Fragment-based Lead Generation Research Articles

Photochemical Methods Applied to DNA Encoded Library (DEL) Synthesis.

DNA-encoded library technology (DELT) is a new screening modality that allows efficient, cost-effective, and rapid identification of small molecules with potential biological activity. This emerging technique represents an enormous advancement that, in combination with other technologies such as high-throughput screening (HTS), fragment-based lead generation, and structure-based drug design, has the potential to transform how drug discovery is carried out. DELT is a hybrid technique in which chemically synthesized compounds are linked to unique genetic tags (or "barcodes") that contain readable information. In this way, millions to billions of building blocks (BBs) attached on-DNA via split-and-pool synthesis can be evaluated against a biological target in a single experiment. Polymerase chain reaction (PCR) amplification and next-generation sequencing (NGS) analysis of the unique sequence of oligonucleotides in the DNA tag are used to identify those ligands with high affinity for the target. This innovative fusion of genetic and chemical technologies was conceived in 1992 by Brenner and Lerner (Proc. Natl. Acad. Sci. 1992, 89, 5381-5383) and is under accelerated development with the implementation of new synthetic techniques and protocols that are compatible with DNA. In fact, reaction compatibility is a key parameter to increasing the chances of identification of a drug target ligand, and a central focus has been the development of new transformations and the transition to robust protocols for on-DNA synthesis. Because the sole use of the DNA tag is as an amplifiable identification barcode, its structural integrity during a new chemical process is mandatory. As such, the use of these sensitive, polyfunctional biological molecules as substrates typically requires aqueous solutions within defined pH and temperature ranges, which is considered a notable challenge in DEL synthesis.Using low-energy visible light as the driving force to promote chemical transformations represents an attractive alternative to classical synthetic methods, and it is an important and well-established synthetic tool for forging chemical bonds in a unique way via radical intermediates. Recent advances in the field of photocatalysis are extraordinary, and this powerful research arena is still under continuous development. Several applications taking advantage of the mild reaction conditions of photoinduced transformations have been directed toward DEL synthesis, allowing the expansion of chemical space available for the evaluation of new building blocks on-DNA. There are no doubts that visible-light-driven reactions have become one of the most powerful approaches for DELT, given the easy way they provide to construct new bonds and the challenges to achieve equal success via classical protocols.Key characteristics of photocatalytic synthesis include the short reaction times and efficiency, which translate into retention of DNA integrity. In this Account, we describe recent advances in the photoinduced diversification of building blocks prepared on-DNA, highlighting the amenability of the techniques employed for preserving the genetic structure of the molecules. We demonstrate with recent research from our group the applicability of photocatalysis to the field and include in the summary a table containing all the photoinduced methods reported to date for DELT, demonstrating their key aspects such as scope, applications, and DNA compatibilities. With this information, practitioners are provided with compelling reasons for developing/choosing photocatalytic methods for DELT applications.

Fragment-Based Design of a Potent MAT2a Inhibitor and in Vivo Evaluation in an MTAP Null Xenograft Model.

MAT2a is a methionine adenosyltransferase that synthesizes the essential metabolite S-adenosylmethionine (SAM) from methionine and ATP. Tumors bearing the co-deletion of p16 and MTAP genes have been shown to be sensitive to MAT2a inhibition, making it an attractive target for treatment of MTAP-deleted cancers. A fragment-based lead generation campaign identified weak but efficient hits binding in a known allosteric site. By use of structure-guided design and systematic SAR exploration, the hits were elaborated through a merging and growing strategy into an arylquinazolinone series of potent MAT2a inhibitors. The selected in vivo tool compound 28 reduced SAM-dependent methylation events in cells and inhibited proliferation of MTAP-null cells in vitro. In vivo studies showed that 28 was able to induce antitumor response in an MTAP knockout HCT116 xenograft model.

Fragment-Based Discovery of Pyrazolopyridones as JAK1 Inhibitors with Excellent Subtype Selectivity.

