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Herbst C, Endres S, Würz R, Sotriffer C. Assessment of fragment docking and scoring with the endothiapepsin model system. Arch Pharm (Weinheim) 2024; 357:e2400061. [PMID: 38631672 DOI: 10.1002/ardp.202400061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Fragment-based screening has become indispensable in drug discovery. Yet, the weak binding affinities of these small molecules still represent a challenge for the reliable detection of fragment hits. The extent of this issue was illustrated in the literature for the aspartic protease endothiapepsin: When seven biochemical and biophysical in vitro screening methods were applied to screen a library of 361 fragments, very poor overlap was observed between the hit fragments identified by the individual approaches, resulting in high levels of false positive and/or false negative results depending on the mutually compared methods. Here, the reported in vitro findings are juxtaposed with the results from in silico docking and scoring approaches. The docking programs GOLD and Glide were considered with the scoring functions ASP, ChemScore, ChemPLP, GoldScore, DSXCSD, and GlideScore. First, the ranking power and scoring power were assessed for the named scoring functions. Second, the capability of reproducing the crystallized fragment binding modes was tested in a structure-based redocking approach. The redocking success notably depended on the ligand efficiency of the considered fragments. Third, a blinded virtual screening approach was employed to evaluate whether in silico screening can compete with in vitro methods in the enrichment of fragment databases.
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Affiliation(s)
- Carina Herbst
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Sara Endres
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Rebecca Würz
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
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2
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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:10669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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Affiliation(s)
| | | | | | | | - Sangeeta Tiwari
- Department of Biological Sciences & Border Biomedical Research Centre, University of Texas at El Paso, El Paso, TX 79968, USA
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Synthesis of oleanolic acid hydrazide-hydrazone hybrid derivatives and investigation of their cytotoxic effects on A549 human lung cancer cells. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Behera BK, Sahu AK, Devi NR, Saikia AK. K 2S 2O 8-Mediated Synthesis of Highly Functionalized Pyrroles via Oxidative Self-Dimerization of N-Propargylamines. J Org Chem 2021; 86:12481-12493. [PMID: 34463507 DOI: 10.1021/acs.joc.1c00471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient methodology has been developed for the synthesis of tetra- and pentasubstituted pyrroles via oxidative self-dimerization of N-propargylamines catalyzed by silver benzoate in the presence of K2S2O8 in good yields. The protocol provides a simple route for the synthesis of both tetra- and pentasubstituted pyrroles with two carbonyl groups in the side chain. The methodology can be extended toward the synthesis of pyrrolo[3,4-d]pyridazine.
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Affiliation(s)
- Bipin Kumar Behera
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Archana Kumari Sahu
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Ngangbam Renubala Devi
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Anil K Saikia
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India
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Rathod B, Chak S, Patel S, Shard A. Tumor pyruvate kinase M2 modulators: a comprehensive account of activators and inhibitors as anticancer agents. RSC Med Chem 2021; 12:1121-1141. [PMID: 34355179 PMCID: PMC8292966 DOI: 10.1039/d1md00045d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
Pyruvate kinase M2 (PKM2) catalyzes the conversion of phosphoenolpyruvate (PEP) to pyruvate. It plays a central role in the metabolic reprogramming of cancer cells and is expressed in most human tumors. It is essential in indiscriminate proliferation, survival, and tackling apoptosis in cancer cells. This positions PKM2 as a hot target in cancer therapy. Despite its well-known structure and several reported modulators targeting PKM2 as activators or inhibitors, a comprehensive review focusing on such modulators is lacking. Herein we summarize modulators of PKM2, the assays used to detect their potential, the preferable tense (T) and relaxed (R) states in which the enzyme resides, lacunae in existing modulators, and several strategies that may lead to effective anticancer drug development targeting PKM2.
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Affiliation(s)
- Bhagyashri Rathod
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad Opposite Air Force Station Gandhinagar Gujarat 382355 India
| | - Shivam Chak
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad Opposite Air Force Station Gandhinagar Gujarat 382355 India
| | - Sagarkumar Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad Opposite Air Force Station Gandhinagar Gujarat 382355 India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad Opposite Air Force Station Gandhinagar Gujarat 382355 India
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Rana A, Galmés B, Frontera A, Biswal HS, Chopra D. Unravelling the electronic nature of C-FO-C non-covalent interaction in proteins and small molecules in the solid state. Phys Chem Chem Phys 2020; 22:25704-25711. [PMID: 33146185 DOI: 10.1039/d0cp05280a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The participation of organic fluorine as a halogen bond donor is rare and is sensitive to the electronic environment in the vicinity of the fluorine atom. The enhancement in the electropositive character (the σ-hole formalism) in fluorine is established by the presence of electron withdrawing groups and this has been examined in the solid-state structures in small molecules and proteins. Short, directional FO contacts have been observed and physical insights obtained, from quantum mechanical calculations, via the molecular electrostatic potential, an analysis of their topological features from atoms-in-molecules, and donor-acceptor characteristics from natural bond orbital analyses. It was observed that such contacts, cooperatively act in the presence of other interactions, and the formed aggregates are stabilizing in nature. In addition, the FO has a bonding character and is attractive in nature. The halogen bonding character of fluorine is relevant in supramolecular chemistry.
