Medicinal Chemistry Design Research Articles

Asymmetric Total Synthesis of (-)-Phaeocaulisin A.

The therapeutic properties of Curcuma (ginger and turmeric’s family) have long been known in traditional medicine. However, only recently have guaiane-type sesquiterpenes extracted from Curcuma phaeocaulis been submitted to biological testing, and their enhanced bioactivity was highlighted. Among these compounds, phaeocaulisin A has shown remarkable anti-inflammatory and anticancer activity, which appears to be tied to the unique bridged acetal moiety embedded in its tetracyclic framework. Prompted by the promising biological profile of phaeocaulisin A and by the absence of a synthetic route for its provision, we have implemented the first enantioselective total synthesis of phaeocaulisin A in 17 steps with 2% overall yield. Our route design builds on the identification of an enantioenriched lactone intermediate, tailored with both a ketone moiety and a conjugated alkene system. Taking advantage of the umpolung carbonyl-olefin coupling reactivity enabled by the archetypal single-electron transfer (SET) reductant samarium diiodide (SmI2), the lactone intermediate was submitted to two sequential SmI2-mediated cyclizations to stereoselectively construct the polycyclic core of the natural product. Crucially, by exploiting the innate inner-sphere nature of carbonyl reduction using SmI2, we have used a steric blocking strategy to render sites SET-unreceptive and thus achieve chemoselective reduction in a complex substrate. Our asymmetric route enabled elucidation of the naturally occurring isomer of phaeocaulisin A and provides a synthetic platform to access other guaiane-type sesquiterpenes from C. phaeocaulis—as well as their synthetic derivatives—for medicinal chemistry and drug design.

Systematic identification of activity cliffs with dual-atom replacements and their rationalization on the basis of single-atom replacement analogs and X-ray structures.

Very small chemical changes in active compounds causing large potency effects are of particular interest in medicinal chemistry and drug design. We have systematically searched active compounds with available high-confidence activity data for pairs of structural analogs with dual-atom replacements and additional analogs with corresponding single-atom replacements. From ~287,000 unique qualifying compounds with activity against nearly 1900 unique targets, ~3500 target-based analog pairs with dual-atom replacements were identified. These included 852 pairs with significant differences in compound potency, representing a set of previously unobserved activity cliffs. Comparing these pairs with corresponding single-atom replacement analogs, which were frequently identified, made it possible to systematically analyze how potency changes propagated from single- to dual-atom replacements. The analysis uncovered different potency effects and revealed that individual atom replacements were often decisive for activity cliff formation. For a limited number of activity cliffs, X-ray structures of targets in complex with cliff compounds were available, which aided in rationalizing potency alterations among analogs with single- or dual-atom replacements. The analog pairs identified herein provide a rich resource of structure-activity relationship information and attractive test cases for calibrating computational methods.

Front Cover: Constitutional Dynamic Inhibition/Activation of Carbonic Anhydrases (ChemPlusChem 11/2021)

The cover shows an artistic concept describing an evolutional approach to the generation of dynamic inhibitors and activators of Carbonic Anhydrase on both the molecular and supramolecular levels through the implementation of reversible covalent reactions and non-covalent intermolecular interactions within inner active catalytic center and on the outer enzyme microenvironment, respectively. They open up wide perspectives to construct a fundamental transition from molecular/supramolecular medicinal chemistry design toward constitutional self-selection CDC strategies, for the discovery of powerful drug molecules and of dynamic polymers for efficient enzyme encapsulation for CO2 capture applications, respectively. More information can be found in the Minireview by M. Barboiu and co-workers.

Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors.

The emergence of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents an urgent public health crisis. Without available targeted therapies, treatment options remain limited for COVID-19 patients. Using medicinal chemistry and rational drug design strategies, we identify a 2-phenyl-1,2-benzoselenazol-3-one class of compounds targeting the SARS-CoV-2 main protease (Mpro). FRET-based screening against recombinant SARS-CoV-2 Mpro identified six compounds that inhibit proteolysis with nanomolar IC50 values. Preincubation dilution experiments and molecular docking determined that the inhibition of SARS-CoV-2 Mpro can occur by either covalent or noncovalent mechanisms, and lead E04 was determined to inhibit Mpro competitively. Lead E24 inhibited viral replication with a nanomolar EC50 value (844 nM) in SARS-CoV-2-infected Vero E6 cells and was further confirmed to impair SARS-CoV-2 replication in human lung epithelial cells and human-induced pluripotent stem cell-derived 3D lung organoids. Altogether, these studies provide a structural framework and mechanism of Mpro inhibition that should facilitate the design of future COVID-19 treatments.

