Drug design with a new transition state analog of the hydrated carbonyl: silicon-based inhibitors of the HIV protease

Synthesis of unsymmetrical dialkoxydiarylsilanes and diarylsilanediols from tetraalkoxysilane having a dioxasilepane unit

The tetraalkoxysilane carrying a stable seven-membered dioxasilepane moiety and two trifluoroethoxy groups undergoes reliable iterative substitution of the two trifluoroethoxy groups by sequential treatment with different aryl Grignard reagents while keeping the seven-membered structure intact. The process results in the synthesis of unsymmetrical dialkoxydiarylsilanes and eventually diarylsilanediols after proper hydrolysis.

Oligo-Condensation Reactions of Silanediols with Conservation of Solid-State-Structural Features

Oligo- and polysiloxanes are usually prepared by condensation reactions in solvents without control of stereochemistry. Here we present a solventless thermal condensation of stable organosilanols. We investigated the condensation reactions of organosilanediols with different organic substituents, having in common at least one aromatic group. The condensation kinetics of the precursors observed by NMR spectroscopy revealed a strong dependence on temperature, time, and substitution pattern at the silicon atom. SEC measurements showed that chain length increases with increasing condensation temperature and time and lower steric demand of the substituents, which also influences the glass transition temperatures (Tg) of the resulting oligo- or polymers. X-ray diffraction studies of the crystalline silanediols and their condensation products revealed a structural correlation between the substituent location in the crystalline precursors and the formed macromolecules induced by the hydrogen bonding pattern. In certain cases, it is possible to carry out topotactic polymerization in the solid-state, which has its origin in the crystal structure.

Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology

Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active-site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues that reduced catalysis had little or no impact on TSA binding and many even increased tungstate affinity. These disparate effects can be accounted for by a model in which distal mutations alter the enzyme's conformational landscape, increasing the occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this ensemble model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity (but not more likely to impact catalysis), presumably due to increased conformational flexibility that allows previously disfavored microstates to increase in occupancy. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration of distal residues that shape the enzyme's conformational landscape and fine-tune active-site residues. Biologically, the evolution of extensive communication between the active site and remote residues to aid catalysis may have provided the foundation for allostery to make it a highly evolvable trait.

Synthesis and Hydrogen-Bond Patterns of Aryl-Group Substituted Silanediols and -triols from Alkoxy- and Chlorosilanes

Organosilanols typically show a high condensation tendency and only exist as stable isolable molecules under very specific steric and electronic conditions at the silicon atom. In the present work, various novel representatives of this class of compounds were synthesized by hydrolysis of alkoxy‐ or chlorosilanes. Phenyl, 1‐naphthyl, and 9‐phenanthrenyl substituents at the silicon atom were applied to systematically study the influence of the aromatic substituents on the structure and reactivity of the compounds. Chemical shifts in ²⁹Si NMR spectroscopy in solution, correlated well with the expected electronic situation induced by the substitution pattern on the Si atom. ¹H NMR studies allowed the detection of strong intermolecular hydrogen bonds. Single‐crystal X‐ray structures of the alkoxides and the chlorosilanes are dominated by π‐π interactions of the aromatic systems, which are substituted by strong hydrogen bonding interactions representing various structural motifs in the respective silanol structures.

The development of an Amber-compatible organosilane force field for drug-like small molecules

As members of the group IVA elements, silicon and carbon have long been thought of as isosteres of each other in drug design. However, the lack of silicon parameters in current main stream force fields hinders the computational study of this important element in drug discovery. Thus, in this study, we attempted to supplement the parameters of organosilanes in the General Amber Force Field (GAFF2). The parameters have been designed following the principles of GAFF2 to make it compatible with the Amber force field family. The accuracy of the parameters was discussed by comparing the pair interaction energy, the liquid properties, and the structures and alchemical binding free energy differences for a set of protein-ligand complexes.

