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Recent Advances in Drug Design
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Recent Advances in Drug Design

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 11129

Special Issue Editor

Dr. George Lambrinidis

E-Mail Website
Guest Editor
Department of Pharmacy, School of Health Sciences, National & Kapodistrian University of Athens, Athens, Greece
Interests: rational drug design; computational chemistry; structural pharmacology; systems pharmacology; bioinformatics

Special Issue Information

Dear Colleagues,

Pharmaceutical companies and labs in academia invest in advanced drug discovery methods in order to reduce time and cost for research and development. Rational drug design methods can guide to the “correct analogs” before synthesis for drug development. Structure-based drug design (SBDD) uses the experimental/theoretical-modelled structure of the protein target, while ligand-based drug design (LBDD) is based on the physicochemical properties and structure of known binders and decoys datasets, applied in 2D- or 3D-QSAR. Both SBDD and LBDD methods aim at description of an accurate “pharmacophore model” that will be used as a template for compounds screening. Hardware innovations on computer science such as multithreading computing and GPU accelerated processing units have led to the development of algorithms that allow the efficient calculation of descriptors and similarity indices used in LBDD or the description of conformational space using advanced docking and molecular dynamics simulation method which are useful in SBDD. However, this Special Issue will focus on recent improvements on water mapping algorithms for SBDD and machine learning algorithms (neural networks, support vector machine, etc/) from researchers involved in computer science, which will suggest molecular descriptors of binding phenomena and tools from graph theory for mapping the binding area, aiming at filtering the best candidate molecules during a virtual screening procedure. Additionally, manuscripts that mainly describe computational studies should be accompanied by experimental validation.

Dr. George Lambrinidis
Guest Editor

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. Molecules 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 2700 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

  • Rational drug design
  • Structure-based design
  • Ligand-based design
  • Artificial intelligence
  • Experimental validation

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Published Papers (3 papers)

