1
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Eguida M, Bret G, Sindt F, Li F, Chau I, Ackloo S, Arrowsmith C, Bolotokova A, Ghiabi P, Gibson E, Halabelian L, Houliston S, Harding RJ, Hutchinson A, Loppnau P, Perveen S, Seitova A, Zeng H, Schapira M, Rognan D. Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2. J Chem Inf Model 2024; 64:5344-5355. [PMID: 38916159 DOI: 10.1021/acs.jcim.4c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
We herewith applied a priori a generic hit identification method (POEM) for difficult targets of known three-dimensional structure, relying on the simple knowledge of physicochemical and topological properties of a user-selected cavity. Searching for local similarity to a set of fragment-bound protein microenvironments of known structure, a point cloud registration algorithm is first applied to align known subpockets to the target cavity. The resulting alignment then permits us to directly pose the corresponding seed fragments in a target cavity space not typically amenable to classical docking approaches. Last, linking potentially connectable atoms by a deep generative linker enables full ligand enumeration. When applied to the WD40 repeat (WDR) central cavity of leucine-rich repeat kinase 2 (LRRK2), an unprecedented binding site, POEM was able to quickly propose 94 potential hits, five of which were subsequently confirmed to bind in vitro to LRRK2-WDR.
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Affiliation(s)
- Merveille Eguida
- Laboratoire d'innovation thérapeutique, UMR7200 CNRS-Université de Strasbourg, F-67400 Illkirch, Strasbourg, France
| | - Guillaume Bret
- Laboratoire d'innovation thérapeutique, UMR7200 CNRS-Université de Strasbourg, F-67400 Illkirch, Strasbourg, France
| | - François Sindt
- Laboratoire d'innovation thérapeutique, UMR7200 CNRS-Université de Strasbourg, F-67400 Illkirch, Strasbourg, France
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Albina Bolotokova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Pegah Ghiabi
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Elisa Gibson
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Sumera Perveen
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Almagul Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Didier Rognan
- Laboratoire d'innovation thérapeutique, UMR7200 CNRS-Université de Strasbourg, F-67400 Illkirch, Strasbourg, France
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2
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Almuqdadi HTA, Kifayat S, Anwer R, Alrehaili J, Abid M. Fragment-based virtual screening identifies novel leads against Plasmepsin IX (PlmIX) of Plasmodium falciparum: Homology modeling, molecular docking, and simulation approaches. Front Pharmacol 2024; 15:1387629. [PMID: 38846093 PMCID: PMC11153788 DOI: 10.3389/fphar.2024.1387629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/24/2024] [Indexed: 06/09/2024] Open
Abstract
Despite continuous efforts to develop safer and efficient medications, malaria remains a major threat posing great challenges for new drug discovery. The emerging drug resistance, increased toxicities, and impoverished pharmacokinetic profiles exhibited by conventional drugs have hindered the search for new entities. Plasmepsins, a group of Plasmodium-specific, aspartic acid protease enzymes, are involved in many key aspects of parasite biology, and this makes them interesting targets for antimalarial chemotherapy. Among different isoforms, PlmIX serves as an unexplored antimalarial drug target that plays a crucial role along with PlmV and X in the parasite's survival by digesting hemoglobin in the host's erythrocytes. In this study, fragment-based virtual screening was performed by modeling the three-dimensional structure of PlmIX and predicting its ligand-binding pocket by using the Sitemap tool. Screening identified the fragments with the XP docking score ≤ -3 kcal/mol from the OTAVA General Fragment Library (≈16,397 fragments), and the selected fragments were chosen for ligand breeding. The resulting ligands (≈69,858 ligands) were subsequently subjected to filtering based on the QikProp properties along with carcinogenicity testing performed using CarcinoPred-EL and then docked in the SP (≈14,078 ligands) as well as XP mode (≈3,104 ligands), and compared with that of control ligands 49C and I0L. The top-ranked ligands were taken further for the calculation of the free energy of binding using Prime MM-GBSA. Overall, a total of six complexes were taken further for MD simulation studies performed at 100 ns to attain a better understanding of the binding mechanisms, and compounds 3 and 4 were found to be the most efficient ones in silico. The analysis of compound 3 revealed that the carbonyl group present in position 1 on the isoindoline moiety (Arg554) was responsible for inhibitory activity against PlmIX. However, the analysis of compound 4 revealed that the amide linkage sandwiched between the phenyl ring and isoquinoline moiety (Lys555 and Ser226) as well as carbonyl oxygen of the carbamoyl group present at position 2 of the pyrazole ring (Gln222) were responsible for PlmIX inhibitory activity, owing to their crucial interactions with key amino acid residues.
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Affiliation(s)
- Haider Thaer Abdulhameed Almuqdadi
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- Department of Chemistry, College of Science, Al-Nahrain University, Baghdad, Iraq
| | - Sumaiya Kifayat
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Jihad Alrehaili
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
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3
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Vemula V, Marudamuthu AS, Prasad S, B M S, S E M, A S, Seal P, Alagumuthu M. Fragment-based design and MD simulations of human papilloma virus-16 E6 protein inhibitors. J Biomol Struct Dyn 2024; 42:288-297. [PMID: 37098806 DOI: 10.1080/07391102.2023.2203775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/10/2023] [Indexed: 04/27/2023]
Abstract
The main objective of this study is to screen potential small molecule inhibitors against HPV (Human Papilloma Virus)-16 E6 protein (HPV16 E6P) using a fragment-based approach. Twenty-six natural HPV inhibitors were selected based on the review of the literature. Among them, Luteolin was selected as the reference compound. These 26 compounds were used to generate novel inhibitors against HPV16 E6P. Fragment script and BREED of Schrodinger software were used to build novel inhibitor molecules. The result in 817 novel molecules was docked into the active binding site of HPV E6 protein and the top ten compounds were screened based on binding affinity compared to Luteolin for further study. Compounds Cpd5, Cpd7, and Cpd10 were the most potent inhibitors of HPV16 E6P and these were non-toxic and showed high Gastrointestinal (GI) absorption and positive drug-likeness score. Complexes of these compounds were stable in the 200 ns Molecular Dynamics (MD) simulation. These 3 HPV16 E6P inhibitors could be the lead molecules as new drugs for HPV-related diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vani Vemula
- Department of Microbiology, M. S. Ramaiah College of Arts, Science and Commerce, Bengaluru, India
| | | | - Sanjay Prasad
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru, India
| | - Suman B M
- Department of Microbiology, M. S. Ramaiah College of Arts, Science and Commerce, Bengaluru, India
| | - Mamatha S E
- Department of Microbiology, M. S. Ramaiah College of Arts, Science and Commerce, Bengaluru, India
| | - Swathi A
