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1.
J Cheminform ; 14(1): 22, 2022 Apr 12.
Article in English | MEDLINE | ID: covidwho-1785168

ABSTRACT

We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy's graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 50000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year.

2.
ChemMedChem ; 17(7): e202100641, 2022 04 05.
Article in English | MEDLINE | ID: covidwho-1705258

ABSTRACT

The pentafluorosulfanyl (-SF5 ) functional group is of increasing interest as a bioisostere in medicinal chemistry. A library of SF5 -containing compounds, including amide, isoxazole, and oxindole derivatives, was synthesised using a range of solution-based and solventless methods, including microwave and ball-mill techniques. The library was tested against targets including human dihydroorotate dehydrogenase (HDHODH). A subsequent focused approach led to synthesis of analogues of the clinically used disease modifying anti-rheumatic drugs (DMARDs), Teriflunomide and Leflunomide, considered for potential COVID-19 use, where SF5 bioisostere deployment led to improved inhibition of HDHODH compared with the parent drugs. The results demonstrate the utility of the SF5 group in medicinal chemistry.


Subject(s)
Chemistry, Pharmaceutical , Amides , Humans
3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-314304

ABSTRACT

There is an increasingly urgent need for new antibiotics, yet there is a significant and persistent economic problem when it comes to developing such medicines. The problem stems from the perceived need for a “market” to drive commercial antibiotic development. In this article, we explore abandoning the market as a prerequisite for successful antibiotic research and development. Once one stops trying to fix a market model that has stopped functioning, one is free to carry out research and development (R&D) in ways that are more openly collaborative, a mechanism that has been demonstrably effective for the R&D underpinning the response to the COVID pandemic. New “open source” research models have great potential for the development of medicines for areas of public health where the traditional profit-driven model struggles to deliver. New financial initiatives, including major push/pull incentives, aimed at fixing the broken antibiotics market provide one possible means for funding an openly collaborative approach to drug development. We argue that now is therefore the time to evaluate, at scale, whether such methods can deliver new medicines through to patients, in a timely manner.

4.
Cell Chem Biol ; 28(12): 1795-1806.e5, 2021 12 16.
Article in English | MEDLINE | ID: covidwho-1599513

ABSTRACT

Designing covalent inhibitors is increasingly important, although it remains challenging. Here, we present covalentizer, a computational pipeline for identifying irreversible inhibitors based on structures of targets with non-covalent binders. Through covalent docking of tailored focused libraries, we identify candidates that can bind covalently to a nearby cysteine while preserving the interactions of the original molecule. We found âˆ¼11,000 cysteines proximal to a ligand across 8,386 complexes in the PDB. Of these, the protocol identified 1,553 structures with covalent predictions. In a prospective evaluation, five out of nine predicted covalent kinase inhibitors showed half-maximal inhibitory concentration (IC50) values between 155 nM and 4.5 µM. Application against an existing SARS-CoV Mpro reversible inhibitor led to an acrylamide inhibitor series with low micromolar IC50 values against SARS-CoV-2 Mpro. The docking was validated by 12 co-crystal structures. Together these examples hint at the vast number of covalent inhibitors accessible through our protocol.


Subject(s)
Drug Design , Protein Kinase Inhibitors/chemistry , SARS-CoV-2/enzymology , Viral Matrix Proteins/antagonists & inhibitors , Acrylamide/chemistry , Acrylamide/metabolism , Binding Sites , COVID-19/pathology , COVID-19/virology , Catalytic Domain , Computational Biology/methods , Databases, Protein , Humans , Inhibitory Concentration 50 , Molecular Docking Simulation , Protein Kinase Inhibitors/metabolism , SARS-CoV-2/isolation & purification , Viral Matrix Proteins/metabolism
5.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-295875

ABSTRACT

A common challenge in drug design pertains to finding chemical modifications to a ligand that increases its affinity to the target protein. An underutilised advance is the increase in structural biology throughput, which has progressed from an artisanal endeavour to a monthly throughput of up to 100 different ligands against a protein in modern synchrotrons. However, the missing piece is a framework that turns high throughput crystallography data into predictive models for ligand design. Here we designed a simple machine learning approach that predicts protein-ligand affinity from experimental structures of diverse ligands against a single protein paired with biochemical measurements. Our key insight is using physics-based energy descriptors to represent protein-ligand complexes, and a learning-to-rank approach that infers the relevant differences between binding modes. We ran a high throughput crystallography campaign against the SARS-CoV-2 Main Protease (M Pro ), obtaining parallel measurements of over 200 protein-ligand complexes and the binding activity. This allows us to design a one-step library syntheses which improved the potency of two distinct micromolar hits by over 10-fold, arriving at a non-covalent and non-peptidomimetic inhibitor with 120 nM antiviral efficacy. Crucially, our approach successfully extends ligands to unexplored regions of the binding pocket, executing large and fruitful moves in chemical space with simple chemistry.