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Research

24 pages, 24860 KiB  
Article
In Silico Screening of Semi-Synthesized Compounds as Potential Inhibitors for SARS-CoV-2 Papain-like Protease: Pharmacophoric Features, Molecular Docking, ADMET, Toxicity and DFT Studies
by Mohamed S. Alesawy, Eslam B. Elkaeed, Aisha A. Alsfouk, Ahmed M. Metwaly and Ibrahim H. Eissa
Molecules 2021, 26(21), 6593; https://doi.org/10.3390/molecules26216593 - 30 Oct 2021
Cited by 44 | Viewed by 3421
Abstract
Papain-like protease is an essential enzyme in the proteolytic processing required for the replication of SARS-CoV-2. Accordingly, such an enzyme is an important target for the development of anti-SARS-CoV-2 agents which may reduce the mortality associated with outbreaks of SARS-CoV-2. A set of [...] Read more.
Papain-like protease is an essential enzyme in the proteolytic processing required for the replication of SARS-CoV-2. Accordingly, such an enzyme is an important target for the development of anti-SARS-CoV-2 agents which may reduce the mortality associated with outbreaks of SARS-CoV-2. A set of 69 semi-synthesized molecules that exhibited the structural features of SARS-CoV-2 papain-like protease inhibitors (PLPI) were docked against the coronavirus papain-like protease (PLpro) enzyme (PDB ID: (4OW0). Docking studies showed that derivatives 34 and 58 were better than the co-crystallized ligand while derivatives 17, 28, 31, 40, 41, 43, 47, 54, and 65 exhibited good binding modes and binding free energies. The pharmacokinetic profiling study was conducted according to the four principles of the Lipinski rules and excluded derivative 31. Furthermore, ADMET and toxicity studies showed that derivatives 28, 34, and 47 have the potential to be drugs and have been demonstrated as safe when assessed via seven toxicity models. Finally, comparing the molecular orbital energies and the molecular electrostatic potential maps of 28, 34, and 47 against the co-crystallized ligand in a DFT study indicated that 28 is the most promising candidate to interact with the target receptor (PLpro). Full article
(This article belongs to the Special Issue Recent Advances in Drug Design)
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16 pages, 1973 KiB  
Article
Design of Multifaceted Antioxidants: Shifting towards Anti-Inflammatory and Antihyperlipidemic Activity
by Ariadni Tzara, George Lambrinidis and Angeliki Kourounakis
Molecules 2021, 26(16), 4928; https://doi.org/10.3390/molecules26164928 - 14 Aug 2021
Cited by 5 | Viewed by 2775
Abstract
Oxidative stress and inflammation are two conditions that coexist in many multifactorial diseases such as atherosclerosis and neurodegeneration. Thus, the design of multifunctional compounds that can concurrently tackle two or more therapeutic targets is an appealing approach. In this study, the basic NSAID [...] Read more.
Oxidative stress and inflammation are two conditions that coexist in many multifactorial diseases such as atherosclerosis and neurodegeneration. Thus, the design of multifunctional compounds that can concurrently tackle two or more therapeutic targets is an appealing approach. In this study, the basic NSAID structure was fused with the antioxidant moieties 3,5-di-tert-butyl-4-hydroxybenzoic acid (BHB), its reduced alcohol 3,5-di-tert-butyl- 4-hydroxybenzyl alcohol (BHBA), or 6-hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid (Trolox), a hydrophilic analogue of α-tocopherol. Machine learning algorithms were utilized to validate the potential dual effect (anti-inflammatory and antioxidant) of the designed analogues. Derivatives 1–17 were synthesized by known esterification methods, with good to excellent yields, and were pharmacologically evaluated both in vitro and in vivo for their antioxidant and anti-inflammatory activity, whereas selected compounds were also tested in an in vivo hyperlipidemia protocol. Furthermore, the activity/binding affinity of the new compounds for lipoxygenase-3 (LOX-3) was studied not only in vitro but also via molecular docking simulations. Experimental results demonstrated that the antioxidant and anti-inflammatory activities of the new fused molecules were increased compared to the parent molecules, while molecular docking simulations validated the improved activity and revealed the binding mode of the most potent inhibitors. The purpose of their design was justified by providing a potentially safer and more efficient therapeutic approach for multifactorial diseases. Full article
(This article belongs to the Special Issue Recent Advances in Drug Design)
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16 pages, 3856 KiB  
Article
Structure-Based Virtual Screening Identifies Multiple Stable Binding Sites at the RecA Domains of SARS-CoV-2 Helicase Enzyme
by Sajjad Ahmad, Yasir Waheed, Saba Ismail, Saadia Bhatti, Sumra Wajid Abbasi and Khalid Muhammad
Molecules 2021, 26(5), 1446; https://doi.org/10.3390/molecules26051446 - 7 Mar 2021
Cited by 18 | Viewed by 3777
Abstract
With the emergence and global spread of the COVID-19 pandemic, the scientific community worldwide has focused on search for new therapeutic strategies against this disease. One such critical approach is targeting proteins such as helicases that regulate most of the SARS-CoV-2 RNA metabolism. [...] Read more.
With the emergence and global spread of the COVID-19 pandemic, the scientific community worldwide has focused on search for new therapeutic strategies against this disease. One such critical approach is targeting proteins such as helicases that regulate most of the SARS-CoV-2 RNA metabolism. The purpose of the current study was to predict a library of phytochemicals derived from diverse plant families with high binding affinity to SARS-CoV-2 helicase (Nsp13) enzyme. High throughput virtual screening of the Medicinal Plant Database for Drug Design (MPD3) database was performed on SARS-CoV-2 helicase using AutoDock Vina. Nilotinib, with a docking value of −9.6 kcal/mol, was chosen as a reference molecule. A compound (PubChem CID: 110143421, ZINC database ID: ZINC257223845, eMolecules: 43290531) was screened as the best binder (binding energy of −10.2 kcal/mol on average) to the enzyme by using repeated docking runs in the screening process. On inspection, the compound was disclosed to show different binding sites of the triangular pockets collectively formed by Rec1A, Rec2A, and 1B domains and a stalk domain at the base. The molecule is often bound to the ATP binding site (referred to as binding site 2) of the helicase enzyme. The compound was further discovered to fulfill drug-likeness and lead-likeness criteria, have good physicochemical and pharmacokinetics properties, and to be non-toxic. Molecular dynamic simulation analysis of the control/lead compound complexes demonstrated the formation of stable complexes with good intermolecular binding affinity. Lastly, affirmation of the docking simulation studies was accomplished by estimating the binding free energy by MMPB/GBSA technique. Taken together, these findings present further in silco investigation of plant-derived lead compounds to effectively address COVID-19. Full article
(This article belongs to the Special Issue Recent Advances in Drug Design)
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