Given its pivotal role in the viral life cycle, blocking integrase (IN) through IN strand transfer inhibitors (INSTIs) represented a breakthrough in the treatment of HIV infection, establishing these antiretroviral regimens as first-line options against AIDS. However, the onset of drug-resistant strains has challenged the efficacy of INSTIs, demanding new efforts in the search for therapeutic tools that work through alternative modes of action. In this context, the discovery of allosteric IN inhibitors (ALLINIs) has highlighted new opportunities to target IN beyond its active site, enhancing antiviral efficacy and the genetic barrier to resistance. Extensive drug discovery campaigns have resulted in the development of effective ALLINIs with both in vitro and in vivo efficacy, two of which are advancing in clinical trials as next-generation therapeutic tools. Nevertheless, advancements in structural biology have critically aided in elucidating the underlying effects of ALLINIs, highlighting a complex, multimodal mode of action that ultimately yields defects in virion maturation. This review focuses on ALLINIs, providing a comprehensive overview of major drug discovery efforts devoted to this field, with an emphasis on the medicinal chemistry and structural biology findings that have revealed unprecedented opportunities for developing innovative and effective anti-HIV drugs.

The SARS-CoV-2 pandemic has posed a tremendous burden globally, highlighting the urgent need for new effective antivirals that are possibly useful against future emerging Coronaviruses (hCoVs). In this context, major efforts were focused on the inhibition of highly conserved and essential targets playing a pivotal role in viral replication. Among them, SARS-CoV-2 nsp13 stands out, being the most conserved enzyme within hCoVs. Following our previous reports describing the identification of indole-based diketo acid (DKA) derivatives as SARS-CoV-2 nsp13 inhibitors endowed with antiviral activity, we applied a scaffold hopping strategy to identify new nsp13 inhibitors. Therefore, we investigated a series of 4-phenyl pyrrolyl DKAs and their structural analogs characterized by molecular simplification or DKA isosteric replacement. The derivatives showed potency against both nsp13-associated activities exhibiting measurable IC50s in the low micromolar/submicromolar range, highlighting a promising dual inhibitory profile accordingly. Structure-activity relationship (SAR) studies were performed, highlighting the main structural features increasing the activity of the different compound classes. Interestingly, SAR trends were confirmed in the presence of the BSA/TCEP system despite variations in potency. To shed light on the interaction of the best acting compounds 13b, 15a, and 17d, docking studies were performed, suggesting a putative binding mode in agreement with our previous findings.

Protein disulfide isomerases (PDIs) play a key role for reduction, oxidation, and isomerization of disulfide bonds within the endoplasmic reticulum. Among them, PDIA1 and PDIA3 have been implicated in diverse pathologies, emerging as promising therapeutic targets. Starting from the scaffold of the known PDI inhibitor 16F16, new molecules were designed, synthesized, and tested against PDIA1 and PDIA3. Based on insulin turbidity and protein thermal shift assays, compounds 2a and 2b showed preferential PDIA1 inhibition, while 2c and 2e inhibited both PDIA1 and PDIA3. Comparative proteomic experiments revealed that both 16F16 and 2e primarily target the first highly conserved Cys-Gly-His-Cys motif in PDIA1, while mainly engaging non-catalytic cysteines in PDIA3. Molecular modeling confirmed thiol reactivity in PDIA1 and PDIA3 and identified binding modes to the most involved protein cysteines. On this basis, here we have reported novel potent PDI inhibitors derived from 16F16 and demonstrated a distinct cysteine modification profile in PDIA1 and PDIA3.

The SARS-CoV-2 pandemic highlighted the urgent need for antivirals targeting essential viral enzymes. Herein, we critically examine the current landscape of small molecule inhibitors targeting the highly conserved non-structural protein 12 (nsp12), the RNA-dependent RNA polymerase, and non-structural protein 13 (nsp13), the helicase, both critical for viral genome replication. Structural and mechanistic features that inform rational inhibitor design, including active sites and cofactor interactions, are discussed. For nsp12, nucleoside analogues derived from a drug repurposing strategy, as well as emerging non-nucleoside inhibitors targeting allosteric sites, are evaluated. Development of ATPase and helicase inhibitors for nsp13 is at an earlier stage, but promising scaffolds have been revealed through high-throughput and structure-based screening. An in-depth analysis of small molecule inhibitors from synthetic and natural sources is presented for both enzymes, highlighting key limitations and strategic directions to advance the development of next-generation antivirals against SARS-CoV-2 through targeted modulation of nsp12 and nsp13.