Herein, we report the discovery of a series of JAK1-selective kinase inhibitors with high potency and excellent JAK family subtype selectivity. A fragment screening hit 1 with a pyrazolopyridone core and a JAK1 bias was selected as the starting point for our fragment-based lead generation efforts. A two-stage strategy was chosen with the dual aims of improving potency and JAK1 selectivity: Optimization of the lipophilic ribose pocket-targeting substituent was followed by the introduction of a variety of P-loop-targeting functional groups. Combining the best moieties from both stages of the optimization afforded compound 40, which showed excellent potency and selectivity. Metabolism studies in vitro and in vivo together with an in vitro safety evaluation suggest that 40 may be a viable lead compound for the development of highly subtype-selective JAK1 inhibitors.

Abstract 19: Design and synthesis of biaryl indolyl benzamides as HDAC1-selective inhibitors via a fragment-based lead generation approach

Abstract Histone deacetylase (HDAC) proteins are epigenetic regulatory enzymes that deacetylate protein substrates, leading to subsequent changes in cell function. HDAC proteins are implicated in cancers and several HDAC inhibitors have been approved by the FDA as anti-cancer drugs. Unfortunately, most of the FDA-approved drugs non-selectively inhibit most of the HDAC isoforms, which may lead to side effects in the clinic and limit their use on the bench top. Isoform-selective HDAC inhibitors may decrease or eliminate the side effects associated with non-selective inhibitors treatment. In addition, isoform-selective HDAC inhibitors can be used as molecular tools to study HDAC-related cancer biology. In this work, several biaryl indolyl benzamide compounds were designed and synthesized based on a fragment-based lead generation approach as potential HDAC1-selective inhibitors. The design was based on combining two different fragments from known HDAC1/2 and HDAC1/3 selective inhibitors. These fragments can discriminate against both HDAC2 and HDAC3 and possibly impart selectivity towards HDAC1. Docking studies were performed to validate the design of the inhibitors and to understand the binding of different isoform-selective inhibitors to HDAC1, HDAC2, and HDAC3. Potency and isoform selectivity of the new compounds were assessed via in vitro screening with different HDAC isoforms. All analogs showed modest selectivity for HDAC1 over HDAC2. Bnz-3 was identified as the best compound in terms of potency and selectivity. In particular, Bnz-3 displayed roughly 10- to 100-fold higher potency than the other compounds, with an IC50 value of 548 nM with HDAC1. In terms of selectivity, Bnz-3 showed about 10.6-fold selectivity for HDAC1 over HDAC2, with almost no inhibition of either HDAC3 or HDAC6. The new biaryl indolyl benzamide HDAC inhibitors represent potential lead compounds that can help to further develop more selective HDAC1 inhibitors. Citation Format: Ahmed T. Negmeldin, Mary Kay H. Pflum. Design and synthesis of biaryl indolyl benzamides as HDAC1-selective inhibitors via a fragment-based lead generation approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 19.

Fragment-Based Lead Generation of 5-Phenyl-1H-pyrazole-3-carboxamide Derivatives as Leads for Potent Factor Xia Inhibitors.

FXIa is suggested as a major target for anticoagulant drug discovery because of reduced risk of bleeding. In this paper, we defined 5-phenyl-1H-pyrazole-3-carboxylic acid derivatives as privileged fragments for FXIa inhibitors’ lead discovery. After replacing the (E)-3-(5-chloro-2-(1H-tetrazol-1-yl)phenyl)acrylamide moiety in compound 3 with 5-(3-chlorophenyl)-1H-pyrazole-3-carboxamide, we traveled from FXIa inhibitor 3 to a scaffold that fused the privileged fragments into a pharmacophore for FXIa inhibitors. Subsequently, we synthesized and assessed the FXIa inhibitory potency of a series of 5-phenyl-1H-pyrazole-3-carboxamide derivatives with different P1, P1′ and P2′moiety. Finally, the SAR of them was systematically investigated to afford the lead compound 7za (FXIa Ki = 90.37 nM, 1.5× aPTT in rabbit plasma = 43.33 μM) which exhibited good in vitro inhibitory potency against FXIa and excellent in vitro coagulation activities. Furthermore, the binding mode of 7za with FXIa was studied and the results suggest that the 2-methylcyclopropanecarboxamide group of 7za makes 2 direct hydrogen bonds with Tyr58B and Thr35 in the FXIa backbone, making 7za binds to FXIa in a highly efficient manner.

