of computational chemistry in biochemical and biomolecular sciences has progressively grown with significant developments in methodology, software, and computer hardware. Computational chemistry methods range from molecular mechanics (MM) and molecular dynamics (MD) calculations based on approximate classical potentials to ab initio approaches based on quantum chemistry. By providing insight into the systems under study at the atomic level, computational chemistry is used to rationalize the experimentally obtained data, but also to guide future experiments by predicting some new features and behaviors.

Molecular docking is a simplified form of MM and MD calculations used to search for the most energetically and geometrically suitable complex between two or more molecules, e.g., ligands and proteins. Therefore, it plays an important and irreplaceable role in rational drug design. Although originally developed and used as a stand-alone method, docking is now mostly employed in combination with other computational methods as part of integrated workflows to improve search accuracy.

This Special Issue is dedicated to presenting the results of recent developments in the methods and application of computational chemistry techniques for studying the structure, dynamics, and function of biological macromolecules. Of particular interest are computational methods aimed at understanding the formation of intermolecular complexes and providing an efficient tool for the discovery of novel protein-targeted drugs.

Dr. Antonija Tomić
Prof. Dr. Snezana Agatonovic-Kustrin
Dr. Dejan Agić
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Applied Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular modelling
  • molecular dynamics simulations
  • advanced methods
  • hybrid methods
  • biological macromolecules, proteins, enzymes
  • molecular docking
  • drug design
  • enzyme catalyzed reactions
  • protein-ligand interactions
  • protein-protein interactions

Published Papers (3 papers)

