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Advanced Methods and Technologies in Drug Discovery
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Advanced Methods and Technologies in Drug Discovery

A special issue of Methods and Protocols (ISSN 2409-9279).

Deadline for manuscript submissions: 20 February 2026 | Viewed by 5384

Special Issue Editors

Prof. Dr. Fernando Albericio

E-Mail Website
Guest Editor
School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
Interests: antimicrobial peptides; solid-phase chemistry; combinatorial chemistry; drug delivery systems; peptide drug conjugates; orthogonal chemistry; drug discovery; biomaterials
Special Issues, Collections and Topics in MDPI journals
Dr. Philip Hublitz

E-Mail Website
Guest Editor
Evotec International GmbH, Marie-Curie-Straße 7, D-37079 Göttingen, Germany
Interests: cell therapy; genome engineering; CRISPR technology; hiPSCs; clinically relevant model systems; drug discovery
Special Issues, Collections and Topics in MDPI journals
Dr. Ivana Šagud

E-Mail Website
Guest Editor
1. Agency for Drugs and Drug Products of the Republic of Croatia (HALMED), Ksaverska Cesta 4, 10000 Zagreb, Croatia
2. Faculty of Biotechnology and Drug Development, Radmile Matejčić 2, 51000 Rijeka, Croatia
Interests: organic chemistry; pharmacology; photochemistry; drug development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Drug discovery is a constantly evolving field with the goal of identifying novel therapeutic agents for a wide range of diseases with unmet medical needs. The process of drug discovery and development is complex and costly and includes various chemical and pharmaceutical strategies. These can even include serendipitous discovery, high-throughput screening of target molecule libraries, selective optimization of existing drugs or natural products, repurposing of known drugs, rational drug design, or the synthesis of new molecular entities based on information derived from crystal structures or in silico modeling techniques (QSAR). The process constantly evolves, with new technologies opening new and unprecedented entrance points. 

The application of drug identification strategies can, yield promising candidates that, subsequently, require an optimization process to enhance their properties, such as increasing affinity and selectivity for the target, ensuring non-toxicity and improving bioavailability, and enabling transformation into lead compounds and, ultimately, effective and safe drug products.

In this Special Issue, “Advanced Methods and Technologies in Drug Discovery”, we aim to focus on the most recent and most significant technical advancements in the field of drug discovery. Methods and Protocols aims to predominantly attract the submission of high-quality protocols, reviews, and original articles in the scope of this topic. This compendium aims to provide valuable insights from every angle of drug discovery and to highlight cutting-edge trends for the future of medicine.

Prof. Dr. Fernando Albericio
Dr. Philip Hublitz
Dr. Ivana Šagud
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 250 words) can be sent to the Editorial Office for assessment.

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. Methods and Protocols 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 1800 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
  • drug development
  • medicinal chemistry
  • disease prevention
  • therapeutic innovation
  • artificial intelligence in drug discovery
  • high-throughput screening
  • omics technologies
  • drug delivery systems
  • novel therapeutic strategies
  • drug design
  • nanomedicine
  • methodology for drug synthesis

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  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