- Department of Microbiology, M. S. Ramaiah College of Arts, Science and Commerce, Bengaluru, India
| | - Priyanka Seal
- Department of Microbiology, M. S. Ramaiah College of Arts, Science and Commerce, Bengaluru, India
| | - Manikandan Alagumuthu
- Department of Microbiology, M. S. Ramaiah College of Arts, Science and Commerce, Bengaluru, India
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4
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Lotfi B, Mebarka O, Alhatlani BY, Abdallah EM, Kawsar SMA. Pharmacoinformatics and Breed-Based De Novo Hybridization Studies to Develop New Neuraminidase Inhibitors as Potential Anti-Influenza Agents. Molecules 2023; 28:6678. [PMID: 37764457 PMCID: PMC10534564 DOI: 10.3390/molecules28186678] [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: 08/26/2023] [Revised: 09/09/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza represents a profoundly transmissible viral ailment primarily afflicting the respiratory system. Neuraminidase inhibitors constitute a class of antiviral therapeutics employed in the management of influenza. These inhibitors impede the liberation of the viral neuraminidase protein, thereby impeding viral dissemination from the infected cell to host cells. As such, neuraminidase has emerged as a pivotal target for mitigating influenza and its associated complications. Here, we apply a de novo hybridization approach based on a breed-centric methodology to elucidate novel neuraminidase inhibitors. The breed technique amalgamates established ligand frameworks with the shared target, neuraminidase, resulting in innovative inhibitor constructs. Molecular docking analysis revealed that the seven synthesized breed molecules (designated Breeds 1-7) formed more robust complexes with the neuraminidase receptor than conventional clinical neuraminidase inhibitors such as zanamivir, oseltamivir, and peramivir. Pharmacokinetic evaluations of the seven breed molecules (Breeds 1-7) demonstrated favorable bioavailability and optimal permeability, all falling within the specified parameters for human application. Molecular dynamics simulations spanning 100 nanoseconds corroborated the stability of these breed molecules within the active site of neuraminidase, shedding light on their structural dynamics. Binding energy assessments, which were conducted through MM-PBSA analysis, substantiated the enduring complexes formed by the seven types of molecules and the neuraminidase receptor. Last, the investigation employed a reaction-based enumeration technique to ascertain the synthetic pathways for the synthesis of the seven breed molecules.
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Affiliation(s)
- Bourougaa Lotfi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 70700, Algeria;
| | - Ouassaf Mebarka
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 70700, Algeria;
| | - Bader Y. Alhatlani
- Unit of Scientific Research, Applied College, Qassim University, Buraydah 52571, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia;
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh;
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5
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Bryan DR, Kulp JL, Mahapatra MK, Bryan RL, Viswanathan U, Carlisle MN, Kim S, Schutte WD, Clarke KV, Doan TT, Kulp JL. BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation. J Chem Inf Model 2023; 63:4229-4236. [PMID: 37406353 DOI: 10.1021/acs.jcim.3c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Fragment-based drug design uses data about where, and how strongly, small chemical fragments bind to proteins, to assemble new drug molecules. Over the past decade, we have been successfully using fragment data, derived from thermodynamically rigorous Monte Carlo fragment-protein binding simulations, in dozens of preclinical drug programs. However, this approach has not been available to the broader research community because of the cost and complexity of doing simulations and using design tools. We have developed a web application, called BMaps, to make fragment-based drug design widely available with greatly simplified user interfaces. BMaps provides access to a large repository (>550) of proteins with 100s of precomputed fragment maps, druggable hot spots, and high-quality water maps. Users can also employ their own structures or those from the Protein Data Bank and AlphaFold DB. Multigigabyte data sets are searched to find fragments in bondable orientations, ranked by a binding-free energy metric. The designers use this to select modifications that improve affinity and other properties. BMaps is unique in combining conventional tools such as docking and energy minimization with fragment-based design, in a very easy to use and automated web application. The service is available at https://www.boltzmannmaps.com.
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Affiliation(s)
- Daniel R Bryan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - John L Kulp
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Zymergen, Inc., 430 E. 29th Street, Suite 625, New York, New York 10016, United States
| | - Manoj K Mahapatra
- Kanak Manjari Institute of Pharmaceutical Sciences, Rourkela 769015, Odisha, India
| | - Richard L Bryan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Usha Viswanathan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Micah N Carlisle
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Surim Kim
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Zymergen, Inc., 430 E. 29th Street, Suite 625, New York, New York 10016, United States
| | - William D Schutte
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Kevaughn V Clarke
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Tony T Doan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - John L Kulp
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
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6
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Wills S, Sanchez-Garcia R, Dudgeon T, Roughley SD, Merritt A, Hubbard RE, Davidson J, von Delft F, Deane CM. Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search. J Chem Inf Model 2023. [PMID: 37229647 DOI: 10.1021/acs.jcim.3c00276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fragment merging is a promising approach to progressing fragments directly to on-scale potency: each designed compound incorporates the structural motifs of overlapping fragments in a way that ensures compounds recapitulate multiple high-quality interactions. Searching commercial catalogues provides one useful way to quickly and cheaply identify such merges and circumvents the challenge of synthetic accessibility, provided they can be readily identified. Here, we demonstrate that the Fragment Network, a graph database that provides a novel way to explore the chemical space surrounding fragment hits, is well-suited to this challenge. We use an iteration of the database containing >120 million catalogue compounds to find fragment merges for four crystallographic screening campaigns and contrast the results with a traditional fingerprint-based similarity search. The two approaches identify complementary sets of merges that recapitulate the observed fragment-protein interactions but lie in different regions of chemical space. We further show our methodology is an effective route to achieving on-scale potency by retrospective analyses for two different targets; in analyses of public COVID Moonshot and Mycobacterium tuberculosis EthR inhibitors, potential inhibitors with micromolar IC50 values were identified. This work demonstrates the use of the Fragment Network to increase the yield of fragment merges beyond that of a classical catalogue search.