Where Do Recent Small Molecule Clinical Development Candidates Come From?

An analysis of 66 published clinical candidates from Journal of Medicinal Chemistry has been conducted to shed light on which lead generation strategies are most frequently employed in identifying drug candidates. The most frequent lead generation strategy (producing a drug candidate) was based on starting points derived from previously known compounds (43%) followed by random high throughput screening (29%). The remainder of approaches included focused screening, structure-based drug design (SBDD), fragment-based lead generation (FBLG), and DNA-encoded library screening (DEL). An analysis of physicochemical properties on the hit-to-clinical pairs shows an average increase in molecular weight (ΔMW = +85) but no change in lipophilicity (ΔclogP = -0.2), although exceptions are noted. The majority (>50%) of clinical candidates were found to be structurally very different from their starting point and were more complex. Finally, several reports of noncovalent scaffolds modified by a covalent warhead using SBDD approaches are discussed.

Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.

NMR binding assays are routinely applied in hit finding and validation during early stages of drug discovery, particularly for fragment-based lead generation. To this end, compound libraries are screened by ligand-observed NMR experiments such as STD, T1ρ, and CPMG to identify molecules interacting with a target. The analysis of a high number of complex spectra is performed largely manually and therefore represents a limiting step in hit generation campaigns. Here we report a novel integrated computational procedure that processes and analyzes ligand-observed proton and fluorine NMR binding data in a fully automated fashion. A performance evaluation comparing automated and manual analysis results on (19)F- and (1)H-detected data sets shows that the program delivers robust, high-confidence hit lists in a fraction of the time needed for manual analysis and greatly facilitates visual inspection of the associated NMR spectra. These features enable considerably higher throughput, the assessment of larger libraries, and shorter turn-around times.

Creating novel activated factor XI inhibitors through fragment based lead generation and structure aided drug design.

Activated factor XI (FXIa) inhibitors are anticipated to combine anticoagulant and profibrinolytic effects with a low bleeding risk. This motivated a structure aided fragment based lead generation campaign to create novel FXIa inhibitor leads. A virtual screen, based on docking experiments, was performed to generate a FXIa targeted fragment library for an NMR screen that resulted in the identification of fragments binding in the FXIa S1 binding pocket. The neutral 6-chloro-3,4-dihydro-1H-quinolin-2-one and the weakly basic quinolin-2-amine structures are novel FXIa P1 fragments. The expansion of these fragments towards the FXIa prime side binding sites was aided by solving the X-ray structures of reported FXIa inhibitors that we found to bind in the S1-S1’-S2’ FXIa binding pockets. Combining the X-ray structure information from the identified S1 binding 6-chloro-3,4-dihydro-1H-quinolin-2-one fragment and the S1-S1’-S2’ binding reference compounds enabled structure guided linking and expansion work to achieve one of the most potent and selective FXIa inhibitors reported to date, compound 13, with a FXIa IC50 of 1.0 nM. The hydrophilicity and large polar surface area of the potent S1-S1’-S2’ binding FXIa inhibitors compromised permeability. Initial work to expand the 6-chloro-3,4-dihydro-1H-quinolin-2-one fragment towards the prime side to yield molecules with less hydrophilicity shows promise to afford potent, selective and orally bioavailable compounds.

Structure guided lead generation for M. tuberculosis thymidylate kinase (Mtb TMK): discovery of 3-cyanopyridone and 1,6-naphthyridin-2-one as potent inhibitors.

M. tuberculosis thymidylate kinase (Mtb TMK) has been shown in vitro to be an essential enzyme in DNA synthesis. In order to identify novel leads for Mtb TMK, we performed a high throughput biochemical screen and an NMR based fragment screen through which we discovered two novel classes of inhibitors, 3-cyanopyridones and 1,6-naphthyridin-2-ones, respectively. We describe three cyanopyridone subseries that arose during our hit to lead campaign, along with cocrystal structures of representatives with Mtb TMK. Structure aided optimization of the cyanopyridones led to single digit nanomolar inhibitors of Mtb TMK. Fragment based lead generation, augmented by crystal structures and the SAR from the cyanopyridones, enabled us to drive the potency of our 1,6-naphthyridin-2-one fragment hit from 500 μM to 200 nM while simultaneously improving the ligand efficiency. Cyanopyridone derivatives containing sulfoxides and sulfones showed cellular activity against M. tuberculosis. To the best of our knowledge, these compounds are the first reports of non-thymidine-like inhibitors of Mtb TMK.