AIM:To evaluate the efficacy of two nitrofuran derivatives against biofilms formed by two strains of Histoplasma capsulatum and to study the toxicity of these compounds in alternative models: Caenorhabditis elegans, Galleria mellonella, and zebrafish. METHODS:The metabolic activity of biofilms was measured after treatment using the XTT reduction assay. Scanning electron microscopy (SEM) and confocal microscopy were used to observe damage to mature biofilms. Survival curves were generated for G. mellonella, while percentage survival was determined for C. elegans and zebrafish. RESULTS:The compounds showed efficacy against early and mature biofilms at concentrations equal to or up to two times higher than those required to eliminate planktonic fungal cells (3.90 to 31.25 μg/mL). Micrographs showed a reduction in metabolic activity, biofilm thickness, and extracellular matrix. In addition, the compounds showed little or no toxicity in alternative models, even at the highest concentrations tested. CONCLUSION:These results are promising for the development of new therapeutic alternatives, especially for species, such as H. capsulatum, which are recognized as high-priority pathogens. Few studies have investigated resistance and antifungal treatment targeting biofilms of this species, making this work a relevant contribution to future approaches.

COVID-19 pandemic stimulated tremendous efforts to develop therapeutic strategies targeting SARS-CoV-2, leading to the evaluation of a wide range of potential treatments in clinical trials. However, effective therapeutics remain elusive when the development of new variants and the limits of antiviral drugs is considered. Therefore, the development of antiviral drugs against SARS-CoV-2 is of paramount importance. Among potential drug targets, the SARS-CoV-2 nsp13 is highly attractive thanks to its pivotal role in viral replication. Pursuing our studies on the development of nsp13 inhibitors, in this work we describe the design, synthesis, and biological evaluation of novel inhibitors targeting SARS-CoV-2 nsp13. The newly designed N-benzyl indole derivatives were active against both enzymatic activities showing measurable IC50 under 30 μM concentration, while N-alkyl derivatives showed less promising results. Interestingly, the tested compounds blocked viral replication with no cytotoxicity. Docking studies predicted their binding into an allosteric conserved site located in the RecA2 domain.

Terminal deoxynucleotidyl transferase (TdT) is overexpressed in some cancer types, where it drives the mutagenic repair of double strand breaks through non canonical non-homologous end joining pathway. The TdT enzyme belongs to the X family of polymerases, together with the DNA polymerase λ (pol λ) and β (pol β). However, TdT exclusively displays template-independent nucleotide polymerisation. Pursuing our studies in developing TdT inhibitors, herein we deepened the structure-activity relationships of new structural analogues of our previously identified hit compounds. The diketo hexenoic acid derivatives here analysed showed high selectivity towards TdT and inhibition potencies spanning from the low micromolar range to the nanomolar. Docking studies highlighted the chemical features involved in the TdT binding, well contributing to the rationalisation of the structural requirements needed for the enzymatic inhibition.

It has been more than four years since the first report of SARS-CoV-2, the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, the scientific community is focused on vaccine development in an exceptionally rapid time frame, as well as the evaluation of a wide range of potential treatments in clinical trials, a few of which have also reached the market. However, these drugs are characterized by several limits (including low response to treatment in some patients, low effectiveness against the new variants, severe side effects, etc.), thus underscoring the need to speed up the research. Among potential antiviral targets, the SARS-CoV-2 nonstructural protein 13 (nsp13) is highly promising thanks to its pivotal role in viral replication. Pursuing the studies on the development of nsp13 inhibitors, herein, the design, synthesis, and biological evaluation of new SARS-CoV-2 nsp13 inhibitors are reported. In general, the newly designed dikehexenoic derivatives are proven active against both the enzymatic activities showing measurable IC50 under 30 mu M concentration, while the diketobutanoic series shows less promising results. Moreover, the tested compounds are capable of blocking viral replication without exerting cytotoxicity. Docking studies predict their binding into an allosteric pocket within the RecA2 domain.