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Affiliation(s)
- Stephanie Wills
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
- Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ruben Sanchez-Garcia
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
- Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Tim Dudgeon
- Informatics Matters, Ltd., Perch Coworking, Franklins House, Bicester OX26 6JU, United Kingdom
| | - Stephen D Roughley
- Vernalis (R&D) Limited, Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom
| | - Andy Merritt
- LifeArc, Lynton House, 7-12 Tavistock Square, London WC1H 9LT, United Kingdom
| | - Roderick E Hubbard
- Vernalis (R&D) Limited, Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom
| | - James Davidson
- Vernalis (R&D) Limited, Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, United Kingdom
- Diamond Light Source, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
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7
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He F, Wang X, Wu Q, Liu S, Cao Y, Guo X, Yin S, Yin N, Li B, Fang M. Identification of potential ATP-competitive cyclin-dependent kinase 1 inhibitors: De novo drug generation, molecular docking, and molecular dynamics simulation. Comput Biol Med 2023; 155:106645. [PMID: 36774892 DOI: 10.1016/j.compbiomed.2023.106645] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Cyclin-dependent kinases 1 (CDK1) has been identified as a potential target for the search for new antitumor drugs. However, no clinically effective CDK1 inhibitors are now available for cancer treatment. Therefore, this study aimed to offer potential CDK1 inhibitors using de novo drug generation, molecular docking, and molecular dynamics (MD) simulation studies. We first utilized the BREED algorithm (a de novo drug generation approach) to produce a novel library of small molecules targeting CDK1. To initially obtain novel potential CDK1 inhibitors with favorable physicochemical properties and excellent druggability, we performed a virtual rule-based rational drug screening on our generated library and found ten initial hits. Then, the molecular interactions and dynamic stability of these ten initial hits and CDK1 complexes during their all-atom MD simulations (total 18 μs) and binding pose metadynamics simulations were investigated, resulting in five final hits. Furthermore, another MD simulation (total 2.1 μs) with different force fields demonstrated the binding ability of the five hits to CDK1. It was found that these five hits, CBMA001 (ΔG = -29.88 kcal/mol), CBMA002 (ΔG = -34.89 kcal/mol), CBMA004 (ΔG = -32.47 kcal/mol), CBMA007 (ΔG = -31.16 kcal/mol), and CBMA008 (ΔG = -34.78 kcal/mol) possessed much greater binding affinity to CDK1 than positive compound Flavopiridol (FLP, ΔG = -25.38 kcal/mol). Finally, CBMA002 and CBMA004 were identified as excellent selective CDK1 inhibitors in silico. Together, this study provides a workflow for rational drug design and two promising selective CDK1 inhibitors that deserve further investigation.
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Affiliation(s)
- Fengming He
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiumei Wang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Qiaoqiong Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Shunzhi Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Yin Cao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaodan Guo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Sihang Yin
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Na Yin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, University Town, Guangzhou, 510006, China
| | - Baicun Li
- National Center for Respiratory Medicine Laboratories, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, 100029, China; National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Meijuan Fang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China.
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8
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Wang M, Wang J, Weng G, Kang Y, Pan P, Li D, Deng Y, Li H, Hsieh CY, Hou T. ReMODE: a deep learning-based web server for target-specific drug design. J Cheminform 2022; 14:84. [PMID: 36510307 PMCID: PMC9743675 DOI: 10.1186/s13321-022-00665-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Deep learning (DL) and machine learning contribute significantly to basic biology research and drug discovery in the past few decades. Recent advances in DL-based generative models have led to superior developments in de novo drug design. However, data availability, deep data processing, and the lack of user-friendly DL tools and interfaces make it difficult to apply these DL techniques to drug design. We hereby present ReMODE (Receptor-based MOlecular DEsign), a new web server based on DL algorithm for target-specific ligand design, which integrates different functional modules to enable users to develop customizable drug design tasks. As designed, the ReMODE sever can construct the target-specific tasks toward the protein targets selected by users. Meanwhile, the server also provides some extensions: users can optimize the drug-likeness or synthetic accessibility of the generated molecules, and control other physicochemical properties; users can also choose a sub-structure/scaffold as a starting point for fragment-based drug design. The ReMODE server also enables users to optimize the pharmacophore matching and docking conformations of the generated molecules. We believe that the ReMODE server will benefit researchers for drug discovery. ReMODE is publicly available at http://cadd.zju.edu.cn/relation/remode/ .
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Affiliation(s)
- Mingyang Wang
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China ,CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Jike Wang
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China ,CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Gaoqi Weng
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China ,CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Yu Kang
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
| | - Peichen Pan
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
| | - Dan Li
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
| | - Yafeng Deng
- CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Honglin Li
- grid.28056.390000 0001 2163 4895Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237 People’s Republic of China
| | - Chang-Yu Hsieh
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
| | - Tingjun Hou
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
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9
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Prentis LE, Singleton CD, Bickel JD, Allen WJ, Rizzo RC. A molecular evolution algorithm for ligand design in DOCK. J Comput Chem 2022; 43:1942-1963. [PMID: 36073674 PMCID: PMC9623574 DOI: 10.1002/jcc.26993] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/13/2022] [Accepted: 08/03/2022] [Indexed: 01/11/2023]
Abstract
As a complement to virtual screening, de novo design of small molecules is an alternative approach for identifying potential drug candidates. Here, we present a new 3D genetic algorithm to evolve molecules through breeding, mutation, fitness pressure, and selection. The method, termed DOCK_GA, builds upon and leverages powerful sampling, scoring, and searching routines previously implemented into DOCK6. Three primary experiments were used during development: Single-molecule evolution evaluated three selection methods (elitism, tournament, and roulette), in four clinically relevant systems, in terms of mutation type and crossover success, chemical properties, ensemble diversity, and fitness convergence, among others. Large scale benchmarking assessed performance across 651 different protein-ligand systems. Ensemble-based evolution demonstrated using multiple inhibitors simultaneously to seed growth in a SARS-CoV-2 target. Key takeaways include: (1) The algorithm is robust as demonstrated by the successful evolution of molecules across a large diverse dataset. (2) Users have flexibility with regards to parent input, selection method, fitness function, and molecular descriptors. (3) The program is straightforward to run and only requires a single executable and input file at run-time. (4) The elitism selection method yields more tightly clustered molecules in terms of 2D/3D similarity, with more favorable fitness, followed by tournament and roulette.
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Affiliation(s)
- Lauren E. Prentis
- Department of Biochemistry & Cell BiologyStony Brook UniversityStony BrookNew YorkUSA
| | | | - John D. Bickel
- Department of ChemistryStony Brook UniversityStony BrookNew YorkUSA
| | - William J. Allen
- Department of Applied Mathematics & StatisticsStony Brook UniversityStony BrookNew YorkUSA
| | - Robert C. Rizzo
- Department of Applied Mathematics & StatisticsStony Brook UniversityStony BrookNew YorkUSA,Institute of Chemical Biology & Drug DiscoveryStony Brook UniversityStony BrookNew YorkUSA,Laufer Center for Physical & Quantitative BiologyStony Brook UniversityStony BrookNew YorkUSA
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10
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Wang H, Pan X, Zhang Y, Wang X, Xiao X, Ji C. MolHyb: A Web Server for Structure-Based Drug Design by Molecular Hybridization. J Chem Inf Model 2022; 62:2916-2922. [PMID: 35695435 DOI: 10.1021/acs.jcim.2c00443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular hybridization is a widely used ligand design method in drug discovery. In this study, we present MolHyb, a web server for structure-based ligand design by molecular hybridization. The input of MolHyb is a protein file and a seed compound file. MolHyb tries to generate novel ligands through hybridizing the seed compound with helper compounds that bind to the same protein target or similar proteins. To facilitate the job of getting helper compounds, we compiled a modeled protein-ligand structure database as an extension to crystal structures in the PDB database by placing the bioactive compounds in ChEMBL into their corresponding 3D protein binding pocket properly. MolHyb works by searching for helper compounds from the protein-ligand structure database and migrating chemical moieties from helper compounds to the seed compound efficiently. Hybridization is performed at both cyclic and acyclic bonds. The users can also input their own helper compounds to MolHyb. We hope that MolHyb will be a useful tool for rational drug design. MolHyb is freely available at http://molhyb.xundrug.cn/.
