Drug Design Strategies Research Articles

Fluorescence theranostic PROTACs for real-time visualization of ERα degradation

Proteolysis targeting chimera (PROTAC) technology, a groundbreaking strategy for degradation of pathogenic proteins by hijacking of the ubiquitin-proteasome-system has become a promising strategy in drug design. However, the real-time monitoring and visualization of protein degradation processes have been long-standing challenges in the realm of drug development. In this research, we sought to amalgamate the highly efficient protein-degrading capabilities of PROTAC technology with the visualization attributes of fluorescent probes, with the potential to pave the path for the design and development of a novel class of visual PROTACs. These novel PROTACs uniquely possess both fluorescence imaging and therapeutic characteristics, all with the goal of enabling real-time observations of protein degradation processes. Our approach involved the utilization of a high ER-targeting fluorescent probe, previously reported in our laboratory, which served as a warhead that specifically binds to the protein of interest (POI). Additionally, a VHL ligand for recruiting E3 ligase and linkers of various lengths were incorporated to synthesize a series of novel ER-inherent fluorescence PROTACs. Among them, compound A3 demonstrated remarkable efficiency in degrading ERα proteins (DC50 = 0.12 μM) and displaying exceptional anti-proliferative activity against MCF-7 cells (IC50 = 0.051 μM). Furthermore, it exhibited impressive fluorescence imaging performance, boasting an emission wavelength of up to 582 nm, a Stokes shift of 116 nm, and consistent optical properties. These attributes make it especially suitable for the real-time, in situ tracking of ERα protein degradation processes, thus may serve as a privileged visual theranostic PROTAC for ERα+ breast cancer. This study not only broadens the application spectrum of PROTAC technology but also introduces a novel approach for real-time visualization of protein degradation processes, ultimately enhancing the diagnostic and treatment efficacy of PROTACs.

Drug Design Strategies, Modes of Action, Synthesis and Industrial Challenges Behind Trifluoromethylated New Chemical Entities

Medicinal plants have been an inspiration source for developing new chemical entities, providing diverse chemical structures and modes of action for medicinal chemistry strategies. Modern medicinal chemistry approaches promote functional group changes to improve NCE’s biological activity. Incorporating the trifluoromethyl (-CF3) group into organic compounds is crucial in modern drug design. It may affect the compound's lipophilicity, solubility, stability, molecular conformation, and pKa, changes that may lead to the discovery of new medicines to treat diseases of our times. For this reason, this chemical transformation is currently a hot topic in the organic chemistry field. Chemists are competing to develop better methods to carry out this transformation efficiently, less hazardously, and cost-effectively. The high number of annual scientific publications on trifluoromethylation evidences the competition. This review profiles 21 trifluoromethylated New Chemical Entities (NCE) selected in December 2020 from the GlobalData database, mainly in late stages of clinical trials (Phase II and III) or already in the commercial phase, containing one or two -CF3 groups in para or meta positions of benzene, or a pyridine ring. Synthetic approaches, therapeutic applications, and manufacturing industrial challenges are provided.

Structure-property Relationships Reported for the New Drugs Approved in 2022.

The structure-property relationship illustrates how modifying the chemical structure of a pharmaceutical compound influences its absorption, distribution, metabolism, excretion, and other related properties. Understanding structure-property relationships of clinically approved drugs could provide useful information for drug design and optimization strategies. Among new drugs approved around the world in 2022, including 37 in the US, structure- property relationships of seven drugs were compiled from medicinal chemistry literature, in which detailed pharmacokinetic and/or physicochemical properties were disclosed not only for the final drug but also for its key analogues generated during drug development. The discovery campaigns for these seven drugs demonstrate extensive design and optimization efforts to identify suitable candidates for clinical development. Several strategies have been successfully employed, such as attaching a solubilizing group, bioisosteric replacement, and deuterium incorporation, resulting in new compounds with enhanced physicochemical and pharmacokinetic properties. The structure-property relationships hereby summarized illustrate how proper structural modifications could successfully improve the overall drug-like properties. The structure-property relationships of clinically approved drugs are expected to continue to provide valuable references and guides for the development of future drugs.

Metal complexes bearing EGFR-inhibiting ligands as promising anticancer agents.

