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Drug Design II

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

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 11944

Special Issue Editor

Center for Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
Interests: medicinal chemistry; drug discovery and development; organic synthesis; drug design; drug resistance; antimicrobials; natural products; peptides
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues

Thanks to the very positive response to the first Special Issue on Drug Design, I am pleased to launch the second edition on this exciting subject.

The severe challenges that our healthcare systems are currently facing remind us of how important it is to be able to develop targeted medicines. Fortunately, we have made significant progress in our capability for a targeted design of specific drug properties on a broad front: fine-tuning of potency and selectivity or pharmacokinetic properties have become possible because of collaborative research efforts in academia and industry.

Drug design is a central component in the drug discovery and development process in order to provide pharmacologically active substances with defined functionality. This highly creative process appeals to chemists and biologists alike. The molecular repertoire ranges from classical small molecules to large molecules such as antibodies and biologics.

This second Special Edition aims to bring together medicinal chemistry, molecular modeling, synthetic chemistry, and the pharmaceutical and biological disciplines involved in the multidisciplinary endeavor of drug research to identify and discuss state-of-the-art research into new ways of designing safe and effective medicines.

Original research articles and reviews addressing the topics listed below are particularly welcome.

I look forward to your contribution!

Prof. Dr. Rainer Riedl
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

  • Drug discovery
  • Lead optimization
  • Clinical candidate development
  • Molecular modelling
  • De novo drug design
  • Structure-based drug design
  • Ligand-based drug design
  • Computer-aided drug design
  • ADMET
  • Pharmacophores
  • Polypharmacology
  • Chemical biology
  • Protein–protein interactions
  • Small molecule drugs
  • Antibodies
  • Protein–drug conjugates (ADCs/PDCs)
  • Fragment-based drug discovery
  • Structure–activity relationships

Published Papers (3 papers)

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Research

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14 pages, 561 KiB  
Article
8-Amino-6-Methoxyquinoline—Tetrazole Hybrids: Impact of Linkers on Antiplasmodial Activity
by Patrick Hochegger, Johanna Dolensky, Werner Seebacher, Robert Saf, Marcel Kaiser, Pascal Mäser and Robert Weis
Molecules 2021, 26(18), 5530; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26185530 - 12 Sep 2021
Cited by 3 | Viewed by 1762
Abstract
A new series of compounds was prepared from 6-methoxyquinolin-8-amine or its N-(2-aminoethyl) analogue via Ugi-azide reaction. Their linkers between the quinoline and the tert-butyltetrazole moieties differ in chain length, basicity and substitution. Compounds were tested for their antiplasmodial activity against Plasmodium [...] Read more.
A new series of compounds was prepared from 6-methoxyquinolin-8-amine or its N-(2-aminoethyl) analogue via Ugi-azide reaction. Their linkers between the quinoline and the tert-butyltetrazole moieties differ in chain length, basicity and substitution. Compounds were tested for their antiplasmodial activity against Plasmodium falciparum NF54 as well as their cytotoxicity against L-6-cells. The activity and the cytotoxicity were strongly influenced by the linker and its substitution. The most active compounds showed good activity and promising selectivity. Full article
(This article belongs to the Special Issue Drug Design II)
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17 pages, 3825 KiB  
Article
In Silico Design and Selection of New Tetrahydroisoquinoline-Based CD44 Antagonist Candidates
by Angel J. Ruiz-Moreno, Atilio Reyes-Romero, Alexander Dömling and Marco A. Velasco-Velázquez
Molecules 2021, 26(7), 1877; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26071877 - 26 Mar 2021
Cited by 3 | Viewed by 3082
Abstract
CD44 promotes metastasis, chemoresistance, and stemness in different types of cancer and is a target for the development of new anti-cancer therapies. All CD44 isoforms share a common N-terminal domain that binds to hyaluronic acid (HA). Herein, we used a computational approach to [...] Read more.
CD44 promotes metastasis, chemoresistance, and stemness in different types of cancer and is a target for the development of new anti-cancer therapies. All CD44 isoforms share a common N-terminal domain that binds to hyaluronic acid (HA). Herein, we used a computational approach to design new potential CD44 antagonists and evaluate their target-binding ability. By analyzing 30 crystal structures of the HA-binding domain (CD44HAbd), we characterized a subdomain that binds to 1,2,3,4-tetrahydroisoquinoline (THQ)-containing compounds and is adjacent to residues essential for HA interaction. By computational combinatorial chemistry (CCC), we designed 168,190 molecules and compared their conformers to a pharmacophore containing the key features of the crystallographic THQ binding mode. Approximately 0.01% of the compounds matched the pharmacophore and were analyzed by computational docking and molecular dynamics (MD). We identified two compounds, Can125 and Can159, that bound to human CD44HAbd (hCD44HAbd) in explicit-solvent MD simulations and therefore may elicit CD44 blockage. These compounds can be easily synthesized by multicomponent reactions for activity testing and their binding mode, reported here, could be helpful in the design of more potent CD44 antagonists. Full article
(This article belongs to the Special Issue Drug Design II)
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Review

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46 pages, 10526 KiB  
Review
The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents
by Gustavo R. Villas-Boas, Vanessa C. Rescia, Marina M. Paes, Stefânia N. Lavorato, Manoel F. de Magalhães-Filho, Mila S. Cunha, Rafael da C. Simões, Roseli B. de Lacerda, Renilson S. de Freitas-Júnior, Bruno H. da S. Ramos, Ana M. Mapeli, Matheus da S. T. Henriques, William R. de Freitas, Luiz A. F. Lopes, Luiz G. R. Oliveira, Jonatas G. da Silva, Saulo E. Silva-Filho, Ana P. S. da Silveira, Katyuscya V. Leão, Maria M. de S. Matos, Jamille S. Fernandes, Roberto K. N. Cuman, Francielli M. de S. Silva-Comar, Jurandir F. Comar, Luana do A. Brasileiro, Jussileide N. dos Santos and Silvia A. Oesterreichadd Show full author list remove Hide full author list
Molecules 2020, 25(18), 4086; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25184086 - 07 Sep 2020
Cited by 12 | Viewed by 6516
Abstract
On March 11, 2020, the World Health Organization (WHO) officially declared the outbreak caused by the new coronavirus (SARS-CoV-2) a pandemic. The rapid spread of the disease surprised the scientific and medical community. Based on the latest reports, news, and scientific articles published, [...] Read more.
On March 11, 2020, the World Health Organization (WHO) officially declared the outbreak caused by the new coronavirus (SARS-CoV-2) a pandemic. The rapid spread of the disease surprised the scientific and medical community. Based on the latest reports, news, and scientific articles published, there is no doubt that the coronavirus has overloaded health systems globally. Practical actions against the recent emergence and rapid expansion of the SARS-CoV-2 require the development and use of tools for discovering new molecular anti-SARS-CoV-2 targets. Thus, this review presents bioinformatics and molecular modeling strategies that aim to assist in the discovery of potential anti-SARS-CoV-2 agents. Besides, we reviewed the relationship between SARS-CoV-2 and innate immunity, since understanding the structures involved in this infection can contribute to the development of new therapeutic targets. Bioinformatics is a technology that assists researchers in coping with diseases by investigating genetic sequencing and seeking structural models of potential molecular targets present in SARS-CoV2. The details provided in this review provide future points of consideration in the field of virology and medical sciences that will contribute to clarifying potential therapeutic targets for anti-SARS-CoV-2 and for understanding the molecular mechanisms responsible for the pathogenesis and virulence of SARS-CoV-2. Full article
(This article belongs to the Special Issue Drug Design II)
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