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Research

17 pages, 5926 KiB  
Article
Let’s Talk about Sex Hormone Receptors and Their Physical Interaction with Sonic Hedgehog Protein: A Computational Study with Emphasis on Progesterone Receptor
by Antonija Tomić, Josipa Čonkaš and Petar Ozretić
Appl. Sci. 2024, 14(2), 562; https://doi.org/10.3390/app14020562 - 09 Jan 2024
Viewed by 847
Abstract
The mature form of the sonic hedgehog protein (SHH-N) is the main canonical activator of the Hedgehog-GLI signaling pathway whose aberrant activity can lead to the development of hormone-dependent cancers like breast or prostate cancer. In this study, we employed computational methods to [...] Read more.
The mature form of the sonic hedgehog protein (SHH-N) is the main canonical activator of the Hedgehog-GLI signaling pathway whose aberrant activity can lead to the development of hormone-dependent cancers like breast or prostate cancer. In this study, we employed computational methods to explore the potential binding of SHH-N with the progesterone receptor (PR), the sole member of the nuclear sex hormone receptor (SHRs) subfamily not previously linked to SHH-N. Through a combination of molecular docking, robust molecular dynamics (MD) simulations, and free energy calculations, we predicted a stable binding between SHH-N-cholesterol and PR. To validate our findings, we extended our in silico investigation to encompass the complexes between SHH-N-cholesterol and estrogen receptor alpha (ERα) and androgen receptor (AR)—complexes that have been experimentally confirmed in our prior studies. The calculations not only confirmed the stable binding of SHH-N-cholesterol with both ERα and AR but also revealed the strongest binding occurred with ERα, followed by AR and PR, suggesting a non-canonical interaction with potential biological significance. Microsecond-long MD simulations unveiled tight cholesterol binding in the SHRs’ binding sites, and we gained insights into sub-molecular interactions contributing to protein-protein stabilization in complexes involving PR and ERα for the first time. The MM/PBSA calculations indicated comparable binding affinities of PR for progesterone and SHH-N-cholesterol, with ERα exhibiting a more favorable enthalpy of binding with SHH-N-cholesterol than with estradiol. Full article
(This article belongs to the Special Issue Latest Advances in Computational Chemistry and Molecular Docking for Biological Macromolecules)
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27 pages, 18516 KiB  
Article
Pharmacoinformatics Analysis Reveals Flavonoids and Diterpenoids from Andrographis paniculata and Thespesia populnea to Target Hepatocellular Carcinoma Induced by Hepatitis B Virus
by Vishal S. Patil, Darasaguppe R. Harish, Umashankar Vetrivel, Sanjay H. Deshpande, Pukar Khanal, Harsha V. Hegde, Subarna Roy and Sunil S. Jalalpure
Appl. Sci. 2022, 12(21), 10691; https://doi.org/10.3390/app122110691 - 22 Oct 2022
Cited by 10 | Viewed by 2278
Abstract
Herbs are widely utilized in the Western Ghats region of India to treat liver diseases and viral-like infections. However, such practices lack scientific evidence at the molecular level and may often pose adverse drug reactions. This study intends to identify phytocompounds with druggability [...] Read more.
Herbs are widely utilized in the Western Ghats region of India to treat liver diseases and viral-like infections. However, such practices lack scientific evidence at the molecular level and may often pose adverse drug reactions. This study intends to identify phytocompounds with druggability and non-toxic profiles with potential activity against hepatitis B virus-induced hepatocellular carcinoma. The details of phytocompounds in traditionally utilized herbs in the Western Ghats region were collated from chemical databases and publications. The druggability and toxicity of these compounds were predicted using MolSoft and ADVERpred, respectively. The probable targets of these phytocompounds were predicted using BindingDB. Moreover, compound-gene set pathways, cellular processes, and functional enrichment analyses were also performed using STRING and KEGG pathway databases. Subsequently, herb–compound–target–disease pathway networks were constructed using Cytoscape. The potential hub protein was virtually screened against the ligand dataset using the POAP pipeline. Finally, molecular dynamics (MD) simulations of the most potential protein–ligand complexes were performed in triplicate using Schrödinger Desmond. Amongst 274 compounds from 16 herbs studied, 36 showed drug-likeness with nontoxic properties and were also predicted to modulate 16 potential targets involved in the pathogenesis of HBV-induced HCC. Among all the molecules screened, flavonoids and diterpenoids from Andrographis paniculata and Thespesia populnea scored the highest edge count via modulating multiple targets and pathways. Moreover, molecular docking and MD simulation (100ns) also inferred that the top-ranking Andrographin and Gossypetin exhibit stable intermolecular interactions with EGFR protein, which was identified as a highly connected hub protein in the constructed network. All these findings are suggestive of identified moieties as potential therapeutics for targeting HBV-associated HCC sans adverse drug reactions. Full article
(This article belongs to the Special Issue Latest Advances in Computational Chemistry and Molecular Docking for Biological Macromolecules)
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16 pages, 6118 KiB  
Article
Spectroscopic and Molecular Docking Analysis of π-Acceptor Complexes with the Drug Barbital
by Abdulhakeem S. Alamri, Majid Alhomrani, Walaa F. Alsanie, Hussain Alyami, Sonam Shakya, Hamza Habeeballah, Osama Abdulaziz, Abdulwahab Alamri, Heba A. Alkhatabi, Raed I. Felimban, Abdulhameed Abdullah Alhabeeb, Moamen S. Refat and Ahmed Gaber
Appl. Sci. 2022, 12(19), 10130; https://doi.org/10.3390/app121910130 - 09 Oct 2022
Cited by 2 | Viewed by 1371
Abstract
The drug barbital (Bar) has a strong sedative–hypnotic effect. The intermolecular charge transfer compounds associated with the chemical reactions between Bar and some π acceptors, such as 2,6-dibromoquinone-4-chloroimide (DBQ), tetracyanoquinodimethane (TCNQ), chloranil (CHL), and chloranilic acid (CLA), have been synthesized and isolated in [...] Read more.
The drug barbital (Bar) has a strong sedative–hypnotic effect. The intermolecular charge transfer compounds associated with the chemical reactions between Bar and some π acceptors, such as 2,6-dibromoquinone-4-chloroimide (DBQ), tetracyanoquinodimethane (TCNQ), chloranil (CHL), and chloranilic acid (CLA), have been synthesized and isolated in solid state. The synthesized products have the molecular formulas (Bar–DBQ), (Bar–TCNQ), (Bar–CHL), and (Bar–CLA) with 1:1 stoichiometry based on Raman, IR, TG, 1H NMR, XRD, SEM, and UV-visible analysis techniques. Additionally, the comparative analysis of molecular docking between the donor reactant moiety, Bar, and its four CT complexes was conducted using two neurotransmitter receptors (dopamine and serotonin). The docking results obtained from AutoDockVina software were investigated by a molecular dynamics simulation technique with 100ns run. The molecular mechanisms behind receptor–ligand interactions were also looked into. The DFT computations were conducted using theory at the B3LYP/6-311G++ level. In addition, the HOMO LUMO electronic energy gap and the CT complex’s optimal geometry and molecule electrostatic potential were examined. Full article
(This article belongs to the Special Issue Latest Advances in Computational Chemistry and Molecular Docking for Biological Macromolecules)
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