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

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 22877

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Prof. Dr. Adel Nefzi

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Department of Cellular Biology & Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
Interests: organic chemistry; medicinal chemistry; small molecules; drug-like compounds; tethered and fused diazacyclic compounds; heterocyclic peptidomimetics; combinatorial chemistry; solid phase organic synthesis
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Dear Colleagues,

The last two decades have witnessed major breakthroughs in the identification of genes, gene products, metabolic pathways, and signalling pathways, as well as progress in miniaturization and robotics, enabling the development of high-throughput mechanism-based biological assays. How does one approach the challenge of generating diverse small-molecule libraries that are likely to provide robust hits against a wide variety of molecular targets and, at the same time, are sound platforms for rapid optimization, affording potent and selective chemical probes that reside within a novel and biologically relevant chemical space? Since no single library can possibly occupy the entire universe of chemical space, there is a widespread agreement that increased access to chemical diversity is needed to target the whole biological space and thus increase the number of targets that are considered “druggable”. The search for new therapeutic entities can proceed along three principal paths of exploration: random walks, building on existing active structures, and using macromolecules as templates for molecular assembly.

Furthermore, there are several practical considerations involved in the efficient production of new entities designed to provide novel chemical probes. For example, the starting materials should be readily available and inexpensive; the synthetic steps must be straightforward, efficient, and reproducible on a multigram scale, the intermediates and final target species must be readily purified, preferably resulting from clean, high-yielding reactions that require minimal purification.

Because of high attrition rates, especially during the clinical phases of drug development, more attention is needed in the early drug design process on selecting candidate drugs whose physicochemical properties are predicted to result in fewer complications during development and, hence, are more likely to lead to an approved, marketed drug. Techniques such as in vitro experiments complemented with computation methods are increasingly used in early drug discovery to select compounds with more favorable ADME and toxicological profiles.

Prof. Dr. Adel Nefzi
Guest Editor

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Keywords

drug design
diversity-oriented synthesis
combinatorial chemistry
computationally guided synthesis
drug-like compounds
computer modeling techniques

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Published Papers (11 papers)

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Research

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29 pages, 14720 KiB

Open AccessArticle

The Parallel Structure–Activity Relationship Screening of Three Compounds Identifies the Common Agonist Pharmacophore of Pyrrolidine Bis-Cyclic Guanidine Melanocortin-3 Receptor (MC3R) Small-Molecule Ligands

by Mark D. Ericson, Katie T. Freeman, Travis M. LaVoi, Haley M. Donow, Radleigh G. Santos, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten and Carrie Haskell-Luevano

Int. J. Mol. Sci. 2023, 24(12), 10145; https://doi.org/10.3390/ijms241210145 - 14 Jun 2023

Viewed by 971

Abstract

The melanocortin receptors are involved in numerous physiological pathways, including appetite, skin and hair pigmentation, and steroidogenesis. In particular, the melanocortin-3 receptor (MC3R) is involved in fat storage, food intake, and energy homeostasis. Small-molecule ligands developed for the MC3R may serve as therapeutic lead compounds for treating disease states of energy disequilibrium. Herein, three previously reported pyrrolidine bis-cyclic guanidine compounds with five sites for molecular diversity (R1–R5) were subjected to parallel structure–activity relationship studies to identify the common pharmacophore of this scaffold series required for full agonism at the MC3R. The R2, R3, and R5 positions were required for full MC3R efficacy, while truncation of either the R1 or R4 positions in all three compounds resulted in full MC3R agonists. Two additional fragments, featuring molecular weights below 300 Da, were also identified that possessed full agonist efficacy and micromolar potencies at the mMC5R. These SAR experiments may be useful in generating new small-molecule ligands and chemical probes for the melanocortin receptors to help elucidate their roles in vivo and as therapeutic lead compounds. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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15 pages, 1491 KiB

Open AccessArticle

Benzoquinoline Derivatives: An Attractive Approach to Newly Small Molecules with Anticancer Activity

by Liliana Oniciuc, Dorina Amăriucăi-Mantu, Dumitrela Diaconu, Violeta Mangalagiu, Ramona Danac, Vasilichia Antoci and Ionel I. Mangalagiu

Int. J. Mol. Sci. 2023, 24(9), 8124; https://doi.org/10.3390/ijms24098124 - 01 May 2023

