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Pharmaceuticals
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New Perspectives on Chemoinformatics and Drug Design
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New Perspectives on Chemoinformatics and Drug Design

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (25 July 2024) | Viewed by 17363

Special Issue Editors

Dr. Bruno Silva Andrade

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Guest Editor
Department of Biological Sciences, State University of Southwest of Bahia, Jequié 45208-091, BA, Brazil
Interests: drug discovery; molecular dynamics; ligand screening; artificial intelligence; bioinformatics
Prof. Dr. Vasco Azevedo

E-Mail Website
Guest Editor
Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
Interests: animal health; veterinary microbiology; bacterial genetics; genomics; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Debmalya Barh

E-Mail Website
Guest Editor
Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
Interests: multiomics; bioinformatics; target discovery; targeted drug development
Dr. Aristóteles Góes-Neto

E-Mail Website
Guest Editor
Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 30270-901, Brazil
Interests: bioinformatics; genomics; vaccinology; antifungals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Traditional drug discovery and development is generally a highly time-consuming and expensive process. Over the last three decades, computational methods have been assisting the development of new chemical compounds to mitigate many diseases and issues related to human and veterinary health, using traditional molecular modeling approaches including protein homology modeling as well as lead discovery using ligand screening with large molecular databases including the structure and pharmacophore-based ligand comparisons. In addition, molecular dynamics (MD) using molecular mechanics (MM) and quantum molecular mechanics (QMM) methods coupled to PBSA and GBSA approaches has been extensively used for describing molecular interactions between small molecules and their pharmacological targets. On the other hand, the increasing number of health and environmental issues, such as new emerging infectious diseases, antimicrobial resistance, and new pharmacological targets for life-style diseases urges for a faster and more accurate response from the scientific community to provide better drug candidates against all these pathogeneses.

We invite authors to submit original research and review articles in the fields of drug discovery and cheminformatics focused on, but not restricted to:

  • Artificial intelligence (AI) methods for ligand-based virtual screening and receptor-based virtual screening, fragment-based drug development, ligand clustering and classification, drug repurposing, and structural characterization of new pharmacological protein targets;
  • Novel approaches in applied molecular dynamics for drug discovery, including the description of protein–ligand interactions, protein structure and small molecule structural elucidation, metadynamics, and accelerating molecular dynamic methods applied in drug interactions;
  • Drug repurposing methods using cheminformatics approaches;
  • Novel drugs against antibiotic resistance;
  • Novel drug design and reverse vaccinology against emerging infectious diseases;
  • Peptidomics-, nano-chemoinformatics-, and immunoinformatics-based drug discovery;
  • Tools and databases for drug design and cheminformatics.

We especially encourage authors from the Global South (countries from Latin America, Africa, Asia, Oceania, and developing countries) to showcase their research, innovations, and contribution in this field. 

All accepted manuscripts will be published as a Special Issue in Pharmaceuticals, allowing the scientific community to have a wide view of new approaches in computational chemistry and drug development.

Dr. Bruno Silva Andrade
Dr. Vasco Azevedo
Dr. Debmalya Barh
Dr. Aristóteles Góes-Neto
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. Pharmaceuticals is an international peer-reviewed open access monthly 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 2900 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
  • cheminformatics
  • artificial intelligence
  • drug repurposing
  • ligand screening
  • molecular dynamics
  • computational methods
  • emerging viruses
  • antibiotics
  • reverse vaccinology

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

Published Papers (6 papers)

