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Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials

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

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 29961

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Dr. Dmitry Aminin

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G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
Interests: biochemistry; cell biology; structure and function of biological membranes; mechanism of biological activity of natural and synthetic biologically active substances; new drug discovery; molecular targets; toxicology; ecotoxicology; biomarkers; biosensors
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Special Issue Information

Dear Colleagues,

This Special Issue will focus on new drug discovery aspects including the search for new molecular targets of various diseases, the creation of new modern methods for diagnosing diseases, the development of new test systems and kits for assessing the selectivity and effectiveness of new drugs, the study of the molecular mechanisms of biologically active compounds, the formulation of new drugs, and pharmacokinetic and pharmacodynamic studies. Preclinical trials of important molecules are also appreciated.

The main topics of interest are listed below:

The discovery of new molecular targets including receptors, enzymes, ion channels, proteins, genes, etc.;
The application of modern methods for drug discovery including SPR, optical molecular imaging, MRI, PET, SPECT, CT, ultrasound molecular imaging, MS imaging and multimodality imaging;
New methods of developing sensitive and selective test systems and assays to detect drug interactions with specific molecular targets related to different diseases;
Drug modulation of specific signaling pathways involved in disease genesis and progression;
Pharmacokinetic and pharmacodynamic behavior of substances;
Computer modeling of drug interaction with molecular targets, docking, molecular dynamics, QSAR, etc.;
Drug delivery systems including targeted molecules, liposomes, nanoparticles, and cells as a carrier;
Preclinical trials of important molecules on animal models of diseases including xenografts.

Dr. Dmitry Aminin
Guest Editor

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Keywords

new drug discovery
molecular targets
signaling pathways
methods for diagnosing diseases
test systems
pharmacokinetics and pharmacodynamic
computer modeling, drug delivery
preclinical trials

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Published Papers (12 papers)

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Editorial

Jump to: Research, Review

3 pages, 185 KiB

Open AccessEditorial

Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials

by Dmitry Aminin

Int. J. Mol. Sci. 2023, 24(9), 8321; https://doi.org/10.3390/ijms24098321 - 5 May 2023

Viewed by 1301

Abstract

The intention of this Special Issue is to focus on new aspects of drug discovery, including the search for new molecular targets of various diseases, the creation of new modern methods for diagnosing diseases, the development of new test systems and kits for assessing the selectivity and effectiveness of new drugs, the study of the molecular mechanisms of biologically active compounds, the formulation of new drugs, pharmacokinetic and pharmacodynamic studies and preclinical trials of important molecules [...] Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

Research

Jump to: Editorial, Review

18 pages, 3874 KiB

Open AccessArticle

Impact of Hydrophobic Chains in Five-Coordinate Glucoconjugate Pt(II) Anticancer Agents

by Alfonso Annunziata, Paola Imbimbo, Maria Elena Cucciolito, Giarita Ferraro, Vincenzo Langellotti, Alessandra Marano, Massimo Melchiorre, Gabriella Tito, Marco Trifuoggi, Daria Maria Monti, Antonello Merlino and Francesco Ruffo

Int. J. Mol. Sci. 2023, 24(3), 2369; https://doi.org/10.3390/ijms24032369 - 25 Jan 2023

Cited by 3 | Viewed by 1558

Abstract

This study describes new platinum(II) cationic five-coordinate complexes (1-R,R’) of the formula [PtR(NHC)(dmphen)(ethene)]CF₃SO₃ (dmphen = 2,9-dimethyl-1,10-phenanthroline), containing in their axial positions an alkyl group R (methyl or octyl) and an imidazole-based NHC-carbene ligand with a substituent R’ of variable length (methyl or octyl) on one nitrogen atom. The Pt–carbene bond is stable both in DMSO and in aqueous solvents. In DMSO, a gradual substitution of dmphen and ethene is observed, with the formation of a square planar solvated species. Octanol/water partitioning studies have revealed the order of hydrophobicity of the complexes (1-Oct,Me > 1-Oct,Oct > 1-Me,Oct > 1-Me,Me). Their biological activity was investigated against two pairs of cancer and non-cancer cell lines. The tested drugs were internalized in cancer cells and able to activate the apoptotic pathway. The reactivity of 1-Me,Me with DNA and protein model systems was also studied using UV–vis absorption spectroscopy, fluorescence, and X-ray crystallography. The compound binds DNA and interacts in various ways with the model protein lysozyme. Remarkably, structural data revealed that the complex can bind lysozyme via non-covalent interactions, retaining its five-coordinate geometry. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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20 pages, 4241 KiB