From fragments to leads: novel bacterial NAD+-dependent DNA ligase inhibitors

Bacterial NAD+-dependent DNA ligase (LigA) is an essential enzyme involved in the repair, replication, and recombination of DNA in all bacteria, making it an attractive target in antibacterial drug discovery. A novel series of LigA inhibitors was discovered by combining information from fragment-based lead generation, X-ray crystal structures of previously discovered inhibitors bound to the adenosine binding site of LigA bound to and established structure–activity relationships of LigA inhibitors. The compounds described here were evaluated in a variety of Gram-positive and Gram-negative pathogens as well as evaluation of physical properties.

Fragment-Based Lead Discovery and Design

Fragment-based lead discovery and design has and continues to show increasing promise in drug discovery. In this article, the current state of the art in terms of hot-spot characterization, fragment screening techniques, and fragment-based design is discussed. Three overall fragment-based lead generation strategies are explored and involve the chemical biology characterization of biological targets via fragment screening, fragment screening as a complementary approach to high-throughput screening of drug-like compounds, and direct fragment-based drug discovery, respectively. The evolution and development of fragment libraries is described. With an emphasis on computational approaches and the strategies applied at AstraZeneca, the review illustrates how integration of data from one regime can inform the design of experiments in the other, ultimately leading to the discovery of high quality chemical matter.

Design and Synthesis of Novel Lactate Dehydrogenase A Inhibitors by Fragment-Based Lead Generation

Lactate dehydrogenase A (LDHA) catalyzes the conversion of pyruvate to lactate, utilizing NADH as a cofactor. It has been identified as a potential therapeutic target in the area of cancer metabolism. In this manuscript we report our progress using fragment-based lead generation (FBLG), assisted by X-ray crystallography to develop small molecule LDHA inhibitors. Fragment hits were identified through NMR and SPR screening and optimized into lead compounds with nanomolar binding affinities via fragment linking. Also reported is their modification into cellular active compounds suitable for target validation work.

Pyrrolamide DNA Gyrase Inhibitors: Fragment-Based Nuclear Magnetic Resonance Screening To Identify Antibacterial Agents

DNA gyrase is an essential enzyme in bacteria, and its inhibition results in the disruption of DNA synthesis and, subsequently, cell death. The pyrrolamides are a novel class of antibacterial agents targeting DNA gyrase. These compounds were identified by a fragment-based lead generation (FBLG) approach using nuclear magnetic resonance (NMR) screening to identify low-molecular-weight compounds that bind to the ATP pocket of DNA gyrase. A pyrrole hit with a binding constant of 1 mM formed the basis of the design and synthesis of a focused library of compounds that resulted in the rapid identification of a lead compound that inhibited DNA gyrase with a 50% inhibitory concentration (IC(50)) of 3 μM. The potency of the lead compound was further optimized by utilizing iterative X-ray crystallography to yield DNA gyrase inhibitors that also displayed antibacterial activity. Spontaneous mutants were isolated in Staphylococcus aureus by plating on agar plates containing pyrrolamide 4 at the MIC. The resistant variants displayed 4- to 8-fold-increased MIC values relative to the parent strain. DNA sequencing revealed two independent point mutations in the pyrrolamide binding region of the gyrB genes from these variants, supporting the hypothesis that the mode of action of these compounds was inhibition of DNA gyrase. Efficacy of a representative pyrrolamide was demonstrated against Streptococcus pneumoniae in a mouse lung infection model. These data demonstrate that the pyrrolamides are a novel class of DNA gyrase inhibitors with the potential to deliver future antibacterial agents targeting multiple clinical indications.