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Affiliation(s)
- Hao Wang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xiaolin Pan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Yueqing Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xingyu Wang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xudong Xiao
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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11
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Acharyya SR, Sen P, Kandasamy T, Ghosh SS. Designing of disruptor molecules to restrain the protein-protein interaction network of VANG1/SCRIB/NOS1AP using fragment-based drug discovery techniques. Mol Divers 2022:10.1007/s11030-022-10462-0. [PMID: 35648249 DOI: 10.1007/s11030-022-10462-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/11/2022] [Indexed: 11/30/2022]
Abstract
Governing protein-protein interaction networks are the cynosure of cell signaling and oncogenic networks. Multifarious processes when aligned with one another can result in a dysregulated output which can result in cancer progression. In the current research, one such network of proteins comprising VANG1/SCRIB/NOS1AP, which is responsible for cell migration, is targeted. The proteins are modeled using in-silico approaches, and the interaction is visualized utilizing protein-protein docking. Designing drugs for the convoluted protein network can serve as a challenging task that can be overcome by fragment-based drug designing, a recent game-changer in the computational drug discovery strategy for protein interaction networks. The model is exposed to the extraction of hotspots, also known as the restrained regions for small molecular hits. The hotspot regions are subjected to a library of generated fragments, which are then recombined and rejoined to develop small molecular disruptors of the macromolecular assemblage. Rapid screening methods using pharmacokinetic tools and 2D interaction studies resulted in four molecules that could serve the purpose of a disruptor. The final validation is executed by long-range simulations of 100 ns and exploring the stability of the complex using several parameters leading to the emergence of two novel molecules VNS003 and VNS005 that could be used as the disruptors of the protein assembly VANG1/SCRIB/NOS1AP. Also, the molecules were explored as single protein targets approbated via molecular docking and 100 ns molecular dynamics simulation. This concluded VNS003 as the most suitable inhibitor module capable of acting as a disruptor of a macromolecular assembly as well as acting on individual protein chains, thus leading to the primary hindrance in the formation of the protein interaction complex.
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Affiliation(s)
- Suchandra Roy Acharyya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 39, India
| | - Plaboni Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 39, India
| | - Thirukumaran Kandasamy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 39, India
| | - Siddhartha Sankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 39, India. .,Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, 39, India.
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12
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13
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Piticchio SG, Martínez-Cartró M, Scaffidi S, Rachman M, Rodriguez-Arevalo S, Sanchez-Arfelis A, Escolano C, Picaud S, Krojer T, Filippakopoulos P, von Delft F, Galdeano C, Barril X. Discovery of Novel BRD4 Ligand Scaffolds by Automated Navigation of the Fragment Chemical Space. J Med Chem 2021; 64:17887-17900. [PMID: 34898210 DOI: 10.1021/acs.jmedchem.1c01108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fragment-based drug discovery (FBDD) is a very effective hit identification method. However, the evolution of fragment hits into suitable leads remains challenging and largely artisanal. Fragment evolution is often scaffold-centric, meaning that its outcome depends crucially on the chemical structure of the starting fragment. Considering that fragment screening libraries cover only a small proportion of the corresponding chemical space, hits should be seen as probes highlighting privileged areas of the chemical space rather than actual starting points. We have developed an automated computational pipeline to mine the chemical space around any specific fragment hit, rapidly finding analogues that share a common interaction motif but are structurally novel and diverse. On a prospective application on the bromodomain-containing protein 4 (BRD4), starting from a known fragment, the platform yields active molecules with nonobvious scaffold changes. The procedure is fast and inexpensive and has the potential to uncover many hidden opportunities in FBDD.
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Affiliation(s)
- Serena G Piticchio
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Míriam Martínez-Cartró
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Salvatore Scaffidi
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Moira Rachman
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Sergio Rodriguez-Arevalo
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Ainoa Sanchez-Arfelis
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Carmen Escolano
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Frank von Delft
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom.,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom.,Centre for Medicines Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom.,Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Carles Galdeano
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Xavier Barril
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
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14
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Wang M, Sun H, Wang J, Pang J, Chai X, Xu L, Li H, Cao D, Hou T. Comprehensive assessment of deep generative architectures for de novo drug design. Brief Bioinform 2021; 23:6470970. [PMID: 34929743 DOI: 10.1093/bib/bbab544] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/20/2023] Open
Abstract
Recently, deep learning (DL)-based de novo drug design represents a new trend in pharmaceutical research, and numerous DL-based methods have been developed for the generation of novel compounds with desired properties. However, a comprehensive understanding of the advantages and disadvantages of these methods is still lacking. In this study, the performances of different generative models were evaluated by analyzing the properties of the generated molecules in different scenarios, such as goal-directed (rediscovery, optimization and scaffold hopping of active compounds) and target-specific (generation of novel compounds for a given target) tasks. In overall, the DL-based models have significant advantages over the baseline models built by the traditional methods in learning the physicochemical property distributions of the training sets and may be more suitable for target-specific tasks. However, both the baselines and DL-based generative models cannot fully exploit the scaffolds of the training sets, and the molecules generated by the DL-based methods even have lower scaffold diversity than those generated by the traditional models. Moreover, our assessment illustrates that the DL-based methods do not exhibit obvious advantages over the genetic algorithm-based baselines in goal-directed tasks. We believe that our study provides valuable guidance for the effective use of generative models in de novo drug design.
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Affiliation(s)
- Mingyang Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Jike Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Jinping Pang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Xin Chai
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, Jiangsu, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, P. R. China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
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15
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Fragment-to-lead tailored in silico design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:44-57. [PMID: 34916022 DOI: 10.1016/j.ddtec.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became established during the last two decades. Its rationality and low entry costs make it appealing, and the numerous examples of approved drugs discovered through FBDD validate the approach. However, FBDD still faces numerous challenges. Perhaps the most important one is the transformation of the initial fragment hits into viable leads. Fragment-to-lead (F2L) optimization is resource-intensive and is therefore limited in the possibilities that can be actively pursued. In silico strategies play an important role in F2L, as they can perform a deeper exploration of chemical space, prioritize molecules with high probabilities of being active and generate non-obvious ideas. Here we provide a critical overview of current in silico strategies in F2L optimization and highlight their remarkable impact. While very effective, most solutions are target- or fragment- specific. We propose that fully integrated in silico strategies, capable of automatically and systematically exploring the fast-growing available chemical space can have a significant impact on accelerating the release of fragment originated drugs.
