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Computational Studies of Drugs and Biomolecules 2.0
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Computational Studies of Drugs and Biomolecules 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 1842

Special Issue Editors

Prof. Dr. Jesús Vicente de Julián-Ortiz

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Guest Editor
Molecular Topology and Drug Design Research Unit, Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Valencia, Spain
Interests: computational chemistry; medicinal chemistry
Special Issues, Collections and Topics in MDPI journals
Dr. Francisco Torrens

E-Mail Website
Guest Editor
Institut Universitari de Ciència Molecular, Universitat de València, Edifici d’Instituts de Paterna, P.O. Box 22085, E-46071 València, Spain
Interests: physical chemistry; theoretical chemistry; computational chemistry; modelling and simulation; computer-aided drug design and development
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Gloria Castellano

E-Mail Website
Guest Editor
Centro de Investigación Traslacional San Alberto Magno (CITSAM), Catholic University of Valencia San Vicente Mártir, 46001 Valencia, Spain
Interests: natural products; organic chemistry; phytochemistry; medicinal plant chemistry; food chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

There is currently a great, ongoing effort to better understand and treat diseases. Computational modeling is becoming increasingly important in biomedical research for understanding how biomolecules interact at the molecular level, as well as the molecular mechanisms of disease. Regarding their applications in xenobiotics, computational methods are fundamental for the discovery of drugs and the assessment of risks associated with chemicals, due to their multiple uses in the collection, processing, analysis and modeling of data. This means that animal testing is less necessary. Drug design is a multi-objective process in which various characteristics, such as efficacy, pharmacokinetics, and safety, must be optimized. With this in mind, advances in computational intelligence and machine learning are providing a basis for more effective searches of chemical spaces and the prediction of biological properties based on molecular structure. This issue aims to show different approaches and technologies that could be implemented in drug design in the near future.

Prof. Dr. Jesús Vicente de Julián-Ortiz
Dr. Francisco Torrens
Prof. Dr. Gloria Castellano
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 modeling
  • drug design
  • molecular mechanism
  • mathematical chemistry
  • structure–activity relationships
  • molecular descriptors
  • pharmacokinetics
  • toxicity

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Published Papers (1 paper)

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Research

14 pages, 4051 KiB  
Article
Dual-Target Mycobacterium tuberculosis Inhibition: Insights into the Molecular Mechanism of Antifolate Drugs
by Pritika Ramharack, Elliasu Y. Salifu and Clement Agoni
Int. J. Mol. Sci. 2023, 24(18), 14021; https://doi.org/10.3390/ijms241814021 - 13 Sep 2023
Cited by 2 | Viewed by 1327
Abstract
The escalating prevalence of drug-resistant strains of Mycobacterium tuberculosis has posed a significant challenge to global efforts in combating tuberculosis. To address this issue, innovative therapeutic strategies are required that target essential biochemical pathways while minimizing the potential for resistance development. The concept [...] Read more.
The escalating prevalence of drug-resistant strains of Mycobacterium tuberculosis has posed a significant challenge to global efforts in combating tuberculosis. To address this issue, innovative therapeutic strategies are required that target essential biochemical pathways while minimizing the potential for resistance development. The concept of dual targeting has gained prominence in drug discovery against resistance bacteria. Dual targeting recognizes the complexity of cellular processes and disrupts more than one vital pathway, simultaneously. By inhibiting more than one essential process required for bacterial growth and survival, the chances of developing resistance are substantially reduced. A previously reported study investigated the dual-targeting potential of a series of novel compounds against the folate pathway in Mycobacterium tuberculosis. Expanding on this study, we investigated the predictive pharmacokinetic profiling and the structural mechanism of inhibition of UCP1172, UCP1175, and UCP1063 on key enzymes, dihydrofolate reductase (DHFR) and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5′-phosphate reductase (RV2671), involved in the folate pathway. Our findings indicate that the compounds demonstrate lipophilic physiochemical properties that promote gastrointestinal absorption, and may also inhibit the drug-metabolizing enzyme, cytochrome P450 3A4, thus enhancing their biological half-life. Furthermore, key catalytic residues (Serine, Threonine, and Aspartate), conserved in both enzymes, were found to participate in vital molecular interactions with UCP1172, which demonstrated the most favorable free binding energies to both DHFR and RV2671 (−41.63 kcal/mol, −48.04 kcal/mol, respectively). The presence of characteristic loop shifts, which are similar in both enzymes, also indicates a common inhibitory mechanism by UCP1172. This elucidation advances the understanding of UCP1172’s dual inhibition mechanism against Mycobacterium tuberculosis. Full article
(This article belongs to the Special Issue Computational Studies of Drugs and Biomolecules 2.0)
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