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Research

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24 pages, 5014 KiB  
Article
Synthesis and Psychotropic Properties of Novel Condensed Triazines for Drug Discovery
by Ervand G. Paronikyan, Shushanik Sh. Dashyan, Suren S. Mamyan, Ruzanna G. Paronikyan, Ivetta M. Nazaryan, Kristine V. Balyan, Hrachik V. Gasparyan, Sona A. Buloyan, Lernik S. Hunanyan and Nina G. Hobosyan
Pharmaceuticals 2024, 17(7), 829; https://doi.org/10.3390/ph17070829 - 25 Jun 2024
Viewed by 1327
Abstract
The exploration of heterocyclic compounds and their fused analogs, featuring key pharmacophore fragments like pyridine, thiophene, pyrimidine, and triazine rings, is pivotal in medicinal chemistry. These compounds possess a wide array of biological activities, making them an intriguing area of study. The quest [...] Read more.
The exploration of heterocyclic compounds and their fused analogs, featuring key pharmacophore fragments like pyridine, thiophene, pyrimidine, and triazine rings, is pivotal in medicinal chemistry. These compounds possess a wide array of biological activities, making them an intriguing area of study. The quest for new neurotropic drugs among derivatives of these heterocycles with pharmacophore groups remains a significant research challenge. The aim of this research work was to develop a synthesis method for new heterocyclic compounds, evaluate their neurotropic and neuroprotective activities, study histological changes, and perform docking analysis. Classical organic synthesis methods were used in the creation of novel heterocyclic systems containing pharmacophore rings. To evaluate the neurotropic activity of these synthesized compounds, a range of biological assays were employed. Docking analysis was conducted using various software packages and methodologies. The neuroprotective activity of compound 13 was tested in seizures with and without pentylenetetrazole (PTZ) administration. Histopathological examinations were performed in different experimental groups in the hippocampus and the entorhinal cortex. As a result of chemical reactions, 16 new, tetra- and pentacyclic heterocyclic compounds were obtained. The biologically studied compounds exhibited protection against PTZ seizures as well as some psychotropic effects. The biological assays evidenced that 13 of the 16 studied compounds showed a high anticonvulsant activity by antagonism with PTZ. The toxicity of the compounds was low. According to the results of the study of psychotropic activity, it was found that the selected compounds have a sedative effect, except compound 13, which exhibited activating behavior and antianxiety effects (especially compound 13). The studied compounds exhibited antidepressant effects, especially compound 13, which is similar to diazepam. Histopathological examination showed that compound 13 produced moderate changes in the brain and exhibited neuroprotective effects in the entorhinal cortex against PTZ-induced damage, reducing gliosis and neuronal loss. Docking studies revealed that out of 16 compounds, 3 compounds bound to the γ-aminobutyric acid type A (GABAA) receptor. Thus, the selected compounds demonstrated anticonvulsant, sedative, and activating behavior, and at the same time exhibited antianxiety and antidepressant effects. Compound 13 bound to the GABAA receptor and exhibited antianxiety, antidepressant, and neuroprotective effects in the entorhinal cortex against PTZ-induced changes. Full article
(This article belongs to the Special Issue New Perspectives on Chemoinformatics and Drug Design)
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19 pages, 7216 KiB  
Article
In Silico Design of Potential Small-Molecule Antibiotic Adjuvants against Salmonella typhimurium Ortho Acetyl Sulphydrylase Synthase to Address Antimicrobial Resistance
by Oluwadunni F. Elebiju, Gbolahan O. Oduselu, Temitope A. Ogunnupebi, Olayinka O. Ajani and Ezekiel Adebiyi
Pharmaceuticals 2024, 17(5), 543; https://doi.org/10.3390/ph17050543 - 23 Apr 2024
Viewed by 1746
Abstract
The inhibition of O-acetyl sulphydrylase synthase isoforms has been reported to represent a promising approach for the development of antibiotic adjuvants. This occurs via the organism developing an unpaired oxidative stress response, causing a reduction in antibiotic resistance in vegetative and swarm [...] Read more.
The inhibition of O-acetyl sulphydrylase synthase isoforms has been reported to represent a promising approach for the development of antibiotic adjuvants. This occurs via the organism developing an unpaired oxidative stress response, causing a reduction in antibiotic resistance in vegetative and swarm cell populations. This consequently increases the effectiveness of conventional antibiotics at lower doses. This study aimed to predict potential inhibitors of Salmonella typhimurium ortho acetyl sulphydrylase synthase (StOASS), which has lower binding energy than the cocrystalized ligand pyridoxal 5 phosphate (PLP), using a computer-aided drug design approach including pharmacophore modeling, virtual screening, and in silico ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) evaluation. The screening and molecular docking of 4254 compounds obtained from the PubChem database were carried out using AutoDock vina, while a post-screening analysis was carried out using Discovery Studio. The best three hits were compounds with the PubChem IDs 118614633, 135715279, and 155773276, possessing binding affinities of −9.1, −8.9, and −8.8 kcal/mol, respectively. The in silico ADMET prediction showed that the pharmacokinetic properties of the best