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16
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Artificial Intelligence-Enabled De Novo Design of Novel Compounds that Are Synthesizable. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2390:409-419. [PMID: 34731479 DOI: 10.1007/978-1-0716-1787-8_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Development of computer-aided de novo design methods to discover novel compounds in a speedy manner to treat human diseases has been of interest to drug discovery scientists for the past three decades. In the beginning, the efforts were mostly concentrated to generate molecules that fit the active site of the target protein by sequential building of a molecule atom-by-atom and/or group-by-group while exploring all possible conformations to optimize binding interactions with the target protein. In recent years, deep learning approaches are applied to generate molecules that are iteratively optimized against a binding hypothesis (to optimize potency) and predictive models of drug-likeness (to optimize properties). Synthesizability of molecules generated by these de novo methods remains a challenge. This review will focus on the recent development of synthetic planning methods that are suitable for enhancing synthesizability of molecules designed by de novo methods.
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17
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Newly designed compounds from scaffolds of known actives as inhibitors of survivin: computational analysis from the perspective of fragment-based drug design. In Silico Pharmacol 2021; 9:47. [PMID: 34350094 DOI: 10.1007/s40203-021-00108-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Survivin is an apoptosis suppressing protein linked to different forms of cancer. As it stands, there are no approved drugs for the inhibition of survivin in cancer cells despite a number of promising compounds in clinical trials. This study designed a new set of compounds from fragments of active survivin inhibitors to potentiate their binding with survivin at BIR domain. Three hundred and five (305) fragments made from eight potent inhibitors of survivin were reconstructed to form a new set of compounds. The compounds were optimized using R group enumeration and bioisostere replacement after extensive docking analysis. The optimised compounds were filtered by a validated pharmacophore model to reveal how well they are aligned to the pharmacophore sites. Molecular docking of the well aligned compounds revealed the top-scoring compounds; and these compounds were compared with the eight inhibitors used as template for fragment-based design on the basis of binding affinity (rigid and flexible docking), predicted pIC50 and intermolecular interactions. The electronic behaviours (global descriptors, HOMO/LUMO, molecular electrostatic potential and Fukui functions) of newly designed compounds were calculated to investigate their reactivity and atomic sites prone to neutrophilic/electrophilic attack. The nine newly designed compounds had better rigid and flexible docking scores, free energy of binding and intermolecular interactions with survivin at BIR domain than the eight active inhibitors. Based on frontier molecular orbitals, OPE-3 was found to be the most reactive and less stable compound (0.13194 eV), followed by OPE-4 and OPE-9. The global descriptive parameters showed that OPE-3 had highest softness value (7.5245 eV) while OPE-8 recorded the maximum hardness value (0.08486 eV). The well-validated QSAR model also showed that OPE-3, OPE-7 and OPE-8 had the most significant bioactivity of all the inhibitors. This study thus provides new insight into the design of compounds capable of modulating the activity of survivin. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00108-8.
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18
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Targeting RNA structures in diseases with small molecules. Essays Biochem 2021; 64:955-966. [PMID: 33078198 PMCID: PMC7724634 DOI: 10.1042/ebc20200011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/16/2020] [Accepted: 09/30/2020] [Indexed: 01/08/2023]
Abstract
RNA is crucial for gene expression and regulation. Recent advances in understanding of RNA biochemistry, structure and molecular biology have revealed the importance of RNA structure in cellular processes and diseases. Various approaches to discovering drug-like small molecules that target RNA structure have been developed. This review provides a brief introduction to RNA structural biology and how RNA structures function as disease regulators. We summarize approaches to targeting RNA with small molecules and highlight their advantages, shortcomings and therapeutic potential.
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19
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Computational Drug Repurposing Resources and Approaches for Discovering Novel Antifungal Drugs against Candida albicans N-Myristoyl Transferase. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is a yeast that is an opportunistic fungal pathogen and also identified as ubiquitous polymorphic species that is mainly linked with major fungal infections in humans, particularly in the immunocompromised patients including transplant recipients, chemotherapy patients, HIV-infected patients as well as in low-birth-weight infants. Systemic Candida infections have a high mortality rate of around 29 to 76%. For reducing its infection, limited drugs are existing such as caspofungin, fluconazole, terbinafine, and amphotericin B, etc. which contain unlikable side effects and also toxic. This review intends to utilize advanced bioinformatics technologies such as Molecular docking, Scaffold hopping, Virtual screening, Pharmacophore modeling, Molecular dynamics (MD) simulation for the development of potentially new drug candidates with a drug-repurpose approach against Candida albicans within a limited time frame and also cost reductive.
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20
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21
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Sydow D, Schmiel P, Mortier J, Volkamer A. KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. J Chem Inf Model 2020; 60:6081-6094. [PMID: 33155465 DOI: 10.1021/acs.jcim.0c00839] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein kinases play a crucial role in many cell signaling processes, making them one of the most important families of drug targets. In this context, fragment-based drug design strategies have been successfully applied to develop novel kinase inhibitors. These strategies usually follow a knowledge-driven approach to optimize a focused set of fragments to a potent kinase inhibitor. Alternatively, KinFragLib explores and extends the chemical space of kinase inhibitors using data-driven fragmentation and recombination. The method builds on available structural kinome data from the KLIFS database for over 2500 kinase DFG-in structures cocrystallized with noncovalent kinase ligands. The computational fragmentation method splits the ligands into fragments with respect to their 3D proximity to six predefined functionally relevant subpocket centers. The resulting fragment library consists of six subpocket pools with over 7000 fragments, available at https://github.com/volkamerlab/KinFragLib. KinFragLib offers two main applications: on the one hand, in-depth analyses of the chemical space of known kinase inhibitors, subpocket characteristics, and connections, and on the other hand, subpocket-informed recombination of fragments to generate potential novel inhibitors. The latter showed that recombining only a subset of 624 representative fragments generated 6.7 million molecules. This combinatorial library contains, besides some known kinase inhibitors, more than 99% novel chemical matter compared to ChEMBL and 63% molecules compliant with Lipinski's rule of five.