Cited by 4 | Viewed by 1911

Abstract

This study presents the synthesis, structural characterization, and in vitro evaluation of anticancer activity of some newly benzo[f]quinoline derivatives. The synthesis is facile and efficient, involving two steps: quaternization of nitrogen heterocycle followed by a [3+2] dipolar cycloaddition reaction. The synthesized compounds were characterized by FTIR, NMR, and X-ray diffraction on monocrystal in the case of compounds 6c and 7c. An in vitro single-dose anticancer assay of eighteen benzo[f]quinoline compounds, quaternary salts, and cycloadducts, was performed. The results showed that the most active compounds were quaternary salts 3d and 3f with aromatic R substituents. Quaternary salt 3d revealed non-selective activity against all types of cancer cells, while salt 3f exhibited a highly selective activity against leukemia cells. Compound 3d also presented remarkable cytotoxic efficiency against four distinct types of cancer cells—namely, non-small cell lung cancer HOP–92, melanoma LOX IMVI, melanoma SK–MEL–5, and breast cancer MDA–MB–468. Compound 3f was selected for five-dose screening. The study also includes SAR correlations. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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19 pages, 4655 KiB

Open AccessArticle

Structure-Based Virtual Screening and De Novo Design to Identify Submicromolar Inhibitors of G2019S Mutant of Leucine-Rich Repeat Kinase 2

by Hwangseo Park, Taeho Kim, Kewon Kim, Ahyoung Jang and Sungwoo Hong

Int. J. Mol. Sci. 2022, 23(21), 12825; https://doi.org/10.3390/ijms232112825 - 24 Oct 2022

Cited by 5 | Viewed by 1808

Abstract

Missense mutations of leucine-rich repeat kinase 2 (LRRK2), including the G2019S mutant, are responsible for the pathogenesis of Parkinson’s disease. In this work, structure-based virtual screening of a large chemical library was carried out to identify a number of novel inhibitors of the G2019S mutant of LRRK2, the biochemical potencies of which ranged from the low micromolar to the submicromolar level. The discovery of these potent inhibitors was made possible due to the modification of the original protein–ligand binding energy function in order to include an accurate ligand dehydration energy term. The results of extensive molecular docking simulations indicated that the newly identified inhibitors were bound to the ATP-binding site of the G2019S mutant of LRRK2 through the multiple hydrogen bonds with backbone amide groups in the hinge region as well as the hydrophobic interactions with the nonpolar residues in the P-loop, hinge region, and interdomain region. Among 18 inhibitors derived from virtual screening, 4-(2-amino-5-phenylpyrimidin-4-yl)benzene-1,3-diol (Inhibitor 2) is most likely to serve as a new molecular scaffold to optimize the biochemical potency, because it revealed submicromolar inhibitory activity in spite of its low molecular weight (279.3 amu). Indeed, a highly potent inhibitor (Inhibitor 2n) of the G2019S mutant was derived via the structure-based de novo design using the structure of Inhibitor 2 as the molecular core. The biochemical potency of Inhibitor 2n surged to the nanomolar level due to the strengthening of hydrophobic interactions in the ATP-binding site, which were presumably caused by the substitutions of small nonpolar moieties. Due to the high biochemical potency against the G2019S mutant of LRRK2 and the putatively good physicochemical properties, Inhibitor 2n is anticipated to serve as a new lead compound for the discovery of antiparkinsonian medicines. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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23 pages, 4588 KiB

Open AccessArticle

Complementary Dual Approach for In Silico Target Identification of Potential Pharmaceutical Compounds in Cystic Fibrosis

by Liza Vinhoven, Frauke Stanke, Sylvia Hafkemeyer and Manuel Manfred Nietert

Int. J. Mol. Sci. 2022, 23(20), 12351; https://doi.org/10.3390/ijms232012351 - 15 Oct 2022

Cited by 1 | Viewed by 1625

Abstract

Cystic fibrosis is a genetic disease caused by mutation of the CFTR gene, which encodes a chloride and bicarbonate transporter in epithelial cells. Due to the vast range of geno- and phenotypes, it is difficult to find causative treatments; however, small-molecule therapeutics have been clinically approved in the last decade. Still, the search for novel therapeutics is ongoing, and thousands of compounds are being tested in different assays, often leaving their mechanism of action unknown. Here, we bring together a CFTR-specific compound database (CandActCFTR) and systems biology model (CFTR Lifecycle Map) to identify the targets of the most promising compounds. We use a dual inverse screening approach, where we employ target- and ligand-based methods to suggest targets of 309 active compounds in the database amongst 90 protein targets from the systems biology model. Overall, we identified 1038 potential target–compound pairings and were able to suggest targets for all 309 active compounds in the database. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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22 pages, 3715 KiB