Overexpression of the epidermal growth factor receptor (EGFR, erbB1) has been observed in a wide range of solid tumors and has frequently been associated with poor prognosis. As a result, EGFR inhibition has become an attractive anticancer drug design strategy, and a large number of small molecular inhibitors have been developed. Despite the widespread clinical use of EGFR tyrosine kinase inhibitors (TKIs), their drug resistance, inadequate accumulation in tumors, and severe side effects have spurred the search for better antitumor drugs. Metal complexes have attracted much attention because of their different mechanisms compared with EGFR-TKIs. Therefore, the combination of metals and inhibitors is a promising anticancer strategy. For example, Ru and Pt centers are introduced to design complexes with double or multiple targets, while Au complexes are combined with inhibitors to overcome drug resistance. Co complexes are designed as prodrugs with weak side effects and enhanced targeting by the hypoxia activation strategy, and other metals such as Rh and Fe enhance the anticancer effect of the complexes. In addition, the introduction of Ga center is beneficial to the development of nuclear imaging tracers. In this paper, metal EGFR-TKI complexes in the last 15 years are reviewed, their mechanisms are briefly introduced, and their advantages are summarized.

Penambatan Molekul Senyawa Swietemacrophyllanin dari Kulit Batang Mahoni (Swietenia macrophylla King,) sebagai Inhibitor Enzim Alfa Glukosidase

Mahogany (Swietenia macrophylla King.) is one of the plants used as an antidiabetic agent. 96% ethanol extract of S. macrophylla stem bark can inhibit the α-glucosidase enzyme. Methanol and aqueous extracts of S. macrophylla stem bark can reduce rat blood glucose levels induced by streptozotocin. Molecular docking is one of the most widely used structural-based drug design strategies due to its wide application in the analysis of binding energy and molecular interactions between drug compounds and receptors. This study aims to identify the compounds in the stem bark of S. macrophylla and analyze the molecular anchoring of the compounds produced by the aid. The research was carried out by means of the water fraction of the stem bark of S. macrophylla and was purified by column chromatography. Fraction 2 was identified by LCMS-MS. Molecular docking using AutoDock 4.2.6. The results of Fraction 2 showed the presence of catechins, evodionol, swietemacrophyllanin, swietenitin K and β-sitosterol. The results of an in-silico study showed that swietemacrophyllanin provided a better affinity than acarbose with a binding energy value of -8.57 kcal/mol and an inhibition constant of 0.52 µM. Forms hydrogen bonds with catalytic residues (Glu277 and Asp352) from the active site of the α-glucosidase enzyme. Swietemacrophyllanin has potential as an antidiabetic agent

Viruses traverse the human proteome through peptide interfaces that can be biomimetically leveraged for drug discovery

We present a drug design strategy based on structural knowledge of protein-protein interfaces selected through virus-host coevolution and translated into highly potential small molecules. This approach is grounded on Vinland, the most comprehensive atlas of virus-human protein-protein interactions with annotation of interacting domains. From this inspiration, we identified small viral protein domains responsible for interaction with human proteins. These peptides form a library of new chemical entities used to screen for replication modulators of several pathogens. As a proof of concept, a peptide from a KSHV protein, identified as an inhibitor of influenza virus replication, was translated into a small molecule series with low nanomolar antiviral activity. By targeting the NEET proteins, these molecules turn out to be of therapeutic interest in a nonalcoholic steatohepatitis mouse model with kidney lesions. This study provides a biomimetic framework to design original chemistries targeting cellular proteins, with indications going far beyond infectious diseases.

Discovery of N-(1-(6-Oxo-1,6-dihydropyrimidine)-pyrazole) Acetamide Derivatives as Novel Noncovalent DprE1 Inhibitors against Mycobacterium tuberculosis.