Open AccessArticle

Effect of Arylazo Sulfones on DNA: Binding, Cleavage, Photocleavage, Molecular Docking Studies and Interaction with A375 Melanoma and Non-Cancer Cells

by Chrysoula Mikra, Achilleas Mitrakas, Virginia Ghizzani, Katerina R. Katsani, Maria Koffa, Michael Koukourakis, George Psomas, Stefano Protti, Maurizio Fagnoni and Konstantina C. Fylaktakidou

Int. J. Mol. Sci. 2023, 24(3), 1834; https://doi.org/10.3390/ijms24031834 - 17 Jan 2023

Cited by 6 | Viewed by 2406

Abstract

A set of arylazo sulfones, known to undergo N–S bond cleavage upon light exposure, has been synthesized, and their activity in the dark and upon irradiation towards DNA has been investigated. Their interaction with calf-thymus DNA has been examined, and the significant affinity observed (most probably due to DNA intercalation) was analyzed by means of molecular docking “in silico” calculations that pointed out polar contacts, mainly via the sulfonyl moiety. Incubation with plasmid pBluescript KS II revealed DNA cleavage that has been studied over time and concentration. UV-A irradiation considerably improved DNA damage for most of the compounds, whereas under visible light the effect was slightly lower. Moving to in vitro experiments, irradiation was found to slightly enhance the death of the cells in the majority of the compounds. Naphthylazosulfone 1 showed photo-disruptive effect under UV-A irradiation (IC₅₀ ~13 μΜ) followed by derivatives 14 and 17 (IC₅₀ ~100 μΜ). Those compounds were irradiated in the presence of two non-cancer cell lines and were found equally toxic only upon irradiation and not in the dark. The temporal and spatial control of light, therefore, might provide a chance for these novel scaffolds to be useful for the development of phototoxic pharmaceuticals. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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16 pages, 3113 KiB

Open AccessArticle

Combined Administration of Pravastatin and Metformin Attenuates Acute Radiation-Induced Intestinal Injury in Mouse and Minipig Models

by Jung Moon Kim, Hyewon Kim, Su Hyun Oh, Won Il Jang, Seung Bum Lee, Mineon Park, Soyeon Kim, Sunhoo Park, Sehwan Shim and Hyosun Jang

Int. J. Mol. Sci. 2022, 23(23), 14827; https://doi.org/10.3390/ijms232314827 - 27 Nov 2022

Cited by 4 | Viewed by 2133

Abstract

Radiation-induced gastrointestinal (GI) damage is one of the critical factors that serve as basis for the lethality of nuclear accidents or terrorism. Further, there are no Food and Drug Administration-approved agents available to mitigate radiation-induced intestinal injury. Although pravastatin (PS) has been shown to exhibit anti-inflammatory and epithelial reconstructive effects following radiation exposure using mouse and minipig models, the treatment failed to improve the survival rate of high-dose irradiated intestinal injury. Moreover, we previously found that metformin (MF), a common drug used for treating type 2 diabetes mellitus, has a mitigating effect on radiation-induced enteropathy by promoting stem cell properties. In this study, we investigated whether the combined administration of PS and MF could achieve therapeutic effects on acute radiation-induced intestinal injury in mouse and minipig models. We found that the combined treatment markedly increased the survival rate and attenuated histological damage in a radiation-induced intestinal injury mouse model, in addition to epithelial barrier recovery, anti-inflammatory effects, and improved epithelial proliferation with stem cell properties. Furthermore, in minipig models, combined treatment with PS and MF ameliorates gross pathological damage in abdominal organs and attenuated radiation-induced intestinal histological damage. Therefore, the combination of PS and MF effectively alleviated radiation-induced intestinal injury in the mouse and minipig models. We believe that the combined use of PS and MF is a promising therapeutic approach for treating radiation-induced intestinal injury. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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14 pages, 4015 KiB

Open AccessArticle

Diastereoselective Synthesis of Novel Spiro-Phosphacoumarins and Evaluation of Their Anti-Cancer Activity

by Valeriia V. Sennikova, Alena V. Zalaltdinova, Yulia M. Sadykova, Ayrat R. Khamatgalimov, Almir S. Gazizov, Alexandra D. Voloshina, Anna P. Lyubina, Syumbelya K. Amerhanova, Julia K. Voronina, Elena A. Chugunova, Nurbol O. Appazov, Alexander R. Burilov and Michail A. Pudovik