QM/MM-based charge-density analysis of protein–ligand complexes: towards medicinal chemistry and drug design perspective

QM/MM-based charge-density analysis of protein–ligand complexes: towards medicinal chemistry and drug design perspective

Exploring ligand dynamics in protein crystal structures with ensemble refinement.

Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein-ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein-ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and Rfree values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.

Peptide-Based Inhibitors of ADAM and ADAMTS Metalloproteinases.

ADAM and ADAMTS are two large metalloproteinase families involved in numerous physiological processes, such as shedding of cell-surface protein ectodomains and extra-cellular matrix remodelling. Aberrant expression or dysregulation of ADAMs and ADAMTSs activity has been linked to several pathologies including cancer, inflammatory, neurodegenerative and cardiovascular diseases. Inhibition of ADAM and ADAMTS metalloproteinases have been attempted using various small molecules and protein-based therapeutics, each with their advantages and disadvantages. While most of these molecular formats have already been described in detail elsewhere, this mini review focuses solely on peptide-based inhibitors, an emerging class of therapeutic molecules recently applied against some ADAM and ADAMTS members. We describe both linear and cyclic peptide-based inhibitors which have been developed using different approaches ranging from traditional medicinal chemistry and rational design strategies to novel combinatorial peptide-display technologies.

Antiaggregant effects of (1,2,5-oxadiazolyl)azasydnone ring assemblies as novel antiplatelet agents.

A series of biheterocyclic assemblies comprising of 1,2,5-oxadiazole and azasydnone scaffolds were synthesized and biologically evaluated as novel nitric oxide (NO)-donor and antiplatelet agents. Depending on functional substituents at the biheterocyclic core, all studied compounds demonstrated good NO-donor profiles releasing NO in a wide range of concentrations (19.2%-195.1%) according to a Griess assay. (1,2,5-Oxadiazolyl)azasydnones showed excellent antiplatelet activity in the case of ADP and adrenaline used as inducers completely suppressing the aggregate formation even at the lowest test concentration of 0.0375μmol/ml, which is a rather unique feature. Moreover, studied biheterocycles possess a selective mechanism of inhibition of platelet aggregation mediated only by ADP and adrenaline, which are considered to be the main inducers causing thrombus formation. In addition, (1,2,5-oxadiazolyl)azasydnones were found to be completely non-toxic to hybrid endothelial cells EaHy 926. Studies of hydrolytic degradation of the synthesized compounds afforded benzoic acid as a sole detectable decomposition product, which is considered advantageous in drug design. Therefore, (1,2,5-oxadiazolyl)azasydnones represent a novel class of promising drug candidates with improved antiplatelet profile and reduced toxicity enabling their huge potential in medicinal chemistry and drug design.

Geminal Diheteroatomic Motifs: Some Applications of Acetals, Ketals, and Their Sulfur and Nitrogen Homologues in Medicinal Chemistry and Drug Design.

Acetals and ketals and their nitrogen and sulfur homologues are often considered to be unconventional and potentially problematic scaffolding elements or pharmacophores for the design of orally bioavailable drugs. This opinion is largely a function of the perception that such motifs might be chemically unstable under the acidic conditions of the stomach and upper gastrointestinal tract. However, even simple acetals and ketals, including acyclic molecules, can be sufficiently robust under acidic conditions to be fashioned into orally bioavailable drugs, and these structural elements are embedded in many effective therapeutic agents. The chemical stability of molecules incorporating geminal diheteroatomic motifs can be modulated by physicochemical design principles that include the judicious deployment of proximal electron-withdrawing substituents and conformational restriction. In this Perspective, we exemplify geminal diheteroatomic motifs that have been utilized in the discovery of orally bioavailable drugs or drug candidates against the backdrop of understanding their potential for chemical lability.