The HIV-1 integrase (IN) plays a critical role in the viral lifecycle by integrating the viral DNA into the host chromosome. The catalytic function of IN has been exploited as a target, with five drugs acting as active site binders (IN strand transfer inhibitors, INSTIs). However, IN mutations conferring low-level resistance to INSTIs have been reported. Therefore, new IN inhibitors with different mechanisms of action are needed. The allosteric inhibition of IN, exerted by allosteric IN inhibitors (ALLINIs), is gaining interest. ALLINIs inhibit IN by inducing aberrant IN multimerization with different mechanisms. Furthermore, recent discoveries unveiled that IN has an under-studied yet equally vital second function. This involves IN binding to the RNA genome in virions, necessary for proper virion maturation. In this work, we describe a series of quinolinonyl derivatives as inhibitors of both the IN catalytic functions and IN-RNA interactions, which impair both early and late steps of viral replication.

Plasmodium, Leishmania, and Trypanosoma parasites are responsible for infectious diseases threatening millions of people worldwide. Despite more recent efforts devoted to the search for new antiprotozoal agents, efficacy, safety, and resistance issues still hinder the development of suited therapeutic options. The lack of robustly validated targets and the complexity of parasite’s diseases have made phenotypic screening a preferential drug discovery strategy for the identification of new chemical entities. However, via this approach, no information on biological target(s) and mechanisms of action of compounds are provided. Among the target deconvolution strategies useful to fill this gap, photoaffinity labeling (PAL) has emerged as one of most suited to enable investigation in a complex cellular environment. More recently, PAL has been exploited to unravel the molecular basis of bioactive compounds’ function in live parasites, allowing elucidation of the mechanism of action of both approved drugs and new chemical entities. Besides highlighting new potential drug targets, PAL can provide valuable information on efficacy and liabilities of small molecules at the molecular level, which could be exploited to greatly facilitate the rational optimization of compounds in terms of potency and safety. In this review, we will report the most recent studies that have leveraged PAL to disclose the biological targets and mechanism of action of phenotypically active compounds targeting kinetoplastid diseases (i.e., human African trypanosomiasis, leishmaniasis, and Chagas disease) and malaria. Moreover, we will comment on potential perspectives that this innovative approach can provide in aiding the discovery and development of new antiprotozoal drugs.

It has been more than four years since the first report of SARS-CoV-2, and humankind has experienced a pandemic with an unprecedented impact. Moreover, the new variants have made the situation even worse. Among viral enzymes, the SARS-CoV-2 main protease (Mpro) has been deemed a promising drug target vs. COVID-19. Indeed, Mpro is a pivotal enzyme for viral replication, and it is highly conserved within coronaviruses. It showed a high extent of conservation of the protease residues essential to the enzymatic activity, emphasizing its potential as a drug target to develop wide-spectrum antiviral agents effective not only vs. SARS-CoV-2 variants but also against other coronaviruses. Even though the FDA-approved drug nirmatrelvir, a Mpro inhibitor, has boosted the antiviral therapy for the treatment of COVID-19, the drug shows several drawbacks that hinder its clinical application. Herein, we report the synthesis of new thiazolidine-4-one derivatives endowed with inhibitory potencies in the micromolar range against SARS-CoV-2 Mpro. In silico studies shed light on the key structural requirements responsible for binding to highly conserved enzymatic residues, showing that the thiazolidinone core acts as a mimetic of the Gln amino acid of the natural substrate and the central role of the nitro-substituted aromatic portion in establishing π-π stacking interactions with the catalytic His-41 residue.