hits were relatively good. The optimization of the best three hits via scaffold hopping gave rise to 187 compounds, and they were docked against StOASS; this revealed that lead compound 1 had the lowest binding energy (−9.3 kcal/mol) and performed better than its parent compound 155773276. Lead compound 1, with the best binding affinity, has a hydroxyl group in its structure and a change in the core heterocycle of its parent compound to benzimidazole, and pyrimidine introduces a synergistic effect and consequently increases the binding energy. The stability of the best hit and optimized compound at the StOASS active site was determined using RMSD, RMSF, radius of gyration, and SASA plots generated from a molecular dynamics simulation. The MD simulation results were also used to monitor how the introduction of new functional groups of optimized compounds contributes to the stability of ligands at the target active site. The improved binding affinity of these compounds compared to PLP and their toxicity profile, which is predicted to be mild, highlights them as good inhibitors of StOASS, and hence, possible antimicrobial adjuvants. Full article
(This article belongs to the Special Issue New Perspectives on Chemoinformatics and Drug Design)
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16 pages, 4248 KiB  
Article
Evaluating Known Zika Virus NS2B-NS3 Protease Inhibitor Scaffolds via In Silico Screening and Biochemical Assays
by Lucianna H. Santos, Rafael E. O. Rocha, Diego L. Dias, Beatriz M. R. M. Ribeiro, Mateus Sá M. Serafim, Jônatas S. Abrahão and Rafaela S. Ferreira
Pharmaceuticals 2023, 16(9), 1319; https://doi.org/10.3390/ph16091319 - 19 Sep 2023
Cited by 2 | Viewed by 1742
Abstract
The NS2B-NS3 protease (NS2B-NS3pro) is regarded as an interesting molecular target for drug design, discovery, and development because of its essential role in the Zika virus (ZIKV) cycle. Although no NS2B-NS3pro inhibitors have reached clinical trials, the employment of drug-like scaffolds can facilitate [...] Read more.
The NS2B-NS3 protease (NS2B-NS3pro) is regarded as an interesting molecular target for drug design, discovery, and development because of its essential role in the Zika virus (ZIKV) cycle. Although no NS2B-NS3pro inhibitors have reached clinical trials, the employment of drug-like scaffolds can facilitate the screening process for new compounds. In this study, we performed a combination of ligand-based and structure-based in silico methods targeting two known non-peptide small-molecule scaffolds with micromolar inhibitory activity against ZIKV NS2B-NS3pro by a virtual screening (VS) of promising compounds. Based on these two scaffolds, we selected 13 compounds from an initial library of 509 compounds from ZINC15’s similarity search. These compounds exhibited structural modifications that are distinct from previously known compounds yet keep pertinent features for binding. Despite promising outcomes from molecular docking and initial enzymatic assays against NS2B-NS3pro, confirmatory assays with a counter-screening enzyme revealed an artifactual inhibition of the assessed compounds. However, we report two compounds, 9 and 11, that exhibited antiviral properties at a concentration of 50 μM in cellular-based assays. Overall, this study provides valuable insights into the ongoing research on anti-ZIKV compounds to facilitate and improve the development of new inhibitors. Full article
(This article belongs to the Special Issue New Perspectives on Chemoinformatics and Drug Design)
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20 pages, 2379 KiB  
Article
Molecular Multi-Target Approach for Human Acetylcholinesterase, Butyrylcholinesterase and β-Secretase 1: Next Generation for Alzheimer’s Disease Treatment
by Géssica Oliveira Mendes, Samuel Silva da Rocha Pita, Paulo Batista de Carvalho, Michel Pires da Silva, Alex Gutterres Taranto and Franco Henrique Andrade Leite
Pharmaceuticals 2023, 16(6), 880; https://doi.org/10.3390/ph16060880 - 15 Jun 2023
Cited by 3 | Viewed by 2183
Abstract
Alzheimer’s Disease (AD) is a neurodegenerative condition characterized by progressive memory loss and other affected cognitive functions. Pharmacological therapy of AD relies on inhibitors of the enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), offering only a palliative effect and being incapable of stopping or [...] Read more.
Alzheimer’s Disease (AD) is a neurodegenerative condition characterized by progressive memory loss and other affected cognitive functions. Pharmacological therapy of AD relies on inhibitors of the enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), offering only a palliative effect and being incapable of stopping or reversing the neurodegenerative process. However, recent studies have shown that inhibiting the enzyme β-secretase 1 (BACE-1) may be able to stop neurodegeneration, making it a promising target. Considering these three enzymatic targets, it becomes feasible to apply computational techniques to guide the identification and planning of molecules capable of binding to all of them. After virtually screening 2119 molecules from a library, 13 hybrids were built and further screened by triple pharmacophoric model, molecular docking, and molecular dynamics (t = 200 ns). The selected hybrid G meets all stereo-electronic requirements to bind to AChE, BChE, and BACE-1 and offers a promising structure for future synthesis, enzymatic testing, and validation. Full article
(This article belongs to the Special Issue New Perspectives on Chemoinformatics and Drug Design)
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Review