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Affiliation(s)
- Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, 752050, Bhubaneswar, India.
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Li Q. Application of Fragment-Based Drug Discovery to Versatile Targets. Front Mol Biosci 2020; 7:180. [PMID: 32850968 PMCID: PMC7419598 DOI: 10.3389/fmolb.2020.00180] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, China
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Glöckner S, Heine A, Klebe G. A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II. Biomolecules 2020; 10:biom10040518. [PMID: 32235320 PMCID: PMC7226012 DOI: 10.3390/biom10040518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 11/16/2022] Open
Abstract
Fragment screening is a powerful tool to identify and characterize binding pockets in proteins. We herein present the results of a proof-of-concept screening campaign of a versatile 96-entry fragment library from our laboratory against the drug target and model protein human carbonic anhydrase II. The screening revealed a novel chemotype for carbonic anhydrase inhibition, as well as less common non-covalent interaction types and unexpected covalent linkages. Lastly, different runs of the PanDDA tool reveal a practical hint for its application.
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Abstract
Introduction: The development of drug candidates with a defined selectivity profile and a unique molecular structure is of fundamental interest for drug discovery. In contrast to the costly screening of large substance libraries, the targeted de novo design of a drug by using structural information of either the biological target and/or structure-activity relationship data of active modulators offers an efficient and intellectually appealing alternative. Areas covered: This review provides an overview on the different techniques of de novo drug design (ligand-based drug design, structure-based drug design, and fragment-based drug design) and highlights successful examples of this targeted approach toward selective modulators of therapeutically relevant targets. Expert opinion: De novo drug design has established itself as a very efficient method for the development of potent and selective modulators for a variety of different biological target classes. The ever-growing wealth of structural data on therapeutic targets will certainly further enhance the importance of de novo design for the drug discovery process in the future. However, a consistent use of the terminology of de novo drug design in the scientific literature should be sought.
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Affiliation(s)
- Thomas Fischer
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
| | - Silvia Gazzola
- b Dipartimento di Scienza e Alta Tecnologia , Università degli Studi dell'Insubria , Como , Italy
| | - Rainer Riedl
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
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Huang X, Guo J, Liu Q, Gu Q, Xu J, Zhou H. Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes. MEDCHEMCOMM 2018; 9:1619-1629. [PMID: 30429968 DOI: 10.1039/c8md00148k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/03/2018] [Indexed: 12/21/2022]
Abstract
Discovery of new drug binding sites on well-established targets is of great interest as it facilitates the design of new mechanistic inhibitors to overcome the acquired drug resistance. Small chemical fragments can easily enter and bind to the cavities on the protein surface. Thus, they can be used to probe new druggable pockets in proteins. DNA gyrase plays indispensable roles in DNA replication, and both its GyrA and GyrB subunits are clinically validated antibacterial targets. New mechanistic GyrB inhibitors are urgently desired since the withdrawal of novobiocin from the market by the FDA due to its reduced efficiency and other reasons. Here, a fragment library was screened against the E. coli GyrB ATPase domain by combining affinity- and bioactivity-based approaches. The following X-ray crystallographic efforts were made to determine the cocrystal structures of GyrB with ten fragment hits, and three different binding modes were disclosed. Fortunately, a hydrophobic pocket which is previously unknown was identified by two fragments. Fragments that bind to this pocket were shown to inhibit the ATPase activity as well as the DNA topological transition activity of DNA gyrase in vitro. A set of fragment analogs were screened to explore the binding capacity of this pocket and identify the better starting fragments for lead development. Phylogenetic analysis revealed that this pocket is conserved in most Gram-negative and also many Gram-positive human pathogenic bacteria, implying a broad-spectrum antibacterial potential and a lower risk of mutation. Thus, the novel druggable pocket and the starting fragments provide a novel basis for designing new GyrB-targeting therapeutics.
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Affiliation(s)
- Xiaojie Huang
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Junsong Guo
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Qi Liu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Qiong Gu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Jun Xu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Huihao Zhou
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
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11
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Kenny PW. Comment on The Ecstasy and Agony of Assay Interference Compounds. J Chem Inf Model 2017; 57:2640-2645. [DOI: 10.1021/acs.jcim.7b00313] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Peter W. Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
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