Int. J. Mol. Sci. 2022, 23(22), 14348; https://doi.org/10.3390/ijms232214348 - 18 Nov 2022

Cited by 4 | Viewed by 1568

Abstract

Herein we present the regio- and diastereoselective synthesis of novel pyrrolidine-fused spiro-dihydrophosphacoumarins via intermolecular [3 + 2] cycloaddition reaction. The presented approach is complementary to existing ones and provides an easy entry to the otherwise inaccessible derivatives. Additionally, the unprecedented pathway of the reaction of 4-hydroxycoumarin with azomethine ylides is described. The anti-cancer activity of the obtained compounds was tested in vitro, the most potent compound being 2.6-fold more active against the HuTu 80 cell line than the reference 5-fluorouracil, with a selectivity index > 32. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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20 pages, 6084 KiB

Open AccessArticle

Novel Regioisomeric Analogues of Naphthyl-N-Acylhydrazone Derivatives and Their Anti-Inflammatory Effects

by Dayana da Costa Salomé, Rosana Helena Coimbra Nogueira de Freitas, Carlos Alberto Manssour Fraga and Patricia Dias Fernandes

Int. J. Mol. Sci. 2022, 23(21), 13562; https://doi.org/10.3390/ijms232113562 - 5 Nov 2022

Cited by 4 | Viewed by 1382

Abstract

Background: When homeostasis is disturbed it can result in a pathological event named inflammation. The main drugs used in the treatment consist of non-steroidal and steroidal anti-inflammatory drugs. However, the side effects remain an obstacle during the treatments. In this study, we aimed to evaluate three new regioisomers analogues of naphthyl-N-acylhydrazone derivatives. Methods: Acute models of inflammation in vivo (formalin-induced licking and carrageenan-induced inflammation) as well as in vitro were used to evaluate the effects of LASSBio-2039, LASSBio-2040, and LASSBio-2041. Results: All three substances (at 1, 10 or 30 µmol/kg) presented significant effects in the in vivo model reducing leukocyte migration, nitric oxide (NO) and interleukin-1β production. It was observed that only LASSBio-2039 significantly reduced cell migration in vitro. None of the LASSBios affected inducible nitric oxide synthase activity nor presented nitric oxide (NO) scavenger effect. No toxic effect was observed, either in vivo or in vitro. The new regioisomers analogues of naphthyl-N-acylhydrazone derivatives presented significant anti-inflammatory activity, suggesting LASSBio-2039 has a direct effect in leukocytes migratory capacity. Conclusions: Taken together, the data indicate that these substances present promising effects for the development of a prototype for new drugs. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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15 pages, 4535 KiB

Open AccessArticle

An Analysis of the Effects of In Vitro Photodynamic Therapy on Prostate Cancer Tissue by Histopathological Examination and Magnetic Resonance Imaging

by David Aebisher, Michał Osuchowski, Dorota Bartusik-Aebisher, Magdalena Krupka-Olek, Klaudia Dynarowicz and Aleksandra Kawczyk-Krupka

Int. J. Mol. Sci. 2022, 23(19), 11354; https://doi.org/10.3390/ijms231911354 - 26 Sep 2022

Cited by 4 | Viewed by 2103

Abstract

Prostate cancer can significantly shorten the lifetime of a patient, even if he is diagnosed at an early stage. The development of minimally-invasive focal therapies such as photodynamic therapy to reduce the number of neoplastic cells while sparing delicate structures is extremely advantageous for treating prostate cancer. This study investigates the effect of photodynamic therapy performed in prostate tissue samples in vitro, using quantitative magnetic resonance imaging and histopathological analysis. Prostate tissue samples were treated with oxygenated solutions of Rose Bengal (RB) or protoporphyrin IX disodium salt (PpIX), illuminated with visible light, and then analyzed for changes in morphology by microscopy and by measurement of spin–lattice and spin–spin relaxation times at 1.5 Tesla. In the treated prostate tissue samples, histopathological images revealed chromatin condensation and swelling of the stroma, and in some cases, thrombotic necrosis and swelling of the stroma accompanied by pyknotic nuclei occurred. Several samples had protein fragments in the stroma. Magnetic resonance imaging of the treated prostate tissue samples revealed differences in the spin–lattice and spin–spin relaxation times prior to and post photodynamic action. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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14 pages, 19753 KiB