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17 pages, 1275 KiB  
Review
Associations between Nutrigenomic Effects and Incidences of Microbial Resistance against Novel Antibiotics
by Mohamed A. Raslan, Sara A. Raslan, Eslam M. Shehata, Amr S. Mahmoud, Kenneth Lundstrom, Debmalya Barh, Vasco Azevedo and Nagwa A. Sabri
Pharmaceuticals 2023, 16(8), 1093; https://doi.org/10.3390/ph16081093 - 1 Aug 2023
Cited by 1 | Viewed by 2150
Abstract
Nutrigenomics is the study of the impact of diets or nutrients on gene expression and phenotypes using high-throughput technologies such as transcriptomics, proteomics, metabolomics, etc. The bioactive components of diets and nutrients, as an environmental factor, transmit information through altered gene expression and [...] Read more.
Nutrigenomics is the study of the impact of diets or nutrients on gene expression and phenotypes using high-throughput technologies such as transcriptomics, proteomics, metabolomics, etc. The bioactive components of diets and nutrients, as an environmental factor, transmit information through altered gene expression and hence the overall function and traits of the organism. Dietary components and nutrients not only serve as a source of energy but also, through their interactions with genes, regulate gut microbiome composition, the production of metabolites, various biological processes, and finally, health and disease. Antimicrobial resistance in pathogenic and probiotic microorganisms has emerged as a major public health concern due to the presence of antimicrobial resistance genes in various food products. Recent evidence suggests a correlation between the regulation of genes and two-component and other signaling systems that drive antibiotic resistance in response to diets and nutrients. Therefore, diets and nutrients may be alternatively used to overcome antibiotic resistance against novel antibiotics. However, little progress has been made in this direction. In this review, we discuss the possible implementations of nutrigenomics in antibiotic resistance against novel antibiotics. Full article
(This article belongs to the Special Issue New Perspectives on Chemoinformatics and Drug Design)
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18 pages, 2663 KiB  
Review
Advances in the Applications of Bioinformatics and Chemoinformatics
by Mohamed A. Raslan, Sara A. Raslan, Eslam M. Shehata, Amr S. Mahmoud and Nagwa A. Sabri
Pharmaceuticals 2023, 16(7), 1050; https://doi.org/10.3390/ph16071050 - 24 Jul 2023
Cited by 11 | Viewed by 7022
Abstract
Chemoinformatics involves integrating the principles of physical chemistry with computer-based and information science methodologies, commonly referred to as “in silico techniques”, in order to address a wide range of descriptive and prescriptive chemistry issues, including applications to biology, drug discovery, and related molecular [...] Read more.
Chemoinformatics involves integrating the principles of physical chemistry with computer-based and information science methodologies, commonly referred to as “in silico techniques”, in order to address a wide range of descriptive and prescriptive chemistry issues, including applications to biology, drug discovery, and related molecular areas. On the other hand, the incorporation of machine learning has been considered of high importance in the field of drug design, enabling the extraction of chemical data from enormous compound databases to develop drugs endowed with significant biological features. The present review discusses the field of cheminformatics and proposes the use of virtual chemical libraries in virtual screening methods to increase the probability of discovering novel hit chemicals. The virtual libraries address the need to increase the quality of the compounds as well as discover promising ones. On the other hand, various applications of bioinformatics in disease classification, diagnosis, and identification of multidrug-resistant organisms were discussed. The use of ensemble models and brute-force feature selection methodology has resulted in high accuracy rates for heart disease and COVID-19 diagnosis, along with the role of special formulations for targeting meningitis and Alzheimer’s disease. Additionally, the correlation between genomic variations and disease states such as obesity and chronic progressive external ophthalmoplegia, the investigation of the antibacterial activity of pyrazole and benzimidazole-based compounds against resistant microorganisms, and its applications in chemoinformatics for the prediction of drug properties and toxicity—all the previously mentioned—were presented in the current review. Full article
(This article belongs to the Special Issue New Perspectives on Chemoinformatics and Drug Design)
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