Open AccessArticle

The Antidepressant-like Activity, Effects on Recognition Memory Deficits, Bioavailability, and Safety after Chronic Administration of New Dual-Acting Small Compounds Targeting Neuropsychiatric Symptoms in Dementia

by Magdalena Jastrzębska-Więsek, Magdalena Kotańska, Aleksandra Grzeszczak, Anna Jaromin, Maria Walczak, Anna Partyka, Joanna Gdula-Argasińska, Magdalena Smolik and Agnieszka Zagórska

Int. J. Mol. Sci. 2022, 23(19), 11452; https://doi.org/10.3390/ijms231911452 - 28 Sep 2022

Viewed by 1676

Abstract

This study aimed to extend the body of preclinical research on prototype dual-acting compounds combining the pharmacophores relevant for inhibiting cyclic nucleotide phosphodiesterase 10 (PDE10A) and serotonin 5-HT_1A/5-HT₇ receptor (5-HT_1AR/5-HT₇R) activity into a single chemical entity (compounds PQA-AZ4 and PQA-AZ6). After i.v. administration of PQA-AZ4 and PQA-AZ6 to rats, the brain to plasma ratio was 0.9 and 8.60, respectively. After i.g. administration, the brain to plasma ratio was 5.7 and 5.3, respectively. An antidepressant-like effect was observed for PQA-AZ6 in the forced swim test, after chronic 21-day treatment via i.p. administration with 1 mg/kg/day. Both compounds revealed an increased level of brain-derived neurotrophic factor (Bdnf) mRNA in the hippocampus and prefrontal cortex. Moreover, PQA-AZ4 and PQA-AZ6 completely reversed (+)-MK801-induced memory disturbances comparable with the potent PDE10 inhibitor, compound PQ-10. In the safety profile that included measurements of plasma glucose, triglyceride, and total cholesterol concentration, liver enzyme activity, the total antioxidant activity of serum, together with weight gain, compounds exhibited no significant activity. However, the studied compounds had different effects on human normal fibroblast cells as revealed in in vitro assay. The pharmacokinetic and biochemical results support the notion that these novel dual-acting compounds might offer a promising therapeutic tool in CNS-related disorders. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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14 pages, 1813 KiB

Open AccessArticle

Synthesis of Novel α-Trifluoroanisole Derivatives Containing Phenylpyridine Moieties with Herbicidal Activity

by Zengfei Cai, Yangyang Cao and Xiaohua Du

Int. J. Mol. Sci. 2022, 23(19), 11083; https://doi.org/10.3390/ijms231911083 - 21 Sep 2022

Cited by 3 | Viewed by 1222

Abstract

To find novel herbicidal compounds with high activity and broad spectrum, a series of phenylpyridine moiety-containing α-trifluoroanisole derivatives were designed, synthesized, and identified via nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS). Greenhouse-based herbicidal activity assays revealed that compound 7a exhibited > 80% inhibitory activity against Abutilon theophrasti, Amaranthus retroflexus, Eclipta prostrate, Digitaria sanguinalis, and Setaria viridis at a dose of 37.5 g a.i./hm², which was better than fomesafen. Compound 7a further exhibited excellent herbicidal activity against Abutilon theophrasti and Amaranthus retroflexus in this greenhouse setting, with respective median effective dose (ED₅₀) values of 13.32 and 5.48 g a.i./hm², both of which were slightly superior to fomesafen (ED₅₀ = 36.39, 10.09 g a.i./hm²). The respective half-maximal inhibitory concentration (IC₅₀) for compound 7a and fomesafen when used to inhibit the Nicotiana tabacum protoporphyrinogen oxidase (NtPPO) enzyme, were 9.4 and 110.5 nM. The docking result of compound 7a indicated that the introduction of 3-chloro-5-trifluoromethylpyridine and the trifluoromethoxy group was beneficial to the formation of stable interactions between these compounds and NtPPO. This work demonstrated that compound 7a could be further optimized as a PPO herbicide candidate to control various weeds. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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19 pages, 4516 KiB

Open AccessArticle

Bis-Cyclic Guanidine Heterocyclic Peptidomimetics as Opioid Ligands with Mixed μ-, κ- and δ-Opioid Receptor Interactions: A Potential Approach to Novel Analgesics

by Jay P. McLaughlin, Ramanjaneyulu Rayala, Ashley J. Bunnell, Mukund P. Tantak, Shainnel O. Eans, Khadija Nefzi, Michelle L. Ganno, Colette T. Dooley and Adel Nefzi

Int. J. Mol. Sci. 2022, 23(17), 9623; https://doi.org/10.3390/ijms23179623 - 25 Aug 2022