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Affiliation(s)
- Dominique Sydow
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Paula Schmiel
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jérémie Mortier
- Digital Technologies, Computational Molecular Design, Bayer AG, 13342 Berlin, Germany
| | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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22
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Czako B, Marszalek JR, Burke JP, Mandal P, Leonard PG, Cross JB, Mseeh F, Jiang Y, Chang EQ, Suzuki E, Kovacs JJ, Feng N, Gera S, Harris AL, Liu Z, Mullinax RA, Pang J, Parker CA, Spencer ND, Yu SS, Wu Q, Tremblay MR, Mikule K, Wilcoxen K, Heffernan TP, Draetta GF, Jones P. Discovery of IACS-9439, a Potent, Exquisitely Selective, and Orally Bioavailable Inhibitor of CSF1R. J Med Chem 2020; 63:9888-9911. [PMID: 32787110 DOI: 10.1021/acs.jmedchem.0c00936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tumor-associated macrophages (TAMs) have a significant presence in the tumor stroma across multiple human malignancies and are believed to be beneficial to tumor growth. Targeting CSF1R has been proposed as a potential therapy to reduce TAMs, especially the protumor, immune-suppressive M2 TAMs. Additionally, the high expression of CSF1R on tumor cells has been associated with poor survival in certain cancers, suggesting tumor dependency and therefore a potential therapeutic target. The CSF1-CSF1R signaling pathway modulates the production, differentiation, and function of TAMs; however, the discovery of selective CSF1R inhibitors devoid of type III kinase activity has proven to be challenging. We discovered a potent, highly selective, and orally bioavailable CSF1R inhibitor, IACS-9439 (1). Treatment with 1 led to a dose-dependent reduction in macrophages, promoted macrophage polarization toward the M1 phenotype, and led to tumor growth inhibition in MC38 and PANC02 syngeneic tumor models.
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Affiliation(s)
- Barbara Czako
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Joseph R Marszalek
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jason P Burke
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Pijus Mandal
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Paul G Leonard
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jason B Cross
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Faika Mseeh
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Yongying Jiang
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Edward Q Chang
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Erika Suzuki
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jeffrey J Kovacs
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Ningping Feng
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Sonal Gera
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Angela L Harris
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Zhen Liu
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Robert A Mullinax
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jihai Pang
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Connor A Parker
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Nakia D Spencer
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Simon S Yu
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Qi Wu
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Martin R Tremblay
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451, United States
| | - Keith Mikule
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451, United States
| | - Keith Wilcoxen
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451, United States
| | - Timothy P Heffernan
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Philip Jones
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
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23
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Alfaro S, Navarro-Retamal C, Caballero J. Transforming Non-Selective Angiotensin-Converting Enzyme Inhibitors in C- and N-domain Selective Inhibitors by Using Computational Tools. Mini Rev Med Chem 2020; 20:1436-1446. [DOI: 10.2174/1389557520666191224113830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023]
Abstract
The two-domain dipeptidylcarboxypeptidase Angiotensin-I-converting enzyme (EC
3.4.15.1; ACE) plays an important physiological role in blood pressure regulation via the reninangiotensin
and kallikrein-kinin systems by converting angiotensin I to the potent vasoconstrictor angiotensin
II, and by cleaving a number of other substrates including the vasodilator bradykinin and the
anti-inflammatory peptide N-acetyl-SDKP. Therefore, the design of ACE inhibitors is within the priorities
of modern medical sciences for treating hypertension, heart failures, myocardial infarction, and
other related diseases. Despite the success of ACE inhibitors for the treatment of hypertension and
congestive heart failure, they have some adverse effects, which could be attenuated by selective domain
inhibition. Crystal structures of both ACE domains (nACE and cACE) reported over the last decades
could facilitate the rational drug design of selective inhibitors. In this review, we refer to the history
of the discovery of ACE inhibitors, which has been strongly related to the development of molecular
modeling methods. We stated that the design of novel selective ACE inhibitors is a challenge
for current researchers which requires a thorough understanding of the structure of both ACE domains
and the help of molecular modeling methodologies. Finally, we performed a theoretical design of potential
selective derivatives of trandolaprilat, a drug approved to treat critical conditions of hypertension,
to illustrate how to use molecular modeling methods such as de novo design, docking, Molecular
Dynamics (MD) simulations, and free energy calculations for creating novel potential drugs with specific
interactions inside nACE and cACE binding sites.
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Affiliation(s)
- Sergio Alfaro
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Carlos Navarro-Retamal
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
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24
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Patel HM, Shaikh M, Ahmad I, Lokwani D, Surana SJ. BREED based de novo hybridization approach: generating novel T790M/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in non small cell lung cancer (NSCLC). J Biomol Struct Dyn 2020; 39:2838-2856. [PMID: 32276580 DOI: 10.1080/07391102.2020.1754918] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Third generation EGFR inhibitor osimertinib was approved as the first-line treatment for EGFR T790M mutation-positive Non-Small Cell Lung Cancer (NSCLC) patients in 2017. However, EGFR tertiary Cys797 to Ser797 (C797S) point mutation emanate rapidly after treatment of osimertinib, which is undruggable mutation to the all existing drugs. In this work, we have reported the novel T790M/C797S-EGFR Tyrosine Kinase inhibitors using BREED based de novo hybridization approach. BREED generates novel inhibitors from structures of known ligands bound to a common target. Among the generated hybridised breed compounds, the top best scorer breed molecules were breed 436, breed 530, breed 450, breed 562 and breed 313. Molecular Dynamics simulation of breed 436 for 10 ns further suggested that docked compound was stable into the pocket of the T790M/C797S-EGFR Tyrosine Kinase. In silico pharmacokinetic predictions of the breed hybridised compounds were within the defined range described for human use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harun M Patel
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
| | - Matin Shaikh
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
| | - Iqrar Ahmad
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
| | - Deepak Lokwani
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
| | - Sanjay J Surana
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
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25
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Spiegel JO, Durrant JD. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform 2020; 12:25. [PMID: 33431021 PMCID: PMC7165399 DOI: 10.1186/s13321-020-00429-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
We here present AutoGrow4, an open-source program for semi-automated computer-aided drug discovery. AutoGrow4 uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. It is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands. By leveraging recent computational and cheminformatics advancements, AutoGrow4 is faster, more stable, and more modular than previous versions. It implements new docking-program compatibility, chemical filters, multithreading options, and selection methods to support a wide range of user needs. To illustrate both de novo design and lead optimization, we here apply AutoGrow4 to the catalytic domain of poly(ADP-ribose) polymerase 1 (PARP-1), a well characterized DNA-damage-recognition protein. AutoGrow4 produces drug-like compounds with better predicted binding affinities than FDA-approved PARP-1 inhibitors (positive controls). The predicted binding modes of the AutoGrow4 compounds mimic those of the known inhibitors, even when AutoGrow4 is seeded with random small molecules. AutoGrow4 is available under the terms of the Apache License, Version 2.0. A copy can be downloaded free of charge from http://durrantlab.com/autogrow4.![]()
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Affiliation(s)
- Jacob O Spiegel
- Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA.