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24 pages, 4306 KB  
Article
New Approach for Targeting Small-Molecule Candidates for Intrinsically Disordered Proteins
by Milan Senćanski
Methods Protoc. 2025, 8(6), 150; https://doi.org/10.3390/mps8060150 - 10 Dec 2025
Viewed by 694
Abstract
Intrinsically disordered proteins (IDPs), such as the Alzheimer’s-associated tau protein, pose challenges for conventional drug discovery. This study applied the Informational Spectrum Method for Small Molecules (ISM-SM), a computational technique utilizing electron–ion interaction potentials (EIIPs), to identify potential tau modulators. Characteristic interaction frequencies [...] Read more.
Intrinsically disordered proteins (IDPs), such as the Alzheimer’s-associated tau protein, pose challenges for conventional drug discovery. This study applied the Informational Spectrum Method for Small Molecules (ISM-SM), a computational technique utilizing electron–ion interaction potentials (EIIPs), to identify potential tau modulators. Characteristic interaction frequencies derived from known ligands and conserved mammalian tau sequences were used to screen DrugBank and the COCONUT natural product database. The screening identified approved drugs previously reported to indirectly influence tau pathology or Alzheimer’s disease pathways, alongside natural products including Bryostatin-14, which is known to modulate kinases involved in tau phosphorylation. These findings suggest that ISM-SM can serve as an in silico tool to identify candidate small molecules, including repurposed drugs and natural products, with potential relevance to tau function and pathology, complementing other IDP drug discovery strategies. Full article
(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
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12 pages, 597 KB  
Article
AgentMol: Multi-Model AI System for Automatic Drug-Target Identification and Molecule Development
by Piotr Karabowicz, Radosław Charkiewicz, Alicja Charkiewicz, Anetta Sulewska and Jacek Nikliński
Methods Protoc. 2025, 8(6), 143; https://doi.org/10.3390/mps8060143 - 1 Dec 2025
Viewed by 774
Abstract
Drug discovery remains a time-consuming and costly process, necessitating innovative computational approaches to accelerate early stage target identification and compound development. We introduce AgentMol, a modular multimodel AI system that integrates large language models, chemical language modeling, and deep learning–based affinity prediction to [...] Read more.
Drug discovery remains a time-consuming and costly process, necessitating innovative computational approaches to accelerate early stage target identification and compound development. We introduce AgentMol, a modular multimodel AI system that integrates large language models, chemical language modeling, and deep learning–based affinity prediction to automate the discovery pipeline. AgentMol begins with disease-related queries processed through a Retrieval-Augmented Generation system using the Large Language Model to identify protein targets. Protein sequences are then used to condition a GPT-2–based chemical language model, which generates corresponding small-molecule candidates in SMILES format. Finally, a regression convolutional neural network (RCNN) predicts the drug-target interaction by estimating binding affinities (pKi). Models were trained and validated on 470,560 ligand–protein pairs from the BindingDB database. The chemical language model achieved high validity (1.00), uniqueness (0.96), and diversity (0.89), whereas the RCNN model demonstrated robust predictive performance with R2 > 0.6 and Pearson’s R > 0.8. By leveraging LangGraph for orchestration, AgentMol delivers a scalable, interpretable pipeline, effectively enabling the end-to-end generation and evaluation of drug candidates conditioned on protein targets. This system represents a significant step toward practical AI-driven molecular discovery with accessible computational demands. Full article
(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
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Review

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21 pages, 1166 KB  
Review
Biodegradable Microneedle for Enhanced Transdermal Drug Delivery: Trends and Techniques
by Renuka Khatik, Jatin Kumar Sahu, Shuvadip Bhowmik, Isha Rai, Madhu Kumari and Monika Dwivedi
Methods Protoc. 2025, 8(6), 134; https://doi.org/10.3390/mps8060134 - 4 Nov 2025
Viewed by 3161
Abstract
The Transdermal Drug Delivery System (TDDS) offers several benefits, such as enhanced patient adherence, controlled release, reduced gastric irritation, and the bypassing of the first-pass metabolism. However, not all drugs can be delivered through this route in effective doses. Biodegradable microneedles (BMn) are [...] Read more.
The Transdermal Drug Delivery System (TDDS) offers several benefits, such as enhanced patient adherence, controlled release, reduced gastric irritation, and the bypassing of the first-pass metabolism. However, not all drugs can be delivered through this route in effective doses. Biodegradable microneedles (BMn) are designed to improve TDDS. This review outlines various types of BMn and their fabrication methods. BMn are produced in different forms, including hollow, solid, dissolve, and hydrogel-forming versions, which have garnered significant attention. These innovative BMn do not contain drugs themselves but instead absorb interstitial fluid to create continuous channels between the dermal microcirculation and a drug-containing patch. Several types of BMn have been tested and approved by regulatory bodies. The use of BMn technology is rapidly growing in point-of-care applications, attracting significant interest from both researchers and healthcare providers. BMn-based Point-of-care (POC) devices have high efficacy for finding various analytes of clinical interests and transdermal drug administration in a minimally invasive manner owing to BMn’ micro-size sharp tips and ease of use. Porous BMn technology may have a very rising future in the case of a vaccine delivery system. Full article
(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
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