Cited by 2 | Viewed by 2377

Abstract

The design and development of analgesics with mixed-opioid receptor interactions has been reported to decrease side effects, minimizing respiratory depression and reinforcing properties to generate safer analgesic therapeutics. We synthesized bis-cyclic guanidine heterocyclic peptidomimetics from reduced tripeptides. In vitro screening with radioligand competition binding assays demonstrated variable affinity for the mu-opioid receptor (MOR), delta-opioid receptor (DOR), and kappa-opioid receptor (KOR) across the series, with compound 1968-22 displaying good affinity for all three receptors. Central intracerebroventricular (i.c.v.) administration of 1968-22 produced dose-dependent, opioid receptor-mediated antinociception in the mouse 55 °C warm-water tail-withdrawal assay, and 1968-22 also produced significant antinociception up to 80 min after oral administration (10 mg/kg, p.o.). Compound 1968-22 was detected in the brain 5 min after intravenous administration and was shown to be stable in the blood for at least 30 min. Central administration of 1968-22 did not produce significant respiratory depression, locomotor effects or conditioned place preference or aversion. The data suggest these bis-cyclic guanidine heterocyclic peptidomimetics with multifunctional opioid receptor activity may hold potential as new analgesics with fewer liabilities of use. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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11 pages, 2663 KiB

Open AccessArticle

1,5-Disubstituted Acylated 2-Amino-4,5-dihydroimidazoles as a New Class of Retinoic Acid Receptor–Related Orphan Receptor (ROR) Inhibitors

by Maria A. Ortiz, F. Javier Piedrafita and Adel Nefzi

Int. J. Mol. Sci. 2022, 23(8), 4433; https://doi.org/10.3390/ijms23084433 - 17 Apr 2022

Cited by 5 | Viewed by 2185

Abstract

A growing body of evidence suggests a pathogenic role for pro-inflammatory T helper 17 cells (Th17) in several autoimmune diseases, including multiple sclerosis, rheumatoid arthritis, inflammatory bowel disease, type I diabetes, and psoriasis—diseases for which no curative treatment is currently available. The nuclear retinoic acid receptor–related orphan receptors alpha and gamma (RORα/γ), in particular the truncated isoform RORγt that is specifically expressed in the thymus, play a critical role in the activation of a pro-inflammatory Th17 response, and RORγ inverse agonists have shown promise as negative regulators of Th17 for the treatment of autoimmune diseases. Our study underscores the screening of a large combinatorial library of 1,5-disubstituted acylated 2-amino-4,5-dihydroimidazoles using a demonstrated synthetic and screening approach and the utility of the positional scanning libraries strategy for the rapid identification of a novel class of ROR inhibitors. We identified compound 1295-273 with the highest activity against RORγ (3.3 µM IC₅₀) in this series, and almost a two-fold selectivity towards this receptor isoform, with 5.3 and 5.8 µM IC₅₀ against RORα and RORβ cells, respectively. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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17 pages, 6205 KiB

Open AccessArticle

Crystal Structure of an SSB Protein from Salmonella enterica and Its Inhibition by Flavanonol Taxifolin

by En-Shyh Lin, Yen-Hua Huang, Ren-Hong Luo, Zarrin Basharat and Cheng-Yang Huang

Int. J. Mol. Sci. 2022, 23(8), 4399; https://doi.org/10.3390/ijms23084399 - 15 Apr 2022

Cited by 7 | Viewed by 1986

Abstract

Single-stranded DNA (ssDNA)-binding proteins (SSBs) play a central role in cells by participating in DNA metabolism, including replication, repair, recombination, and replication fork restart. SSBs are essential for cell survival and thus an attractive target for potential anti-pathogen chemotherapy. In this study, we determined the crystal structure and examined the size of the ssDNA-binding site of an SSB from Salmonella enterica serovar Typhimurium LT2 (SeSSB), a ubiquitous opportunistic pathogen which is highly resistant to antibiotics. The crystal structure was solved at a resolution of 2.8 Å (PDB ID 7F25), indicating that the SeSSB monomer possesses an oligonucleotide/oligosaccharide-binding (OB) fold domain at its N-terminus and a flexible tail at its C-terminus. The core of the OB-fold in the SeSSB is made of a six-stranded β-barrel capped by an α-helix. The crystal structure of the SeSSB contained two monomers per asymmetric unit, which may indicate the formation of a dimer. However, the gel-filtration chromatography analysis showed that the SeSSB forms a tetramer in solution. Through an electrophoretic mobility shift analysis, we characterized the stoichiometry of the SeSSB complexed with a series of ssDNA dA homopolymers, and the size of the ssDNA-binding site was determined to be around 22 nt. We also found the flavanonol taxifolin, also known as dihydroquercetin, capable of inhibiting the ssDNA-binding activity of the SeSSB. Thus, this result extended the SSB interactome to include taxifolin, a natural product with a wide range of promising pharmacological activities. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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38 pages, 5225 KiB