Decaprenylphosphoryl-β-d-ribose oxidase (DprE1) is a promising target for treating tuberculosis (TB). Currently, most novel DprE1 inhibitors are discovered through high-throughput screening, while computer-aided drug design (CADD) strategies are expected to promote the discovery process. In this study, with the aid of structure-based virtual screening and computationally guided design, a series of novel scaffold N-(1-(6-oxo-1,6-dihydropyrimidine)-pyrazole) acetamide derivatives with significant antimycobacterial activities were identified. Among them, compounds LK-60 and LK-75 are capable of effectively suppressing the proliferation of Mtb with MICMtb values of 0.78-1.56 μM, comparable with isoniazid and much superior to the phase II candidate TBA-7371 (MICMtb = 12.5 μM). LK-60 is also the most active DprE1 inhibitor derived from CADD so far. Further studies confirmed their high affinity to DprE1, good safety profiles to gut microbiota and human cells, and synergy effects with either rifampicin or ethambutol, indicating their broad potential for clinical applications.

Matrix metalloproteinase-8 (MMP-8) and its inhibitors: A minireview

The type-II collagenase, also known as matrix metalloproteinase-8 (MMP-8) plays a vital role in a variety of physiological illnesses namely cardiovascular, musculoskeletal, renal, digestive, and respiratory ailments including cancer. However, numerous novel compounds with effective MMP-8 inhibitory activity have been created by research and academic institutions, pharmaceutical companies, and both. Sadly, despite showing promising results, these compounds have a variety of negative side effects. In this context, a number of MMP-8 inhibitors having potential inhibitory activity with different key structural features such as hydroxamates, carboxylic acid, thiol and mercaptosulfide, phosphonate, and pyrimidine-2,4,6-trione have been discussed. Additionally, various ligand-based and structure-based drug designs that have been previously conducted on a variety of MMP-8 inhibitors have been thoroughly reviewed and that can offer important information regarding the development of novel MMP-8 inhibitors in the future. Therefore, the detailed knowledge about the key structural features of the existing MMP-8 inhibitors can be found, and further with the help of drug design strategies, a novel class of collagenase inhibitors may be identified. In light of this, this work may be beneficial for researchers looking into the processes involved in developing and identifying new potential and promising MMP-8 inhibitors.

Functional implications of unusual NOS and SONOS covalent linkages found in proteins.

The tertiary and quaternary structures of many proteins are stabilized by strong covalent forces, of which disulfide bonds are the most well known. A new type of intramolecular and intermolecular covalent bond has been recently reported, consisting of the Lys and Cys side-chains linked by an oxygen atom (NOS). These post-translational modifications are widely distributed amongst proteins, and are formed under oxidative conditions. Similar linkages are observed during antibiotic biosynthesis, where hydroxylamine intermediates are tethered to the sulfur of enzyme active site Cys residues. These linkages open the way to understanding protein structure and function, give new insights into enzyme catalysis and natural product biosynthesis, and offer new strategies for drug design.

Quinoline-based tetrazolium prochelators: formazan release, iron sequestration, and antiproliferative efficacy in cancer cells.

Iron-binding strategies in anticancer drug design target the key role of iron in cancer growth. The incorporation of a quinoline moiety in the design of tetrazolium-based prochelators facilitates their intracellular reduction/activation to iron-binding formazans. The new prochelators are antiproliferative at submicromolar levels, induce apoptosis and cell cycle arrest, and impact iron signaling in cancer cells.

A machine learning method for predicting the IC50 values of novel designed analogs of Non-Nucleoside Reverse-Transcriptase Inhibitors (NNRTIs) as potentially safer drugs

It is estimated that over four decades since the onset of the AIDS epidemic, a significant number of individuals have been impacted by HIV-1 infection. The latest data shows that 165,000 children were among the 1.5 million people who contracted HIV in 2022. Additionally, it is projected that about 655,000 people will die from AIDS-related illnesses in 2023. Scientists have been working on different methodologies to improve the pharmacological properties of drugs, one of which is rational drug design. To build a robust machine-learning model, this study used computer-aided drug design and virtual screening strategies based on ligand and structure. This allowed us to select the best scaffold for modifying the core of nevirapine. Based on this screening, forty analogs were built, and the prediction of IC50, affinity, and toxicity was performed. The study found that changes should be made to the activated pyridine ring, specifically in the alpha position to the pyridine nitrogen.Moreover, the substitution with the best in silico values was the meta substitution in the carbocyclic ring. It was suggested that these substituents can be either electro-donating or electron-withdrawing groups. This QSAR-SBDD analysis provides a roadmap for synthesizing novel NNRTIs with improved pharmacological profiles.