Open AccessArticle

Transcription Factor MAFB as a Prognostic Biomarker for the Lung Adenocarcinoma

by Omar Samir, Naohiro Kobayashi, Teppei Nishino, Mennatullah Siyam, Manoj Kumar Yadav, Yuri Inoue, Satoru Takahashi and Michito Hamada

Int. J. Mol. Sci. 2022, 23(17), 9945; https://doi.org/10.3390/ijms23179945 - 1 Sep 2022

Cited by 5 | Viewed by 3887

Abstract

MAFB is a basic leucine zipper (bZIP) transcription factor specifically expressed in macrophages. We have previously identified MAFB as a candidate marker for tumor-associated macrophages (TAMs) in human and mouse models. Here, we analyzed single-cell sequencing data of patients with lung adenocarcinoma obtained from the GEO database (GSE131907). Analyzed data showed that general macrophage marker CD68 and macrophage scavenger receptor 1 (CD204) were expressed in TAM and lung tissue macrophage clusters, while transcription factor MAFB was expressed specifically in TAM clusters. Clinical records of 120 patients with lung adenocarcinoma stage I (n = 57), II (n = 21), and III (n = 42) were retrieved from Tsukuba Human Tissue Biobank Center (THB) in the University of Tsukuba Hospital, Japan. Tumor tissues from these patients were extracted and stained with anti-human MAFB antibody, and then MAFB-positive cells relative to the tissue area (MAFB⁺ cells/tissue area) were morphometrically quantified. Our results indicated that higher numbers of MAFB⁺ cells significantly correlated to increased local lymph node metastasis (nodal involvement), high recurrence rate, poor pathological stage, increased lymphatic permeation, higher vascular invasion, and pleural infiltration. Moreover, increased amounts of MAFB⁺ cells were related to poor overall survival and disease-free survival, especially in smokers. These data indicate that MAFB may be a suitable prognostic biomarker for smoker lung cancer patients. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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22 pages, 4210 KiB

Open AccessArticle

Systems Drug Discovery for Diffuse Large B Cell Lymphoma Based on Pathogenic Molecular Mechanism via Big Data Mining and Deep Learning Method

by Shan-Ju Yeh, Tsun-Yung Yeh and Bor-Sen Chen

Int. J. Mol. Sci. 2022, 23(12), 6732; https://doi.org/10.3390/ijms23126732 - 16 Jun 2022

Cited by 4 | Viewed by 2485

Abstract

Diffuse large B cell lymphoma (DLBCL) is an aggressive heterogeneous disease. The most common subtypes of DLBCL include germinal center b-cell (GCB) type and activated b-cell (ABC) type. To learn more about the pathogenesis of two DLBCL subtypes (i.e., DLBCL ABC and DLBCL GCB), we firstly construct a candidate genome-wide genetic and epigenetic network (GWGEN) by big database mining. With the help of two DLBCL subtypes’ genome-wide microarray data, we identify their real GWGENs via system identification and model order selection approaches. Afterword, the core GWGENs of two DLBCL subtypes could be extracted from real GWGENs by principal network projection (PNP) method. By comparing core signaling pathways and investigating pathogenic mechanisms, we are able to identify pathogenic biomarkers as drug targets for DLBCL ABC and DLBCL GCD, respectively. Furthermore, we do drug discovery considering drug-target interaction ability, drug regulation ability, and drug toxicity. Among them, a deep neural network (DNN)-based drug-target interaction (DTI) model is trained in advance to predict potential drug candidates holding higher probability to interact with identified biomarkers. Consequently, two drug combinations are proposed to alleviate DLBCL ABC and DLBCL GCB, respectively. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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23 pages, 5908 KiB

Open AccessArticle

Kunitz-Type Peptides from Sea Anemones Protect Neuronal Cells against Parkinson’s Disease Inductors via Inhibition of ROS Production and ATP-Induced P2X7 Receptor Activation

by Aleksandra Kvetkina, Evgeny Pislyagin, Ekaterina Menchinskaya, Ekaterina Yurchenko, Rimma Kalina, Sergei Kozlovskiy, Leonid Kaluzhskiy, Alexander Menshov, Natalia Kim, Steve Peigneur, Jan Tytgat, Alexis Ivanov, Naira Ayvazyan, Elena Leychenko and Dmitry Aminin