Open AccessArticle

Repurposing Multiple-Molecule Drugs for COVID-19-Associated Acute Respiratory Distress Syndrome and Non-Viral Acute Respiratory Distress Syndrome via a Systems Biology Approach and a DNN-DTI Model Based on Five Drug Design Specifications

by Ching-Tse Ting and Bor-Sen Chen

Int. J. Mol. Sci. 2022, 23(7), 3649; https://doi.org/10.3390/ijms23073649 - 26 Mar 2022

Cited by 5 | Viewed by 2945

Abstract

The coronavirus disease 2019 (COVID-19) epidemic is currently raging around the world at a rapid speed. Among COVID-19 patients, SARS-CoV-2-associated acute respiratory distress syndrome (ARDS) is the main contribution to the high ratio of morbidity and mortality. However, clinical manifestations between SARS-CoV-2-associated ARDS and non-SARS-CoV-2-associated ARDS are quite common, and their therapeutic treatments are limited because the intricated pathophysiology having been not fully understood. In this study, to investigate the pathogenic mechanism of SARS-CoV-2-associated ARDS and non-SARS-CoV-2-associated ARDS, first, we constructed a candidate host-pathogen interspecies genome-wide genetic and epigenetic network (HPI-GWGEN) via database mining. With the help of host-pathogen RNA sequencing (RNA-Seq) data, real HPI-GWGEN of COVID-19-associated ARDS and non-viral ARDS were obtained by system modeling, system identification, and Akaike information criterion (AIC) model order selection method to delete the false positives in candidate HPI-GWGEN. For the convenience of mitigation, the principal network projection (PNP) approach is utilized to extract core HPI-GWGEN, and then the corresponding core signaling pathways of COVID-19-associated ARDS and non-viral ARDS are annotated via their core HPI-GWGEN by KEGG pathways. In order to design multiple-molecule drugs of COVID-19-associated ARDS and non-viral ARDS, we identified essential biomarkers as drug targets of pathogenesis by comparing the core signal pathways between COVID-19-associated ARDS and non-viral ARDS. The deep neural network of the drug–target interaction (DNN-DTI) model could be trained by drug–target interaction databases in advance to predict candidate drugs for the identified biomarkers. We further narrowed down these predicted drug candidates to repurpose potential multiple-molecule drugs by the filters of drug design specifications, including regulation ability, sensitivity, excretion, toxicity, and drug-likeness. Taken together, we not only enlighten the etiologic mechanisms under COVID-19-associated ARDS and non-viral ARDS but also provide novel therapeutic options for COVID-19-associated ARDS and non-viral ARDS. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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Review

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20 pages, 2186 KiB

Open AccessReview

Taurine and Creatine Transporters as Potential Drug Targets in Cancer Therapy

by Dorota Stary and Marek Bajda

Int. J. Mol. Sci. 2023, 24(4), 3788; https://doi.org/10.3390/ijms24043788 - 14 Feb 2023

Cited by 3 | Viewed by 2808

Abstract

Cancer cells are characterized by uncontrolled growth, proliferation, and impaired apoptosis. Tumour progression could be related to poor prognosis and due to this fact, researchers have been working on novel therapeutic strategies and antineoplastic agents. It is known that altered expression and function of solute carrier proteins from the SLC6 family could be associated with severe diseases, including cancers. These proteins were noticed to play important physiological roles through transferring nutrient amino acids, osmolytes, neurotransmitters, and ions, and many of them are necessary for survival of the cells. Herein, we present the potential role of taurine (SLC6A6) and creatine (SLC6A8) transporters in cancer development as well as therapeutic potential of their inhibitors. Experimental data indicate that overexpression of analyzed proteins could be connected with colon or breast cancers, which are the most common types of cancers. The pool of known inhibitors of these transporters is limited; however, one ligand of SLC6A8 protein is currently tested in the first phase of clinical trials. Therefore, we also highlight structural aspects useful for ligand development. In this review, we discuss SLC6A6 and SLC6A8 transporters as potential biological targets for anticancer agents. Full article

(This article belongs to the Special Issue Small Molecule Drug Design and Research)

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