The synthesis and bioactivities of ROCK2 inhibitors with 1,2-dithiolan-3-yl motif.

Rho-associated coiled-coil containing kinase (ROCK) plays an important role in inflammation. Herein, a series of compounds were designed and synthesized as ROCK inhibitors based on the structure-based drug design (SBDD) strategy and were evaluated for cytotoxicity, antioxidant activity and anti-inflammatory activity. Among them, compound DC24 was identified as the optimal hit in enzymatic screening with an IC50 value of 0.124 μM against ROCK2 and 50-fold selectivity over ROCK1. DC24 has a novel lipid amide scaffold with a bis(4-fluorophenyl)methyl substituent, and DC24 is the first ROCK2 inhibitor interacting with the hinge region of ROCK2 via the 1,2-dithiolan-3-yl motif, which has been confirmed by the binding model of DC24 with ROCK2. In a complete Freund's adjuvant (CFA) induced acute inflammation model, DC24 at a dose of 5 mg kg-1 exhibited an anti-inflammatory effect better than that of belumosudil. Furthermore, DC24 exhibits good safety in vivo.

Sulfonamide inhibitors of bacterial carbonic anhydrases.

The increasing prevalence of antibiotic-resistant bacteria necessitates the exploration of novel therapeutic targets. Bacterial carbonic anhydrases (CAs) have been known for decades, but only in the past ten years they have garnered significant interest as drug targets to develop antibiotics having a diverse mechanism of action compared to the clinically used drugs. Significant progress has been made in the field in the past three years, with the validation in vivo of CAs from Neisseria gonorrhoeae, and vancomycin-resistant enterococci as antibiotic targets. This chapter compiles the state-of-the-art research on sulfonamide derivatives described as inhibitors of all known bacterial CAs. A section delves into the mechanisms of action of sulfonamide compounds with the CA classes identified in pathogenic bacteria, specifically α, β, and γ classes. Therefore, the inhibitory profiling of the bacterial CAs with classical and clinically used sulfonamide compounds is reported and analyzed. Another section covers various other series of sulfonamide CA inhibitors studied for the development of new antibiotics. By synthesizing current research findings, this chapter highlights the potential of sulfonamide inhibitors as a novel class of antibacterial agents and paves the way for future drug design strategies.

Designing novel anti-plasmodial quinoline-furanone hybrids: computational insights, synthesis, and biological evaluation targeting Plasmodium falciparum lactate dehydrogenase.

To combat resistance against current antimalarials, modifying key pharmacophores and exploring novel parasite-specific drug targets remained one of the key drug design strategies. The resistance to quinoline-based antimalarials arises often due to the efflux of the drug. Hence, the development of newer agents containing bulkier pharmacophores will enable medicinal chemists to counteract drug resistance. In view of this, herein we designed bulkier quinoline-furanone hybrids. Initially, virtual drug-likeness and ADMET screening were conducted to optimize physicochemical properties followed by docking of the hybrids against the Plasmodium falciparum lactate dehydrogenase (PfLDH) enzyme. The most potent hybrids that emerged from the computational screening were synthesized and screened for their bioactivity against the resistant strain of Plasmodium through Schizont Maturation Inhibition assays. Among the compounds tested, 5g and 6e demonstrated the best activity, with IC50 values similar to chloroquine (CQ), and 5g exhibited superior LDH inhibition compared to CQ. Compounds 5f, 7a, and 7f showed IC50 values comparable to CQ and moderate LDH inhibition. Structure-activity relationship (SAR) analysis revealed that halogen substitutions, particularly Br and Cl, enhanced antimalarial activity, while strong electron-withdrawing (-NO2) or -donating (-OH) groups led to diminished activity. Additionally, bulkier aromatic substitutions were favoured for antimalarial activity and LDH inhibition. The investigation successfully found potent anti-plasmodial quinoline-furanone hybrids, demonstrating promising prospects for combating malaria.

Conformational flexibility driving charge-selective substrate translocation across a bacterial transporter.