Amide Bond Bioisosteres: Strategies, Synthesis, and Successes

The amide functional group plays a key role in the composition of biomolecules, including many clinically approved drugs. Bioisosterism is widely employed in the rational modification of lead compounds, being used to increase potency, enhance selectivity, improve pharmacokinetic properties, eliminate toxicity, and acquire novel chemical space to secure intellectual property. The introduction of a bioisostere leads to structural changes in molecular size, shape, electronic distribution, polarity, pK_a, dipole or polarizability, which can be either favorable or detrimental to biological activity. This approach has opened up new avenues in drug design and development resulting in more efficient drug candidates introduced onto the market as well as in the clinical pipeline. Herein, we review the strategic decisions in selecting an amide bioisostere (the why), synthetic routes to each (the how), and success stories of each bioisostere (the implementation) to provide a comprehensive overview of this important toolbox for medicinal chemists.

On the Potential of Silicon as a Building Block for Life

Despite more than one hundred years of work on organosilicon chemistry, the basis for the plausibility of silicon-based life has never been systematically addressed nor objectively reviewed. We provide a comprehensive assessment of the possibility of silicon-based biochemistry, based on a review of what is known and what has been modeled, even including speculative work. We assess whether or not silicon chemistry meets the requirements for chemical diversity and reactivity as compared to carbon. To expand the possibility of plausible silicon biochemistry, we explore silicon's chemical complexity in diverse solvents found in planetary environments, including water, cryosolvents, and sulfuric acid. In no environment is a life based primarily around silicon chemistry a plausible option. We find that in a water-rich environment silicon's chemical capacity is highly limited due to ubiquitous silica formation; silicon can likely only be used as a rare and specialized heteroatom. Cryosolvents (e.g., liquid N2) provide extremely low solubility of all molecules, including organosilicons. Sulfuric acid, surprisingly, appears to be able to support a much larger diversity of organosilicon chemistry than water.

Bioisosteric Replacement as a Tool in Anti-HIV Drug Design

Bioisosteric replacement is a powerful tool for modulating the drug-like properties, toxicity, and chemical space of experimental therapeutics. In this review, we focus on selected cases where bioisosteric replacement and scaffold hopping have been used in the development of new anti-HIV-1 therapeutics. Moreover, we cover field-based, computational methodologies for bioisosteric replacement, using studies from our group as an example. It is our hope that this review will serve to highlight the utility and potential of bioisosteric replacement in the continuing search for new and improved anti-HIV drugs.

Progress in the medicinal chemistry of silicon: C/Si exchange and beyond

Application of silyl functionalities is one of the most promising strategies among various ‘elements chemistry’ approaches for the development of novel and distinctive drug candidates. Replacement of one or more carbon atoms of various biologically active compounds with silicon (so-called sila-substitution) has been intensively studied for decades, and is often effective for alteration of activity profile and improvement of metabolic profile. In addition to simple C/Si exchange, several novel approaches for utilizing silicon in medicinal chemistry have been suggested in recent years, focusing on the intrinsic differences between silicon and carbon. Sila-substitution offers great potential for enlarging the chemical space of medicinal chemistry, and provides many options for structural development of drug candidates.

Ru(ii)-Pheox-catalyzed Si–H insertion reaction: construction of enantioenriched carbon and silicon centers

We established a highly enantioselective Si–H insertion reaction to construct chiral centers at the carbon and silicon atoms, using a Ru(ii)–Pheox catalyst.