Abstract 1709: Novel small molecule HPK1 inhibitor induces immunogenic anti-tumor effects

Abstract Background Hematopoietic progenitor kinase 1 (HPK1, MAP4K1), a member of the MAP4K family of protein serine/threonine kinases1,2 is a negative regulator of TCR and BCR3. Immunosuppressive mediators PGE2 and adenosine regulate activation of HPK13. In vivo anti-tumor activity by HPK1 gene deletion, kinase dead HPK1 and small molecule HPK1 inhibitors have been demonstrated in multiple immunogenic syngeneic tumor models3,4. Enhanced anti-tumor efficacy in these models was achieved by combining HPK1 inhibitors with immune check-point blockers (ICBs) like anti-PD-1, anti-PD-L1or anti-CTLA4 antibodies3,4. HPK1 inhibition is a target for immuno-oncology treatment in cancers responsive or non-responsive to current ICBs. Methods Creative medicinal chemistry design complemented by structured-based support was used to identify & develop inhibitors of HPK1 with pico/nano-molar potency, optimal kinase selectivity, PK and efficacy profile. Our SAR efforts were guided by biochemical assays, functional read-outs and primary human in vitro T-cell activation assays. In vivo target engagement and pharmacodynamic data was generated using mouse models of the lung (LLC) and colon (MC38 and CT26) cancer. Results We describe novel and potent HPK1 inhibitors that can inhibit pSLP76 and enhance IL-2 production in Jurkat cells, IL-2 and IFN-γ production in human PBMCs, whole blood and primary T cells and TNF-α production by dendritic cells following stimulation. A reversal of PGE2 or adenosine mediated immunosuppression was also achieved by the inhibitors. These compounds on oral dosing showed strong tumor growth inhibition (TGI) in syngeneic models refractory to ICBs (subcutaneous LLC) as well as responsive to ICBs (subcutaneous MC38 and CT26; orthotopic LLC). TGI was accompanied by the immune response of increased cytokine (IL-2/IFNγ) levels and tumor infiltrating lymphocytes (TILs). Combination with ICBs induced enhanced TGI correlating with enhanced cytokine induction and TILs. We confirmed the immune-mediated mechanism of inhibitors by their lack of efficacy in immune-compromised mice. The lead compound demonstrated cardiac safety (hERG assay), lack of genotoxicity and very good safety margins in the mouse exploratory toxicology studies up to 28-days. Conclusion We have discovered a novel, orally active HPK1 inhibitor that demonstrates excellent stand-alone efficacy in multiple tumor models and also offers the potential to enhance current immunotherapy regimens in both responsive and refractory cancers. Further evaluation of our lead molecule towards the clinic is underway. Acknowledgements Sanjib D, Megha M, Jiju M, Sheetal K, Arti J, Swayam M, Srinivas K, Pradeep V, Vikram B, Abhay K, Jagmohan S, Ravi T, Mohammad Y, Rahul B, Ajit J, Sanjay G, Pramod S.

Scaffold-Hopping Strategy on a Series of Proteasome Inhibitors Led to a Preclinical Candidate for the Treatment of Visceral Leishmaniasis.

There is an urgent need for new treatments for visceral leishmaniasis (VL), a parasitic infection which impacts heavily large areas of East Africa, Asia, and South America. We previously reported on the discovery of GSK3494245/DDD01305143 (1) as a preclinical candidate for VL and, herein, we report on the medicinal chemistry program that led to its identification. A hit from a phenotypic screen was optimized to give a compound with in vivo efficacy, which was hampered by poor solubility and genotoxicity. The work on the original scaffold failed to lead to developable compounds, so an extensive scaffold-hopping exercise involving medicinal chemistry design, in silico profiling, and subsequent synthesis was utilized, leading to the preclinical candidate. The compound was shown to act via proteasome inhibition, and we report on the modeling of different scaffolds into a cryo-EM structure and the impact this has on our understanding of the series’ structure–activity relationships.

Ni(II) Schiff-Base Complexes as Chiral Electroauxiliaries and Methodological Platform for Stereoselective Electrochemical Functionalization of Amino Acids.