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26
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Ercan S, Şenses Y. Design and molecular docking studies of new inhibitor candidates for EBNA1 DNA binding site: a computational study. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2019.1709638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Selami Ercan
- Department of Nursing, School of Health Sciences, Batman University, Batman, Turkey
| | - Yusuf Şenses
- Institute of Science, Batman University, Batman, Turkey
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27
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de Souza Neto LR, Moreira-Filho JT, Neves BJ, Maidana RLBR, Guimarães ACR, Furnham N, Andrade CH, Silva FP. In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery. Front Chem 2020; 8:93. [PMID: 32133344 PMCID: PMC7040036 DOI: 10.3389/fchem.2020.00093] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Fragment-based drug (or lead) discovery (FBDD or FBLD) has developed in the last two decades to become a successful key technology in the pharmaceutical industry for early stage drug discovery and development. The FBDD strategy consists of screening low molecular weight compounds against macromolecular targets (usually proteins) of clinical relevance. These small molecular fragments can bind at one or more sites on the target and act as starting points for the development of lead compounds. In developing the fragments attractive features that can translate into compounds with favorable physical, pharmacokinetics and toxicity (ADMET-absorption, distribution, metabolism, excretion, and toxicity) properties can be integrated. Structure-enabled fragment screening campaigns use a combination of screening by a range of biophysical techniques, such as differential scanning fluorimetry, surface plasmon resonance, and thermophoresis, followed by structural characterization of fragment binding using NMR or X-ray crystallography. Structural characterization is also used in subsequent analysis for growing fragments of selected screening hits. The latest iteration of the FBDD workflow employs a high-throughput methodology of massively parallel screening by X-ray crystallography of individually soaked fragments. In this review we will outline the FBDD strategies and explore a variety of in silico approaches to support the follow-up fragment-to-lead optimization of either: growing, linking, and merging. These fragment expansion strategies include hot spot analysis, druggability prediction, SAR (structure-activity relationships) by catalog methods, application of machine learning/deep learning models for virtual screening and several de novo design methods for proposing synthesizable new compounds. Finally, we will highlight recent case studies in fragment-based drug discovery where in silico methods have successfully contributed to the development of lead compounds.
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Affiliation(s)
- Lauro Ribeiro de Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - José Teófilo Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Bruno Junior Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
- Laboratory of Cheminformatics, Centro Universitário de Anápolis – UniEVANGÉLICA, Anápolis, Brazil
| | - Rocío Lucía Beatriz Riveros Maidana
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Carolina Ramos Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Floriano Paes Silva
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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28
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Cardoso MH, Orozco RQ, Rezende SB, Rodrigues G, Oshiro KGN, Cândido ES, Franco OL. Computer-Aided Design of Antimicrobial Peptides: Are We Generating Effective Drug Candidates? Front Microbiol 2020; 10:3097. [PMID: 32038544 PMCID: PMC6987251 DOI: 10.3389/fmicb.2019.03097] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides (AMPs), especially antibacterial peptides, have been widely investigated as potential alternatives to antibiotic-based therapies. Indeed, naturally occurring and synthetic AMPs have shown promising results against a series of clinically relevant bacteria. Even so, this class of antimicrobials has continuously failed clinical trials at some point, highlighting the importance of AMP optimization. In this context, the computer-aided design of AMPs has put together crucial information on chemical parameters and bioactivities in AMP sequences, thus providing modes of prediction to evaluate the antibacterial potential of a candidate sequence before synthesis. Quantitative structure-activity relationship (QSAR) computational models, for instance, have greatly contributed to AMP sequence optimization aimed at improved biological activities. In addition to machine-learning methods, the de novo design, linguistic model, pattern insertion methods, and genetic algorithms, have shown the potential to boost the automated design of AMPs. However, how successful have these approaches been in generating effective antibacterial drug candidates? Bearing this in mind, this review will focus on the main computational strategies that have generated AMPs with promising activities against pathogenic bacteria, as well as anti-infective potential in different animal models, including sepsis and cutaneous infections. Moreover, we will point out recent studies on the computer-aided design of antibiofilm peptides. As expected from automated design strategies, diverse candidate sequences with different structural arrangements have been generated and deposited in databases. We will, therefore, also discuss the structural diversity that has been engendered.
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Affiliation(s)
- Marlon H Cardoso
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Raquel Q Orozco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Instituto de Ciências Biológicas, Departamento de Biologia, Programa de Pós-Graduação em Ciências Biológicas (Imunologia/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Samilla B Rezende
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Gisele Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Karen G N Oshiro
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Elizabete S Cândido
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Octávio L Franco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil.,Instituto de Ciências Biológicas, Departamento de Biologia, Programa de Pós-Graduação em Ciências Biológicas (Imunologia/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
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29
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Bonanni D, Lolli ML, Bajorath J. Computational Method for Structure-Based Analysis of SAR Transfer. J Med Chem 2020; 63:1388-1396. [PMID: 31939664 DOI: 10.1021/acs.jmedchem.9b01931] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The identification of different compound series with corresponding structure-activity relationship (SAR) progression for a given target is referred to as SAR transfer, which is of interest in lead optimization. If difficulties are encountered during multiproperty optimization, the SAR transfer concept can be applied attempting to replace a lead compound with another candidate. For a systematic assessment of SAR transfer, computational approaches are required. So far, SAR transfer has been investigated at the level of compounds and analogue series. Herein, we introduce a new computational method for structure-guided exploration of SAR transfer. The approach relies on a three-dimensional molecular fragmentation and recombination scheme and the identification of analogues of crystallographic ligands. On the basis of spatially aligned X-ray ligands, alternative substituents and compound cores are identified, enabling the detection of multiple SAR transfer events. Application of the methodology across different targets identified SAR transfer events with high frequency.
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Affiliation(s)
- Davide Bonanni
- Department of Drug Science and Technology , University of Turin , via Pietro Giuria 9 , 10125 Turin , Italy.,Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Endenicher Allee 19c , Rheinische Friedrich-Wilhelms-Universität , D-53115 Bonn , Germany
| | - Marco L Lolli
- Department of Drug Science and Technology , University of Turin , via Pietro Giuria 9 , 10125 Turin , Italy
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Endenicher Allee 19c , Rheinische Friedrich-Wilhelms-Universität , D-53115 Bonn , Germany
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30
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Ercan S, Şenyiğit B, Şenses Y. Dual inhibitor design for HIV-1 reverse transcriptase and integrase enzymes: a molecular docking study. J Biomol Struct Dyn 2019; 38:573-580. [DOI: 10.1080/07391102.2019.1700166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Selami Ercan
- School of Health Sciences, Department of Nursing, Batman University, Batman, Turkey
| | | | - Yusuf Şenses
- Institute of Science, Batman University, Batman, Turkey
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31
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Hsu HH, Huang CH, Lin ST. New Data Structure for Computational Molecular Design with Atomic or Fragment Resolution. J Chem Inf Model 2019; 59:3703-3713. [PMID: 31393721 DOI: 10.1021/acs.jcim.9b00478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new molecular data structure and molecular structure operation algorithms are proposed for general purpose molecular design. The data structure allows for a variety of molecular operations for creating new molecules. Two types of molecular operations were developed, unimolecular and bimolecular operations. In unimolecular operations, a child molecule can be created from a parent via addition of a functional group, deletion of a fragment, mutation of an atom, etc. In bimolecular operations, children molecules are generated from two parent molecules through combination or crossover (hybridization). These molecular operations are essential for the creation and modification of molecules for the purpose of molecular design. The data structure is capable of representing linear, branched, multifunctional, and multivalent compounds. Algorithms are developed for deriving the molecular data structure of a molecule from its atomic coordinates and vice versa. We show that this new molecular data structure and the developed algorithms, referred to as Molecular Assembling and Representation Suite, allow one to generate a comprehensive library of new molecules via performing every possible molecular structure modification.