Ferroquine and its derivatives: new generation of antimalarial agents

Malaria has been teasing human populations from a long time. Presently, several classes of antimalarial drugs are available in market, but the issues of toxicity, lower efficacy and the resistance by malarial parasites have decreased their overall therapeutic indices. Thus, the search for new promising antimalarials continues, however, the battle against malaria is far from over. Ferroquine is a derivative of chloroquine with antimalarial properties. It is the most successful of the chloroquine derivatives. Not only ferroquine, but also its derivatives have shown promising potential as antimalarials of clinical interest. Presently, much research is dedicated to the development of ferroquine derivatives as safe alternatives to antimalarial chemotherapy. The present article describes the structural, chemical and biological features of ferroquine. Several classes of ferroquine derivatives including hydroxyferroquines, trioxaferroquines, chloroquine-bridged ferrocenophanes, thiosemicarbazone derivatives, ferrocene dual conjugates, 4-N-substituted derivatives, and others have been discussed. Besides, the mechanism of action of ferroquine has been discussed. A careful observation has been made into pharmacologically significant ferroquine derivatives with better or equal therapeutic effects to that of chloroquine and ferroquine. A brief discussion of the toxicities of ferroquine derivatives has been made. Finally, efforts have been made to discuss the current challenges and future perspectives of ferroquine-based antimalarial drug development.

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Structural, chemical and biological features of ferroquine have been discussed.

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Several classes of ferroquine derivatives have been reviewed.

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Mechanism of action of ferroquine has been described.

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Challenges in ferroquine-based antimalarial drug development have been highlighted.

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Perspectives in ferroquine-based antimalarial drug development have been outlined.

Enantioselective synthesis of α-aminosilanes by copper-catalyzed hydroamination of vinylsilanes

The synthesis of α-aminosilanes by a highly enantio- and regioselective copper-catalyzed hydroamination of vinylsilanes is reported. The system employs Cu-DTBM-SEGPHOS as the catalyst, diethoxymethylsilane as the stoichiometric reductant, and O-benzoylhydroxylamines as the electrophilic nitrogen source. This hydroamination reaction is compatible with differentially substituted vinylsilanes, thus providing access to amino acid mimics and other valuable chiral organosilicon compounds.

Study of the chelating properties of Ge(OH)2 functionality as metal binding group for Zn2+ cation in simplified protease-like environments: a DFT analysis

The development of protease's inhibitors is an active field of research in the pharmaceutical industry. As concerns the design of new inhibitors, the theoretical study of the binding patterns and energies of known metal binding groups (MBGs) toward Zn(2+) using quantum-chemical calculations may offer a better understanding of their interaction models and may be useful for the improvement and design of novel ZBGs. Here the properties of gem-Ge(OH)(2)-based compounds as ZBG were assessed theoretically using DFT calculations. [Zn(Imdz)(2) R - OH(2)](2+) complexes (Imdz =imidazole rings; R = imidazole ring, acetic acid molecule or acetate anion) were used to partially reproduce the coordination sphere in metalloproteases (ACE, amgiotensin converting enzyme, and TLN, thermolysine) being inhibited by related compounds (i.e., silanediols). The MBG- Zn(2+) interaction was analyzed through the energy of the reaction: [Zn(Imdz)(2) R - OH(2)](2+) + L → [Zn(Imdz)(2) R - L](2+) + H(2)O using DFT (M06L/cc-pVDZ) in gas-phase and in solution (IEF-PCM). Although the functional used (M06L) has proven its efficiency to study systems containing transition metal governed by non-covalent interactions, dispersion effects were implemented by the correction of the computed energies using the DFT-D3 program. Accounting for dispersion effects produced a systematic increase of c.a. 13 kJ mol(-1) on the energies, whereas the effect of solvent goes in the opposite direction (i.e., BE under the IEF-PCM model are on average 125 kJ mol(-1) lower). The Ge(OH)(2) - Zn(2+) interaction seems to be similar (or even stronger) than the Si(OH)(2) -Zn(2+). Their better performance as ZBG is explained by the combined NBO-AIM analysis. The results of this work may encourage the preparation, isolation, and experimental assay of the chelating properties of these compounds, which may propose a new family of protease's inhibitors.