The concept of chiral electroauxiliary based on the redox active chiral platform to perform transformations of a redox inactive substrate is suggested and discussed in the context of the targeted stereoselective electrochemical functionalization of amino acids. Tailor-made amino acids are essential structural features of modern medicinal chemistry and drug design; the development of efficient synthetic approaches to these compounds is of topical interest. The modified substrate (an amino acid) is included as a structural motif in the redox active complex (with a possibility to be released after modification) that integrates "a bifunctional linker" (the structural motif capable to "catch" a substrate) and a chiral moiety responsible for asymmetry induction. The amino acid, being included as a part of such ensemble, becomes stable towards redox destruction and its targeted electrochemical modification saving the amino acid skeleton is possible, thus developing new modes of reactivity for well-known compounds.

Trends in peptide drug discovery.

Since the introduction of insulin almost a century ago, more than 80 peptide drugs have reached the market for a wide range of diseases, including diabetes, cancer, osteoporosis, multiple sclerosis, HIV infection and chronic pain. In this Perspective, we summarize key trends in peptide drug discovery and development, covering the early efforts focused on human hormones, elegant medicinal chemistry and rational design strategies, peptide drugs derived from nature, and major breakthroughs in molecular biology and peptide chemistry that continue to advance the field. We emphasize lessons from earlier approaches that are still relevant today as well as emerging strategies such as integrated venomics and peptide-display libraries that create new avenues for peptide drug discovery. We also discuss the pharmaceutical landscape in which peptide drugs could be particularly valuable and analyse the challenges that need to be addressed for them to reach their full potential.

The Playbooks of Medicinal Chemistry Design Moves.

Large databases of biologically relevant molecules, such as ChEMBL, SureChEMBL, or compound collections of pharmaceutical or agrochemical companies, are invaluable sources of medicinal chemistry information, albeit implicit. We developed a modified matched molecular pair approach to systematically and exhaustively extract the transformations in these databases and distill them into snippets of explicit design knowledge that are easily interpretable and directly applicable. The resulting "playbooks of medicinal chemistry design moves" capture the collective pharmaceutical and agrochemical research expertise across multiple chemists, companies, targets, and projects. They can be queried in an automated fashion for systematic prospective design and compound generation. The ChEMBL playbook and an application to exploit it are available at https://github.com/mahendra-awale/medchem_moves.

A Computational and Experimental Investigation of the Origin of Selectivity in the Chiral Phosphoric Acid Catalyzed Enantioselective Minisci Reaction.

The Minisci reaction is one of the most valuable methods for directly functionalizing basic heteroarenes to form carbon–carbon bonds. Use of prochiral, heteroatom-substituted radicals results in stereocenters being formed adjacent to the heteroaromatic system, generating motifs which are valuable in medicinal chemistry and chiral ligand design. Recently a highly enantioselective and regioselective protocol for the Minisci reaction was developed, using chiral phosphoric acid catalysis. However, the precise mechanism by which this process operated and the origin of selectivity remained unclear, making it challenging to develop the reaction more generally. Herein we report further experimental mechanistic studies which feed into detailed DFT calculations that probe the precise nature of the stereochemistry-determining step. Computational and experimental evidence together support Curtin–Hammett control in this reaction, with initial radical addition being quick and reversible, and enantioselectivity being achieved in the subsequent slower, irreversible deprotonation. A detailed survey via DFT calculations assessed a number of different possibilities for selectivity-determining deprotonation of the radical cation intermediate. Computations point to a clear preference for an initially unexpected mode of internal deprotonation enacted by the amide group, which is a crucial structural feature of the radical precursor, with the assistance of the associated chiral phosphate. This unconventional stereodetermining step underpins the high enantioselectivities and regioselectivities observed. The mechanistic model was further validated by applying it to a test set of substrates possessing varied structural features.

Direct Synthesis of N-(1,2,5-Oxadiazolyl)hydrazones through a Diazotization/Reduction/Condensation Cascade.