Over the last decades, bacterial resistance has become one of the emerging health threats. Particularly dangerous are bacterial strains resistant to various antibacterial drugs. Herein, we modified graphene quantum dots (GQDs) to produce efficient photo-induced antibacterial agents. GQDs were modified with (a) ethylene-diamine (EDA), (b) with EDA and gold nanoparticles (AuNPs), and (c) 3-amino-1,2,4-triazole (TA) using carbodiimide coupling. Photo-induced antibacterial activity of modified GQDs was tested against 8 bacterial strains. Treatment with modified GQDs and blue light (wavelength of 470 nm) resulted in remarkable antibacterial activity with minimal inhibitory concentrations (MIC) of 7.81 mu g mL(-1) for K. pneumoniae and S. aureus and 3.9 mu g mL(-1) against MRSA and E. faecalis. Planar organization of GQDs functionalized with AuNPs allowed direct access of molecular oxygen to AuNPs leading to more efficient O-1(2) production as well as the O-1(2) production from excited GQDs. Thus, GQDs functionalized with AuNPs showed outstanding efficiency in the battle against several bacterial strains, particularly those that lead to nosocomial infections.

Background: As a result of the paucity of treatment, Leishmaniasis continues to provoke about 60,000 deaths every year worldwide. New molecules are needed, and drug discovery research is oriented toward targeting proteins crucial for parasite survival. Among them, trypanothione reductase (TR) is of remarkable interest owing to its vital role in Leishmania species protozoan parasite life. Our previously identified compound 1 is a novel chemotype endowed with a unique mode of TR inhibition thanks to its binding to a formerly unknown but druggable site at the entrance of the NADPH binding cavity, absent in human glutathione reductase (hGR). Methods: We designed and synthesized new 3-amino-1-arylpropan-1-one derivatives structurally related to compound 1 and evaluated their potential inhibition activity on TR from Leishmania infantum (LiTR). Cluster docking was performed to assess the binding poses of the compounds. Results: The newly synthesized compounds were screened at a concentration of 100 μM in in vitro assays and all of them proved to be active with residual activity percentages lower than 75%. Conclusions: Compounds 2a and 2b were the most potent inhibitors found, suggesting that an additional aromatic ring might be promising for enzymatic inhibition. Further structure–activity relationships are needed to optimize our compounds activity.

Solid tumors are active tissues containing hypoxic regions and producing metabolic acids. By decreasing pH, cancer cells create a hostile environment for surrounding host cells and foster tumor growth and progression. By governing acid/base regulation, carbonic anhydrases (CAs) are involved in several physiological/pathological processes, including tumors. Indeed, CAs are clinically relevant in cancer therapy as among the fifteen human isoforms, two of them, namely CA IX (overexpressed in solid tumors and associated with increased metastasis and poor prognosis) and CA XII (overexpressed in some tumors) are involved in tumorigenesis. Targeting these two isoforms is considered as a pertinent approach to develop new cancer therapeutics. Several CA inhibitors (CAIs) have been described, even though they are unselective inhibitors of different isoforms. Thus, efforts are needed to find new selective CAIs. In this work, we described new diketo acid derivatives as CAIs, with the best acting compounds 1c and 5 as nanomolar inhibitors of CA IX and XII, being also two orders of magnitude selective over CAs I and II. Molecular modeling studies showed the different binding poses of the best acting CAIs within CA II and IX, highlighting the key structural features that could confer the ability to establish specific interactions within the enzymes. In different tumor cell lines overexpressing CA IX and XII, the tested compounds showed antiproliferative activity already at 24 h treatment, with no effects on somatic not transformed cells.

For RNA viruses, RNA helicases have long been recognized to play critical roles during virus replication cycles, facilitating proper folding and replication of viral RNAs, therefore representing an ideal target for drug discovery. SARS-CoV-2 helicase, the non-structural protein 13 (nsp13) is a highly conserved protein among all known coronaviruses, and, at the moment, is one of the most explored viral targets to identify new possible antiviral agents. In the present study, we present six diketo acids (DKAs) as nsp13 inhibitors able to block both SARS-CoV-2 nsp13 enzymatic functions. Among them four compounds were able to inhibit viral replication in the low micromolar range, being active also on other human coronaviruses such as HCoV229E and MERS CoV. The experimental investigation of the binding mode revealed ATP-non-competitive kinetics of inhibition, not affected by substrate-displacement effect, suggesting an allosteric binding mode that was further supported by molecular modelling calculations predicting the binding into an allosteric conserved site located in the RecA2 domain.