Efficient routes to carbon-silicon bond formation for the synthesis of silicon-containing peptides and azasilaheterocycles

Silasubstitution, where silicon is substituted for carbon at specific sites of the substrate, has become a growing practice in medicinal chemistry. Introducing silicon into bioactive compounds provides slight physical and electronic alterations to the parent compound, which in certain instances could make the substrate a more viable candidate for a drug target. One application is in the field of protease inhibition. Various silane diol isosteres can act as potent inhibitors of aspartic and metalloproteases because of their ability to mimic the high-energy tetrahedral intermediate in peptide bond hydrolysis. In particular, since 1998, the Sieburth group has prepared a number of functionalized peptide silane diol isosteres. In a seminal study, they demonstrated that these molecules can bind to the active site of the enzymes. Inspired by these results, we initiated a study to develop a concise and straightforward route to access highly functionalized silicon diol based peptidomimetic analogs, which we describe in this Account. The synthesis of such analogs is challenging because the dipeptide mimics require the formation of two carbon-silicon bonds as well as two chiral carbon centers. Our first strategy was to assemble the two C-Si bonds from diphenylsilane through an initial regioselective hydrosilylation step of a terminal alkene, followed by lithiation of the formed alkyldiphenylsilane by a simple lithium metal reduction. Subsequent diastereoselective addition of this silyllithium species to a tert-butylsulfinimine provided a rapid method to assemble the dipeptide mimic with stereochemical control at the new chiral carbon center adjacent to the silicon. This strategy worked with a wide range of functional groups. However, there were some limitations with the more elaborate targets. In particular, we needed to exchange the phenyl groups of the diphenylsilane with aryl groups that were more labile under acidic conditions in order to introduce Si-O bonds in the end product. We demonstrated that a variety of Ar(2)SiH(2) compounds with methyl substituents on the aromatic core could effectively undergo hydrosilylation and reductive lithiation with a soluble reducing agent, lithium naphthalenide. The electron-rich aromatic groups were more acid labile and, depending on the conditions, could produce either the silane diol or the silanol. In an alternative strategy, we used a highly regioselective Rh-catalyzed sequential double hydrosilylation to form the two C-Si bonds with a single catalyst. This approach is a more efficient, atom economical way to synthesize a wider range of highly functionalized organosilanes with the added possibility of extending this method into an asymmetric protocol. By this method, various functional groups that were not previously tolerated in the lithiation protocol, including OBn, OAc, furyl, and thiophenes, could now be incorporated. Hydrosilylation of a terminal olefin and a peptide functionalized with an enamide at the C-terminus achieved the desired silane in high yields in a one pot reaction without compromising the stereochemical integrity of the peptide. As an extension of this work, we used these methods to efficiently generate a variety of chiral azasilaheterocycles, including silapiperidines and silaindolizidines.

Efficient, enantioselective assembly of silanediol protease inhibitors

A five-step assembly of silicon-protected dipeptide mimics from commercially available reagents is described. This methodology makes silanediol protease inhibitors readily available for the first time. The sequence features asymmetric hydrosilylation, a novel reduction of a silyl ether to a silyllithium reagent, and addition of this dianion to a sulfinimine, to produce the complete inhibitor skeleton with full control of stereochemistry. Oxidation of the primary alcohol to an acid completes the synthesis.

Silanetriols as in vitro inhibitors for AChE

Three stable silanetriols with increasing steric protection of the silicon atom have been tested for inhibition of acetylcholinesterase (AChE). For all tested silanetriols we found reversible inhibition of the AChE activity at a 100 μM concentration. The highest inhibition rate was found for the sterically least hindered cyclohexylsilanetriol with 45% inhibition relative to galanthamine hydrobromide for which an IC(50) value of 121 ± 3 μM was determined as well. The cytotoxicity of the silanetriols used was found to be negligible at concentrations relevant for inhibition.