7.
Nat Commun ; 12(1): 3201, 2021 05 27.
Article in English | MEDLINE | ID: covidwho-1387343

ABSTRACT

Fragment-based drug design has introduced a bottom-up process for drug development, with improved sampling of chemical space and increased effectiveness in early drug discovery. Here, we combine the use of pharmacophores, the most general concept of representing drug-target interactions with the theory of protein hotspots, to develop a design protocol for fragment libraries. The SpotXplorer approach compiles small fragment libraries that maximize the coverage of experimentally confirmed binding pharmacophores at the most preferred hotspots. The efficiency of this approach is demonstrated with a pilot library of 96 fragment-sized compounds (SpotXplorer0) that is validated on popular target classes and emerging drug targets. Biochemical screening against a set of GPCRs and proteases retrieves compounds containing an average of 70% of known pharmacophores for these targets. More importantly, SpotXplorer0 screening identifies confirmed hits against recently established challenging targets such as the histone methyltransferase SETD2, the main protease (3CLPro) and the NSP3 macrodomain of SARS-CoV-2.


Subject(s)
Coronavirus 3C Proteases/chemistry , Coronavirus Papain-Like Proteases/chemistry , Drug Development/methods , Drug Discovery/methods , High-Throughput Screening Assays/methods , Histone-Lysine N-Methyltransferase/chemistry , Animals , Cell Survival , Chlorocebus aethiops , Computational Chemistry , Crystallography, X-Ray , Databases, Protein , Drug Design , HEK293 Cells , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Ligands , Protein Binding , Receptors, G-Protein-Coupled/chemistry , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , Small Molecule Libraries , Vero Cells
8.
Nat Commun ; 12(1): 4848, 2021 08 11.
Article in English | MEDLINE | ID: covidwho-1354102

ABSTRACT

There is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication. Structural analysis reveals two "druggable" pockets on NSP13 that are among the most conserved sites in the entire SARS-CoV-2 proteome. Here we present crystal structures of SARS-CoV-2 NSP13 solved in the APO form and in the presence of both phosphate and a non-hydrolysable ATP analog. Comparisons of these structures reveal details of conformational changes that provide insights into the helicase mechanism and possible modes of inhibition. To identify starting points for drug development we have performed a crystallographic fragment screen against NSP13. The screen reveals 65 fragment hits across 52 datasets opening the way to structure guided development of novel antiviral agents.


Subject(s)
Methyltransferases/chemistry , RNA Helicases/chemistry , SARS-CoV-2/chemistry , Viral Nonstructural Proteins/chemistry , Adenosine Triphosphate/chemistry , Adenosine Triphosphate/metabolism , Amino Acid Sequence , Apoenzymes/chemistry , Apoenzymes/metabolism , Binding Sites , Crystallography, X-Ray , Drug Design , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Methyltransferases/antagonists & inhibitors , Methyltransferases/metabolism , Models, Molecular , Phosphates/chemistry , Phosphates/metabolism , Protein Conformation , RNA Helicases/antagonists & inhibitors , RNA Helicases/metabolism , RNA, Viral/chemistry , RNA, Viral/metabolism , SARS-CoV-2/enzymology , Structure-Activity Relationship , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/metabolism
9.
Wellcome Open Res ; 6: 146, 2021.
Article in English | MEDLINE | ID: covidwho-1296224

ABSTRACT

There is an increasingly urgent need for new antibiotics, yet there is a significant and persistent economic problem when it comes to developing such medicines. The problem stems from the perceived need for a "market" to drive commercial antibiotic development. In this article, we explore abandoning the market as a prerequisite for successful antibiotic research and development. Once one stops trying to fix a market model that has stopped functioning, one is free to carry out research and development (R&D) in ways that are more openly collaborative, a mechanism that has been demonstrably effective for the R&D underpinning the response to the COVID pandemic. New "open source" research models have great potential for the development of medicines for areas of public health where the traditional profit-driven model struggles to deliver. New financial initiatives, including major push/pull incentives, aimed at fixing the broken antibiotics market provide one possible means for funding an openly collaborative approach to drug development. We argue that now is therefore the time to evaluate, at scale, whether such methods can deliver new medicines through to patients, in a timely manner.

10.
Sci Rep ; 11(1): 13208, 2021 06 24.
Article in English | MEDLINE | ID: covidwho-1281733

ABSTRACT

Effective agents to treat coronavirus infection are urgently required, not only to treat COVID-19, but to prepare for future outbreaks. Repurposed anti-virals such as remdesivir and human anti-inflammatories such as barcitinib have received emergency approval but their overall benefits remain unclear. Vaccines are the most promising prospect for COVID-19, but will need to be redeveloped for any future coronavirus outbreak. Protecting against future outbreaks requires the identification of targets that are conserved between coronavirus strains and amenable to drug discovery. Two such targets are the main protease (Mpro) and the papain-like protease (PLpro) which are essential for the coronavirus replication cycle. We describe the discovery of two non-antiviral therapeutic agents, the caspase-1 inhibitor SDZ 224015 and Tarloxotinib that target Mpro and PLpro, respectively. These were identified through extensive experimental screens of the drug repurposing ReFRAME library of 12,000 therapeutic agents. The caspase-1 inhibitor SDZ 224015, was found to be a potent irreversible inhibitor of Mpro (IC50 30 nM) while Tarloxotinib, a clinical stage epidermal growth factor receptor inhibitor, is a sub micromolar inhibitor of PLpro (IC50 300 nM, Ki 200 nM) and is the first reported PLpro inhibitor with drug-like properties. SDZ 224015 and Tarloxotinib have both undergone safety evaluation in humans and hence are candidates for COVID-19 clinical evaluation.