Bacterial membrane porins facilitate the translocation of small molecules while restricting large molecules, and this mechanism remains elusive at the molecular level. Here, we investigate the selective uptake of large cyclic sugars across an unusual passive membrane transporter, CymA, comprising a charged zone and a constricting N terminus segment. Using a combination of electrical recordings, protein mutagenesis and molecular dynamics simulations, we establish substrate translocation across CymA governed by the electrostatic pore properties and conformational dynamics of the constriction segment. Notably, we show that the variation in pH of the environment resulted in reversible modulation of the substrate binding site in the pore, thereby regulating charge-selective transport of cationic, anionic and neutral cyclic sugars. The quantitative kinetics of cyclic sugar translocation across CymA obtained in electrical recordings at different pHs are comparable with molecular dynamics simulations that revealed the transport pathway, energetics and favorable affinity sites in the pore for substrate binding. We further define the molecular basis of cyclic sugar translocation and establish that the constriction segment is flexible and can reside inside or outside the pore, regulating substrate translocation distinct from the ligand-gated transport mechanism. Our study provides novel insights into energy-independent large molecular membrane transport for targeted drug design strategies.

Computational Drug Design Strategies for Fighting the COVID-19 Pandemic.

The advent of COVID-19 has brought the use of computer tools to the fore in health research. In recent years, computational methods have proven to be highly effective in a variety of areas, including genomic surveillance, host range prediction, drug target identification, and vaccine development. They were also instrumental in identifying new antiviral compounds and repurposing existing therapeutics to treat COVID-19. Using computational approaches, researchers have made significant advances in understanding the molecular mechanisms of COVID-19 and have developed several promising drug candidates and vaccines. This chapter highlights the critical importance of computational drug design strategies in elucidating various aspects of COVID-19 and their contribution to advancing global drug design efforts during the pandemic. Ultimately, the use of computing tools will continue to play an essential role in health research, enabling researchers to develop innovative solutions to combat new and emerging diseases.

Screening of efficient salicylaldoxime reactivators for DFP and paraoxon-inhibited acetylcholinesterase.

Previously we reported two salicylaldoxime conjugates (L7R3 and L7R5) showing equal or even higher reactivating efficiency for both organophosphorus nerve agent and pesticide inhibited acetylcholinesterase in comparison to obidoxime and HI-6. In this study, L7R3 and L7R5 were selected as lead compounds and refined by employing a fragment-based drug design strategy, and a total of 32 novel salicylaldoxime conjugates were constructed and screened for DFP and paraoxon inhibited acetylcholinesterase. The findings demonstrate that the conjugate L73R3, which contains a 4-nitrophenyl group, exhibited a higher reactivation efficacy against paraoxon-inhibited acetylcholinesterase compared to obidoxime and HI-6. It was confirmed that the combination of a 4-pyridinyl or 4-nitrophenyl peripheral site ligand, a piperazine linker and a methyl or chloro-substituted salicylaldoxime could construct efficient nonquaternary oxime reactivators. The results hold promise for developing a new generation of highly effective antidotes for organophosphate poisoning.

Development, biological evaluation, and molecular modelling of some benzene-sulfonamide derivatives as protein tyrosine phosphatase-1B inhibitors for managing diabetes mellitus and associated metabolic disorders.

Exploring new inhibitors with good bioavailability and high selectivity for managing type 2 diabetes mellitus (T2DM) and its associated complications is a major challenge for research, academia, and the pharmaceutical industry. Protein tyrosine phosphatase-1B (PTP1B) arose as an important negative regulator in insulin signaling pathways associated with metabolic disorders, including T2DM and obesity. Novel neutral compounds with a benzene-sulfonamide scaffold were designed and synthesized based on structural- and ligand-based drug design strategies for fragment growth. Promising hits against PTP1B were identified through in vitro enzymology inhibition assay. Mechanistic aspects of the compound's different inhibition activities were rigorously investigated through molecular docking coupled with explicit dynamics simulations. Four identified hits, 3c, 8, 10a, and 11, with sub-micromolar PTP-1B IC50 and significant predicted pharmacokinetic and pharmacodynamic parameters, were further biologically evaluated for their anti-diabetic, anti-obesity, anti-inflammatory, and anti-oxidant effects in a high-fat diet (HFD) + streptozotocin (STZ)-induced T2DM rat model. All these hit compounds exhibited a significant anti-diabetic and anti-obesity effect and a significant efficacy in reducing oxidative stress and increasing anti-oxidant enzymes while reducing inflammatory markers. Improving compound potency was further highlighted by improving the pharmacokinetic profile of the most active compound, 10a, through nano formulation. Compound 10a nano formulation showed the most promising anti-diabetic and anti-obesity effects and a remarkable histopathological improvement in all organs studied.