Further studies toward the stereocontrolled synthesis of silicon-containing peptide mimics

Further studies are reported on the utilization of the versatile reaction between chiral sulfinimines and alkyldiphenylsilyl lithium reagents with the goal of preparing a wide range of silanediol-based protease inhibitors. In particular, focus has been placed to demonstrate how a number of genetically encoded amino acid side chains such as serine, threonine, tyrosine, lysine, proline, arginine, aspartate and asparagine might be incorporated into the overall approach. Efforts to apply this synthetic methodology for accessing biologically relevant silanediol dipeptide mimics are also described. This includes the synthesis of a potential inhibitor of the human neutrophil elastase, as well as a diphenylsilane mimic of a hexapeptide fragment of the human islet amyloid polypeptide.

The future of imaging: developing the tools for monitoring response to therapy in oncology: the 2009 Sir James MacKenzie Davidson Memorial lecture

Since the days of Sir James MacKenzie Davidson, radiology discoveries have been shaping the way patients are managed. The lecture on which this review is based focused not on anatomical imaging, which already has a great impact on patient management, but on the molecular imaging of cancer targets and pathways. In this post-genomic era, we have several tools at our disposal to enable the discovery of new probes for stratifying patients for therapy and for monitoring response to therapy sooner than is possible using conventional cross-sectional imaging methods. I describe a chemical library approach to discovering new imaging agents, as well as novel methods for improving the metabolic stability of existing probes. Finally, I describe the evaluation of these probes for clinical use in both pre-clinical and clinical validation. The chemical library approach is exemplified by the discovery of isatin sulfonamide probes for imaging apoptosis in tumours. This approach allowed important desirable features of radiopharmaceuticals to be incorporated into the design strategy. A lead compound, [(18)F]ICMT11, is selectively taken up in vitro in cancer cells and in vivo in tumours undergoing apoptosis. Improvement of the metabolic stability of a probe is exemplified by work on [(18)F]fluoro-[1,2-(2)H(2)]choline ("[(18)F]-D4-choline"), a novel probe for imaging choline metabolism. Deuterium substitution significantly reduced the systemic metabolism of this compound relative to that of non-deuteriated analogues, supporting its future clinical use. In order for probes to be useful for monitoring response a number of validation and/or qualification studies need to be performed, including assessments of whether the probe measures the target or pathway of interest in a specific and reproducible manner, whether the probe is stable to metabolism in vivo, what is the best time to assess response with these probes and finally whether changes in radiotracer uptake are associated with clinical outcome. [(18)F]Fluorothymidine, a probe for proliferation imaging has been validated and qualified for use in breast cancer. In summary, the ability to create new molecules that can report on specific targets and pathways provides a strategy for studying response to treatment in cancer earlier than it is currently possible. This could fundamentally change the way medicine is practised in the next 5-10 years.

Stereocontrolled synthesis of methyl silanediol peptide mimics

The treatment of chiral sulfinimines with (methyldiphenylsilyl)lithium gives alpha-(methyldiphenylsilyl)sulfinamides with excellent diastereoselectivity, and in good yield. The presence of alpha-protons on the imines is also well tolerated. The sulfinamide auxiliary is easily removed via treatment with methanolic HCl and the resulting amine extended into peptide chains accordingly. The diphenylsilyl moiety is a resilient protecting group for the corresponding silanediol, which can be unmasked via treatment with TfOH, followed by aqueous hydrolysis. The crude silanediol may be isolated and purified as its corresponding bis-TMS siloxane via protection with TMSCl, and converted back to the desired silanediol via hydrolysis with aqueous KOH. Efforts to apply this approach to biologically relevant silanediol peptide mimics, with a view to protease inhibition, are described.

Discovery of potent HIV-1 protease inhibitors incorporating sulfoximine functionality

Based on the unique property of sulfoximine and the homodimeric C(2) structural symmetry of HIV-1 protease, a novel class of sulfoximine-based pseudosymmetric HIV-1 protease inhibitors was designed and synthesized. The sulfoximine moiety was demonstrated to be important for HIV-1 protease inhibitor potency. The most active stereoisomer (2S,2'S) displays a potency of 2.5 nM (IC(50)) against HIV-1 protease and an anti-HIV-1 activity of 408 nM (IC(50)). A possible mode of action is proposed.