Subject(s)
Antiviral Agents/chemistry , COVID-19/drug therapy , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus Papain-Like Proteases/antagonists & inhibitors , Drug Repositioning , Oligopeptides/chemistry , Cell Line , Humans , Serpins/chemistry , Viral Proteins/chemistry
12.
J Vis Exp ; (171)2021 05 29.
Article in English | MEDLINE | ID: covidwho-1268367

ABSTRACT

In fragment-based drug discovery, hundreds or often thousands of compounds smaller than ~300 Da are tested against the protein of interest to identify chemical entities that can be developed into potent drug candidates. Since the compounds are small, interactions are weak, and the screening method must therefore be highly sensitive; moreover, structural information tends to be crucial for elaborating these hits into lead-like compounds. Therefore, protein crystallography has always been a gold-standard technique, yet historically too challenging to find widespread use as a primary screen. Initial XChem experiments were demonstrated in 2014 and then trialed with academic and industrial collaborators to validate the process. Since then, a large research effort and significant beamtime have streamlined sample preparation, developed a fragment library with rapid follow-up possibilities, automated and improved the capability of I04-1 beamline for unattended data collection, and implemented new tools for data management, analysis and hit identification. XChem is now a facility for large-scale crystallographic fragment screening, supporting the entire crystals-to-deposition process, and accessible to academic and industrial users worldwide. The peer-reviewed academic user program has been actively developed since 2016, to accommodate projects from as broad a scientific scope as possible, including well-validated as well as exploratory projects. Academic access is allocated through biannual calls for peer-reviewed proposals, and proprietary work is arranged by Diamond's Industrial Liaison group. This workflow has already been routinely applied to over a hundred targets from diverse therapeutic areas, and effectively identifies weak binders (1%-30% hit rate), which both serve as high-quality starting points for compound design and provide extensive structural information on binding sites. The resilience of the process was demonstrated by continued screening of SARS-CoV-2 targets during the COVID-19 pandemic, including a 3-week turn-around for the main protease.


Subject(s)
Crystallography, X-Ray/methods , Drug Discovery/methods , Proteins/chemistry , Humans
13.
Sci Adv ; 7(16)2021 04.
Article in English | MEDLINE | ID: covidwho-1186193

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate-ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.


Subject(s)
Catalytic Domain/physiology , Protein Binding/physiology , Viral Nonstructural Proteins/metabolism , COVID-19/drug therapy , Catalytic Domain/genetics , Crystallography, X-Ray , Humans , Models, Molecular , Molecular Docking Simulation , Protein Conformation , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Viral Nonstructural Proteins/genetics
15.
Curr Opin Struct Biol ; 65: 209-216, 2020 12.
Article in English | MEDLINE | ID: covidwho-1065572

ABSTRACT

Understanding allosteric regulation of proteins is fundamental to our study of protein structure and function. Moreover, allosteric binding pockets have become a major target of drug discovery efforts in recent years. However, even though the function of almost every protein can be influenced by allostery, it remains a challenge to discover, rationalise and validate putative allosteric binding pockets. This review examines how the discovery and analysis of putative allosteric binding sites have been influenced by the availability of centralised facilities for crystallographic fragment screening, along with newly developed computational methods for modelling low occupancy features. We discuss the experimental parameters required for success, and how new methods could influence the field in the future. Finally, we reflect on the general problem of how to translate these findings into actual ligand development programs.


Subject(s)
Proteins , Allosteric Regulation , Allosteric Site , Humans , Ligands , Protein Binding , Protein Conformation , Proteins/chemistry , Proteins/metabolism
16.
Nat Commun ; 11(1): 5047, 2020 10 07.
Article in English | MEDLINE | ID: covidwho-841208

ABSTRACT

COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.


Subject(s)
Betacoronavirus/chemistry , Cysteine Endopeptidases/chemistry , Peptide Fragments/chemistry , Viral Nonstructural Proteins/chemistry , Betacoronavirus/enzymology , Binding Sites , Catalytic Domain , Coronavirus 3C Proteases , Crystallography, X-Ray , Cysteine Endopeptidases/metabolism , Drug Design , Mass Spectrometry , Models, Molecular , Peptide Fragments/metabolism , Protein Conformation , SARS-CoV-2 , Small Molecule Libraries/chemistry , Small Molecule Libraries/metabolism , Static Electricity , Viral Nonstructural Proteins/metabolism
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