Biophysical Approaches to Discovery of Novel Antibacterial Leads

This presentation will outline biophysical approaches to discovery of antibacterial lead compounds that are designed to address bacterial resistance to many current antibiotics. There are a number of essential enzymes, in key pathways of pathogenic bacteria, which have not been targeted by existing drugs. The potential bacterial selectivity and spectrum of these single gene targets can be validated using structural tools. In addition, inhibiting clinically exploited and validated bacterial enzymes with a different mechanism (e.g., at a different binding site) than those offered by current drugs can be a powerful approach. Target enzymes that have remained unexploited or those that offer alternative binding sites include cell wall biosynthesis and DNA replication enzymes. In our discovery efforts, biophysical studies including X-ray crystallography and NMR spectroscopy are utilized at all stages of lead generation beginning with target selection, validation, selectivity analysis and probing of target binding sites for druggability. This will be exemplified with comparative structures of target enzymes from different pathways. Hits identified through screening of compound and fragment libraries against these targets are progressed towards leads with the help of biophysical and structural analysis of protein-ligand complexes. Development of effective screening assays for enzyme targets requires a thorough understanding of enzyme mechanism. An example will be given of how water LOGSY measurements by NMR explained the mechanism of a multisubstrate cell wall enzyme. Finally, development of a lead series against a bacterial DNA replication enzyme beginning with a fragment based lead generation approach will be presented. In this approach, biochemical, biophysical and structural tools were employed to screen fragment libraries against the target enzyme and progress initial hits to drug-like leads. The availability of high-resolution target structure provided valuable chemistry guidance in designing such leads.

Challenges of fragment screening

Fragment-based screening for lead generation has seen tremendous growth and success in the last few years. Furthermore, the careful design of fragment libraries has ensured both that the coverage of chemical space is as great as possible and also that the included fragments have desirable physical properties. This particular effort has thus enhanced the advantages of a fragment-based approach. Other technological advances and applications have increased the speed of the process, resulting in more successful case studies being presented. Nonetheless challenges still remain. Weak fragment hits are often overlooked in favor of more potent HTS hits that may have poorer physical properties and ligand efficiencies. The timelines necessary to realize success with fragment-based screens can be long relative to other lead generation approaches, since fragment hits need to be given sufficient consideration and may require more cycles for optimization. A robust system for crystallography, which can be difficult to develop, can also dramatically affect the final outcome of a fragment-based lead generation campaign by enabling the determination of high-resolution complex structures that can serve as starting points for structure-based design. Active research is helping to address these challenges. Computational approaches that can aid in the optimization process either through growing or linking of fragments continue to be developed and can play a significant role in reducing the time required for improving the potency of an initial fragment lead. Methods aimed at exploiting fragment hits for uses other than scaffold generation are also being established to take full advantage of this information as well as any associated structural information available for a project. For example, fragment hits can be merged onto an HTS scaffold during the lead optimization process. In addition, for a given target, potential pharmacophores can be derived from fragment hits and later used for virtual screening of databases to enable scaffold hopping. Fragment positioning methods such as GRID [1], MCSS [2–4], SPROUT [5], MUSIC [6], LUDI [7, 8], and Superstar [9] have been in use for over two decades now and are typically employed during the early stage of lead optimization. These methods determine energetically favorable binding site positions for various functional group types or chemical fragments based on molecular mechanics or knowledge-based potentials. ‘‘Hot spots’’ can be calculated for a wide range of functional groups in a given target binding site/region. Such target-derived pharmacophoric points can also be used to guide docking calculations to more finely sample the relevant regions of a binding site (e.g., [10, 11]) or to perform pharmacophore searches of large databases. Caveat [12] and HOOK [13] were among the first ‘‘fragment-linking’’ computational approaches developed in the early 1990s. Newer generation computational methods continue to be developed (e.g., Re-core [14], Allegrow (Boston De Novo Design, Boston, MA, 2009), Confirm [15], MED-SuMo [16], and pharmacophore modeling for scaffold replacement in MOE (Chemical Computing Group, Montreal, Canada, 2009)) and successful uses of these newer programs are being reported. Increasingly, standard molecular docking programs are being utilized to screen large databases of small molecules to created target-focused fragment sets for experimental testing either in a high-concentration biochemical assay or by biophysical means such as NMR, Biacore, mass spectrometry, or X-ray crystallography. Focused fragment sets D. Joseph-McCarthy (&) Infection Computational Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA e-mail: diane.joseph-mccarthy@astrazeneca.com

Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology

For the detection of the precise and unambiguous binding of fragments to a specific binding site on the target protein, we have developed a novel reporter displacement binding assay technology. The application of this technology for the fragment screening as well as the fragment evolution process with a specific modelling based design strategy is demonstrated for inhibitors of the protein kinase p38alpha. In a fragment screening approach seed fragments were identified which were then used to build compounds from the deep-pocket towards the hinge binding area of the protein kinase p38alpha based on a modelling approach. BIRB796 was used as a blueprint for the alignment of the fragments. The fragment evolution of these deep-pocket binding fragments towards the fully optimized inhibitor BIRB796 included the modulation of the residence time as well as the affinity. The goal of our study was to evaluate the robustness and efficiency of our novel fragment screening technology at high fragment concentrations, compare the screening data with biochemical activity data and to demonstrate the evolution of the hit fragments with fast kinetics, into slow kinetic inhibitors in an in silico approach.

Recent progress in the drug discovery of non-peptidic BACE1 inhibitors

Background: β-Secretase, also called BACE1, is a promising molecular target for developing anti-Alzheimer's disease drugs. Several approaches of drug discovery for this therapy have been attempted, for example, substrate-based and structure-based designs, high-throughput screening, fragment-based lead generation and in silico screening. Method: In this review, we describe the design of non-peptidic BACE1 inhibitors from a historical perspective and not by the inhibitor's category. Conclusion: The respective methods have both merits and demerits and should be used in a mutually complementary manner.

Novel Prostaglandin D Synthase Inhibitors Generated by Fragment-Based Drug Design

We describe the discovery of novel inhibitors of prostaglandin D2 synthase (PGDS) through fragment-based lead generation and structure-based drug design. A library of 2500 low-molecular-weight compounds was screened using 2D nuclear magnetic resonance (NMR), leading to the identification of 24 primary hits. Structure determination of protein-ligand complexes with the hits enabled a hit optimization process, whereby we harvested increasingly more potent inhibitors out of our corporate compound collection. Two iterative cycles were carried out, comprising NMR screening, molecular modeling, X-ray crystallography, and in vitro biochemical testing. Six novel high-resolution PGDS complex structures were determined, and 300 hit analogues were tested. This rational drug design procedure culminated in the discovery of 24 compounds with an IC 50 below 1 microM in the in vitro assay. The best inhibitor (IC 50 = 21 nM) is one of the most potent inhibitors of PGDS to date. As such, it may enable new functional in vivo studies of PGDS and the prostaglandin metabolism pathway.

Discovery of a Novel Warhead against β-Secretase through Fragment-Based Lead Generation

Fragment-based lead generation was applied to find novel small-molecule inhibitors of beta-secretase (BACE-1), a key target for the treatment of Alzheimer's disease. Fragment hits coming from a 1D NMR screen were characterized by BIAcore, and the most promising compounds were soaked into protein crystals to help the rational design of more potent hit analogues. Problems arising due to our inability to grow BACE-1 crystals at the biologically relevant pH at which the screen was run were overcome by using endothiapepsin as a surrogate aspartyl protease. Among others, we identified 6-substituted isocytosines as a novel warhead against BACE-1, and the accompanying paper in this journal describes how these were optimized to a lead series of nanomolar inhibitors.1.

Application of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine β-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency

Fragment-based lead generation has led to the discovery of a novel series of cyclic amidine-based inhibitors of beta-secretase (BACE-1). Initial fragment hits with an isocytosine core having millimolar potency were identified via NMR affinity screening. Structure-guided evolution of these fragments using X-ray crystallography together with potency determination using surface plasmon resonance and functional enzyme inhibition assays afforded micromolar inhibitors. Similarity searching around the isocytosine core led to the identification of a related series of inhibitors, the dihydroisocytosines. By leveraging the knowledge of the ligand-BACE-1 recognition features generated from the isocytosines, the dihydroisocytosines were efficiently optimized to submicromolar potency. Compound 29, with an IC50 of 80 nM, a ligand efficiency of 0.37, and cellular activity of 470 nM, emerged as the lead structure for future optimization.