There are diverse methods to extract cannabinoids from Cannabis, including conventional and advanced techniques. In selecting the proper method, several parameters have to be considered, mainly solvents, time of extraction, temperature, pressure, size of the plant material, and matrix/solvents ratio. Basing on the current literature, the use of organic solvents is the most convenient method for cannabis extraction. Among the conventional methods, Soxhlet extraction and dynamic maceration gave the best results, even though these techniques are time-consuming and with harmful environmental impact, furnishing also low yields and low quality of extracts. For this reason, several advanced techniques have been developed, including pressurized liquid extraction, ultrasound-assisted extraction, supercritical fluid extraction, microwave-assisted extraction, enzyme-assisted extraction, pulsed electric field treatment. These are characterized by shorter extraction times, lower amounts of solvent needed, the possibility to work at lower temperatures, and higher adaptability to automation, being therefore more green and sustainable methods.

Developing drugs for brain infection by Naegleria fowleri is an unmet medical need. We used a combination of cheminformatics, target-, and phenotypic-based drug discovery methods to identify inhibitors that target an essential N. fowleri enzyme, sterol 14-demethylase (NfCYP51). A total of 124 compounds preselected in silico were tested against N. fowleri. Nine primary hits with EC50 ≤ 10 μM were phenotypically identified. Cocrystallization with NfCYP51 focused attention on one primary hit, miconazole-like compound 2a. The S-enantiomer of 2a produced a 1.74 Å cocrystal structure. A set of analogues was then synthesized and evaluated to confirm the superiority of the S-configuration over the R-configuration and the advantage of an ether linkage over an ester linkage. The two compounds, S-8b and S-9b, had an improved EC50 and KD compared to 2a. Importantly, both were readily taken up into the brain. The brain-to-plasma distribution coefficient of S-9b was 1.02 ± 0.12, suggesting further evaluation as a lead for primary amoebic meningoencephalitis.

Plants have been known since ancient times for their healing properties, being used as preparations against human diseases of different etiologies. More recently, natural products have been studied and characterized, isolating the phytochemicals responsible for their bioactivity. Most certainly, there are currently numerous active compounds extracted from plants and used as drugs, dietary supplements, or sources of bioactive molecules that are useful in modern drug discovery. Furthermore, phytotherapeutics can modulate the clinical effects of co-administered conventional drugs. In the last few decades, the interest has increased even more in studying the positive synergistic effects between plant-derived bioactives and conventional drugs. Indeed, synergism is a process where multiple compounds act together to exert a merged effect that is greater than that of each of them summed together. The synergistic effects between phytotherapeutics and conventional drugs have been described in different therapeutic areas, and many drugs are based on synergistic interactions with plant derivatives. Among them, caffeine has shown positive synergistic effects with different conventional drugs. Indeed, in addition to their multiple pharmacological activities, a growing body of evidence highlights the synergistic effects of caffeine with different conventional drugs in various therapeutic fields. This review aims to provide an overview of the synergistic therapeutic effects of caffeine and conventional drugs, summarizing the progress reported to date.

BACKGROUND:Heparanase (HPSE) is an endo-β-glucuronidase that cleaves heparan sulfate side chains, leading to the disassembly of the extracellular matrix, facilitating cell invasion and metastasis dissemination. In this research, we investigated the role of a new HPSE inhibitor, RDS 3337, in the regulation of the autophagic process and the balance between apoptosis and autophagy in U87 glioblastoma cells.METHODS:After treatment with RDS 3337, cell lysates were analyzed for autophagy and apoptosis-related proteins by Western blot.RESULTS:We observed, firstly, that LC3II expression increased in U87 cells incubated with RDS 3337, together with a significant increase of p62/SQSTM1 levels, indicating that RDS 3337 could act through the inhibition of autophagic-lysosomal flux of LC3-II, thereby leading to accumulation of lipidated LC3-II form. Conversely, the suppression of autophagic flux could activate apoptosis mechanisms, as revealed by the activation of caspase 3, the increased level of cleaved Parp1, and DNA fragmentation.CONCLUSIONS:These findings support the notion that HPSE promotes autophagy, providing evidence that RDS 3337 blocks autophagic flux. It indicates a role for HPSE inhibitors in the balance between apoptosis and autophagy in U87 human glioblastoma cells, suggesting a potential role for this new class of compounds in the control of tumor growth progression.