Int. J. Mol. Sci. 2022, 23(9), 5115; https://doi.org/10.3390/ijms23095115 - 4 May 2022

Cited by 8 | Viewed by 3012

Abstract

Parkinson’s disease (PD) is a socially significant disease, during the development of which oxidative stress and inflammation play a significant role. Here, we studied the neuroprotective effects of four Kunitz-type peptides from Heteractis crispa and Heteractis magnifica sea anemones against PD inductors. The peptide HCIQ1c9, which was obtained for the first time, inhibited trypsin less than other peptides due to unfavorable interactions of Arg17 with Lys43 in the enzyme. Its activity was reduced by up to 70% over the temperature range of 60–100 °C, while HCIQ2c1, HCIQ4c7, and HMIQ3c1 retained their conformation and stayed active up to 90–100 °C. All studied peptides inhibited paraquat- and rotenone-induced intracellular ROS formation, in particular NO, and scavenged free radicals outside the cells. The peptides did not modulate the TRPV1 channels but they affected the P2X7R, both of which are considered therapeutic targets in Parkinson’s disease. HMIQ3c1 and HCIQ4c7 almost completely inhibited the ATP-induced uptake of YO-PRO-1 dye in Neuro-2a cells through P2X7 ion channels and significantly reduced the stable calcium response in these cells. The complex formation of the peptides with the P2X7R extracellular domain was determined via SPR analysis. Thus, these peptides may be considered promising compounds to protect neuronal cells against PD inductors, which act as ROS production inhibitors and partially act as ATP-induced P2X7R activation inhibitors. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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15 pages, 4609 KiB

Open AccessArticle

QSAR, Docking, and Molecular Dynamics Simulation Studies of Sigmacidins as Antimicrobials against Streptococci

by Jiqing Ye, Xiao Yang and Cong Ma

Int. J. Mol. Sci. 2022, 23(8), 4085; https://doi.org/10.3390/ijms23084085 - 7 Apr 2022

Cited by 6 | Viewed by 2574

Abstract

Streptococci are a family of bacterial species significantly affecting human health. In addition, environmental Streptococci represent one of the major causes of diverse livestock diseases. Due to antimicrobial resistance, there is an urgent need for novel antimicrobial agent discovery against Streptococci. We discovered a class of benzoic acid derivatives named sigmacidins inhibiting the bacterial RNA polymerase-σ factor interaction and demonstrating excellent antimicrobial activity against Streptococci. In this work, a combinational computer approach was applied to gain insight into the structural basis and mechanism of action of sigmacidins as antimicrobials against Streptococcus pneumoniae. Both two- and three-dimensional quantitative structure-active relationships (2D and 3D QSAR) of sigmacidins displayed good predictive ability. Moreover, molecular docking and molecular dynamics simulation studies disclosed possible contacts between the inhibitors and the protein. The results obtained in this study provided understanding and new directions to the further optimizations of sigmacidins as novel antimicrobials. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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Review

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43 pages, 3395 KiB

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Natural Inhibitors of Cholinesterases: Chemistry, Structure–Activity and Methods of Their Analysis

by Natalia Smyrska-Wieleba and Tomasz Mroczek

Int. J. Mol. Sci. 2023, 24(3), 2722; https://doi.org/10.3390/ijms24032722 - 1 Feb 2023

Cited by 17 | Viewed by 4008

Abstract

This article aims to provide an updated description and comparison of the data currently available in the literature (from the last 15 years) on the studied natural inhibitors of cholinesterases (IChEs), namely, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). These data also apply to the likely impact of the structures of the compounds on the therapeutic effects of available and potential cholinesterase inhibitors. IChEs are hitherto known compounds with various structures, activities and origins. Additionally, multiple different methods of analysis are used to determine the cholinesterase inhibitor potency. This summary indicates that natural sources are still suitable for the discovery of new compounds with prominent pharmacological activity. It also emphasizes that further studies are needed regarding the mechanisms of action or the structure–activity correlation to discuss the issue of cholinesterase inhibitors and their medical application. Full article

(This article belongs to the Special Issue Frontiers in New Drug Discovery: From Molecular Targets to Preclinical Trials)

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