A straightforward synthesis of a series of previously unknown N-(1,2,5-oxadiazolyl)hydrazones through the diazotization/reduction/condensation cascade of amino-1,2,5-oxadiazoles was accomplished. The described protocol was suitable for a wide array of target hydrazones, which were prepared in good to high yields under smooth reaction conditions with very good functional group tolerance. Importantly, the presented approach unveils a direct route to in situ generation of previously inaccessible (1,2,5-oxadiazolyl)hydrazines. In addition, a first example of the ionic structure incorporating a protonated hydrazone motif linked to the 1,2,5-oxadiazole 2-oxide subunit was synthesized, indicating the stability of prepared compounds toward acid-promoted hydrolysis. Overall, this method provides a direct access to the isosteric analogues of drug candidates for treatment of various neglected diseases, thus enabling their potential application in medicinal chemistry and drug design.

A Turing Test for Molecular Generators.

Machine learning approaches promise to accelerate and improve success rates in medicinal chemistry programs by more effectively leveraging available data to guide a molecular design. A key step of an automated computational design algorithm is molecule generation, where the machine is required to design high-quality, drug-like molecules within the appropriate chemical space. Many algorithms have been proposed for molecular generation; however, a challenge is how to assess the validity of the resulting molecules. Here, we report three Turing-inspired tests designed to evaluate the performance of molecular generators. Profound differences were observed between the performance of molecule generators in these tests, highlighting the importance of selection of the appropriate design algorithms for specific circumstances. One molecule generator, based on match molecular pairs, performed excellently against all tests and thus provides a valuable component for machine-driven medicinal chemistry design workflows.

Discovery of PF-06835919: A Potent Inhibitor of Ketohexokinase (KHK) for the Treatment of Metabolic Disorders Driven by the Overconsumption of Fructose.

Increased fructose consumption and its subsequent metabolism have been implicated in metabolic disorders such as nonalcoholic fatty liver disease and steatohepatitis (NAFLD/NASH) and insulin resistance. Ketohexokinase (KHK) converts fructose to fructose-1-phosphate (F1P) in the first step of the metabolic cascade. Herein we report the discovery of a first-in-class KHK inhibitor, PF-06835919 (8), currently in phase 2 clinical trials. The discovery of 8 was built upon our originally reported, fragment-derived lead 1 and the recognition of an alternative, rotated binding mode upon changing the ribose-pocket binding moiety from a pyrrolidinyl to an azetidinyl ring system. This new binding mode enabled efficient exploration of the vector directed at the Arg-108 residue, leading to the identification of highly potent 3-azabicyclo[3.1.0]hexane acetic acid-based KHK inhibitors by combined use of parallel medicinal chemistry and structure-based drug design.

Cats and llamas could offer a path to coronavirus therapies

Computation and experimentation also yield possible therapeutic compounds for COVID-19 [ABSTRACT FROM AUTHOR] Copyright of Physics Today is the property of American Institute of Physics and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission However, users may print, download, or email articles for individual use This abstract may be abridged No warranty is given about the accuracy of the copy Users should refer to the original published version of the material for the full abstract (Copyright applies to all Abstracts )

Potential of Gold Candidates against Human Colon Cancer.

Development of novel metallodrugs with pharmacological profile plays a significant role in modern medicinal chemistry and drug design. Metal complexes have shown remarkable clinical results in current cancer therapy. Gold complexes have attained attention due to their high antiproliferative potential. Gold-based drugs are used for the treatment of rheumatoid arthritis. Gold-containing compounds with selective and specific targets are capable to assuage the symptoms of a range of human diseases. Gold (I) species with labile ligands (such as Cl in TEPAuCl) interact with isolated DNA; therefore, this biomolecule has been considered as a target for gold drugs. Gold (I) has a high affinity towards sulfur and selenium. Due to this, gold (I) drugs readily interact with cysteine or selenocysteine residue of the enzyme to form protein-gold(I) thiolate or protein-gold (I) selenolate complexes that lead to inhibition of the enzyme activity. Au(III) compounds due to their square-planner geometriesthe same as found in cisplatin, represent a good source for the development of anti-tumor agents. This article aims to review the most important applications of gold products in the treatment of human colon cancer and to analyze the complex interplay between gold and the human body.