Pre-formulation of an additive combination of two antimicrobial agents, clofazimine and nisin A, to boost antimicrobial activity.

According to the World Health Organization, antimicrobial resistance is one of the top ten issues that pose a major threat to humanity. The lack of investment by the pharmaceutical industry has meant fewer novel antimicrobial agents are in development, exacerbating the problem. Emerging drug design strategies are exploring the repurposing of existing drugs and the utilization of novel drug candidates, like antimicrobial peptides, to combat drug resistance. This proactive approach is crucial in fighting global health threats. In this study, an additive combination of a repurposed anti-leprosy drug, clofazimine, and an antimicrobial peptide, nisin A, are preformulated using liquid antisolvent precipitation to generate a stable amorphous, ionized nanoparticle system to boost antimicrobial activity. The nanotechnology aims to improve the physicochemical properties of the inherently poorly water-soluble clofazimine molecules while also harnessing the previously unreported additive effect of clofazimine and nisin A. The approach transformed clofazimine into a more water-soluble salt, yielding amorphous nanoparticles stabilized by the antimicrobial peptide; and combined the two drugs into a more soluble and more active formulation. Blending pre-formulation strategies like amorphization, salt formation, and nanosizing to improve the inherent low aqueous solubility of drugs can open many new possibilities for the design of new antimicrobial agents. This fusion of pre-formulation technologies in combination with the multi-hurdle approach of selecting drugs with different effects on microbes could be key in the design platform of new antibiotics in the fight against antimicrobial resistance.

Novel computational and drug design strategies for the inhibition of human T-cell leukemia virus 1-associated lymphoma by Astilbin derivatives

Human T-cell leukemia virus 1 (HTLV-1) associated lymphoma is a devastating malignancy triggered by HTLV-1 infections. We employeda comprehensive drug design and computational strategy in this work to explore the inhibitory activitiesof Astilbin derivatives against HTLV-1-associated lymphoma. We evaluated the stability, binding affinities, and various computational analysis of Astilbin derivatives against target proteins, such as HTLV-1 main protease and HTLV-1 capsid protein. The root mean square deviation (RMSD), root mean square fluctuation, radius of gyration, hydrogen bond analysis, principal component analysis (PCA) and dynamic cross-correlation matrix (DCCM) were applied to characterize these protein–ligand interactions further. Ligand-03 and ligand-04 exhibited notable binding affinity to HTLV-1 capsid protein, while ligand-05 displayed high binding affinity to HTLV-1 protease. MD simulation analysis revealed that ligand-03, bound to HTLV-1 capsid protein, demonstrated enhanced stability with lower RMSD values and fewer conformational changes, suggesting a promising binding orientation. Ligand-04, despite stable binding, exhibited increased structural deviations, making it less suitable. Ligand-05 demonstrated stable binding to HTLV-1 protease throughout the simulation period at 100 nanoseconds. Hydrogen bond analysis indicated that ligand-05 formed persistent hydrogen bonds with significantresidues, contributing to its stability. PCA highlighted ligand-03's more remarkable conformational changes, while DCCM showed ligand-05's distinct dynamics, indicating its different behavior in the complex. Furthermore, binding free energy calculations supported the favorable interactions of ligand-03 and ligand-04 with HTLV-1 capsid protein, while ligand-05 showed weaker interactions with HTLV-1 protease. Molecular electrostatic potential and frontier molecular orbital analyses provided insights into these compounds’ charge distribution and stability. In conclusion, this research found Astilbin derivatives as potential inhibitors of HTLV-1-associated lymphoma. Future attempts at drug development will benefit from the steady interaction landscape provided by Ligand-03, Ligand-04 and Ligand-05, which showed the most attractive binding profile with the target protein. These results open up new opportunities for innovative drug development, and more experimental testing should be done between Astilbin derivatives and HTLV-1-associated lymphoma. Communicated by Ramaswamy H. Sarma