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Affiliation(s)
- Hsuan-Hao Hsu
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
| | - Chen-Hsuan Huang
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
| | - Shiang-Tai Lin
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
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32
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Seidel T, Schuetz DA, Garon A, Langer T. The Pharmacophore Concept and Its Applications in Computer-Aided Drug Design. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:99-141. [PMID: 31621012 DOI: 10.1007/978-3-030-14632-0_4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pharmacophore-based techniques currently are an integral part of many computer-aided drug design workflows and have been successfully and extensively applied for tasks such as virtual screening, de novo design, and lead optimization. Pharmacophore models can be derived both in a receptor-based and in a ligand-based manner, and provide an abstract description of essential non-bonded interactions that typically occur between small-molecule ligands and macromolecular targets. Due to their simplistic and abstract nature, pharmacophores are both perfectly suited for efficient computer processing and easy to comprehend by life and physical scientists. As a consequence, they have also proven to be a valuable tool for communicating between computational and medicinal chemists.This chapter aims to provide a short overview of the pharmacophore concept and its applications in modern computer-aided drug design. The chapter is divided into three distinct parts. The first section contains a brief introduction to the pharmacophore concept. The second section provides a description of the most common nonbonded interaction types and their representation as pharmacophoric features. Furthermore, it gives an overview of the various methods for pharmacophore generation and important pharmacophore-based techniques in drug design. This part concludes with examples for recent pharmacophore concept-related research and development. The last section is dedicated to a review of research in the field of natural product chemistry as carried out by employing pharmacophore-based drug design methods.
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Affiliation(s)
- Thomas Seidel
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria.
| | - Doris A Schuetz
- InteLigand GmbH, IRIC-Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, QC, Canada
| | - Arthur Garon
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
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33
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Zhang S, Zhang J, Gao P, Sun L, Song Y, Kang D, Liu X, Zhan P. Efficient drug discovery by rational lead hybridization based on crystallographic overlay. Drug Discov Today 2018; 24:805-813. [PMID: 30529326 DOI: 10.1016/j.drudis.2018.11.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/29/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
In this review, we provide an overview of recent applications of crystallographic overlay-based molecular structure hybridization of lead compounds as a rational strategy for efficient drug discovery, with selected examples, and briefly discuss its advantages compared with other ligand-based methodologies.
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Affiliation(s)
- Shuo Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, 250012, Ji'nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China.
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34
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CoMFA and CoMSIA-based designing of resveratrol derivatives as amyloid-beta aggregation inhibitors against Alzheimer's disease. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2138-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Oglic D, Oatley SA, Macdonald SJF, Mcinally T, Garnett R, Hirst JD, Gärtner T. Active Search for Computer-aided Drug Design. Mol Inform 2018; 37. [PMID: 29388736 DOI: 10.1002/minf.201700130] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/03/2018] [Indexed: 01/08/2023]
Abstract
We consider lead discovery as active search in a space of labelled graphs. In particular, we extend our recent data-driven adaptive Markov chain approach, and evaluate it on a focused drug design problem, where we search for an antagonist of an αv integrin, the target protein that belongs to a group of Arg-Gly-Asp integrin receptors. This group of integrin receptors is thought to play a key role in idiopathic pulmonary fibrosis, a chronic lung disease of significant pharmaceutical interest. As an in silico proxy of the binding affinity, we use a molecular docking score to an experimentally determined αvβ6 protein structure. The search is driven by a probabilistic surrogate of the activity of all molecules from that space. As the process evolves and the algorithm observes the activity scores of the previously designed molecules, the hypothesis of the activity is refined. The algorithm is guaranteed to converge in probability to the best hypothesis from an a priori specified hypothesis space. In our empirical evaluations, the approach achieves a large structural variety of designed molecular structures for which the docking score is better than the desired threshold. Some novel molecules, suggested to be active by the surrogate model, provoke a significant interest from the perspective of medicinal chemistry and warrant prioritization for synthesis. Moreover, the approach discovered 19 out of the 24 active compounds which are known to be active from previous biological assays.
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Affiliation(s)
- Dino Oglic
- School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham, NG8 1BB, United Kingdom.,Institut für Informatik III, Universität Bonn, Römerstraße 164, 53117, Bonn, Germany
| | - Steven A Oatley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Simon J F Macdonald
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Thomas Mcinally
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Roman Garnett
- Department of Computer Science and Engineering Washington University in St. Louis, One Brookings Drive CB 1045, St. Louis, MO, 63130, USA
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Thomas Gärtner
- School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham, NG8 1BB, United Kingdom
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36
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Chevillard F, Rimmer H, Betti C, Pardon E, Ballet S, van Hilten N, Steyaert J, Diederich WE, Kolb P. Binding-Site Compatible Fragment Growing Applied to the Design of β 2-Adrenergic Receptor Ligands. J Med Chem 2018; 61:1118-1129. [PMID: 29364664 DOI: 10.1021/acs.jmedchem.7b01558] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fragment-based drug discovery is intimately linked to fragment extension approaches that can be accelerated using software for de novo design. Although computers allow for the facile generation of millions of suggestions, synthetic feasibility is however often neglected. In this study we computationally extended, chemically synthesized, and experimentally assayed new ligands for the β2-adrenergic receptor (β2AR) by growing fragment-sized ligands. In order to address the synthetic tractability issue, our in silico workflow aims at derivatized products based on robust organic reactions. The study started from the predicted binding modes of five fragments. We suggested a total of eight diverse extensions that were easily synthesized, and further assays showed that four products had an improved affinity (up to 40-fold) compared to their respective initial fragment. The described workflow, which we call "growing via merging" and for which the key tools are available online, can improve early fragment-based drug discovery projects, making it a useful creative tool for medicinal chemists during structure-activity relationship (SAR) studies.
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Affiliation(s)
- Florent Chevillard
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Helena Rimmer
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology, Philipps-University Marburg , Hans-Meerwein-Straße 3, 35032 Marburg, Germany
| | - Cecilia Betti
- Research Group of Organic Chemistry, Departments of Chemistry and Bio-Engineering Sciences, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB , 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel , 1050 Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Departments of Chemistry and Bio-Engineering Sciences, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
| | - Niek van Hilten
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB , 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel , 1050 Brussels, Belgium
| | - Wibke E Diederich
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology, Philipps-University Marburg , Hans-Meerwein-Straße 3, 35032 Marburg, Germany
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
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37
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Abstract
Following the elucidation of the human genome, chemogenomics emerged in the beginning of the twenty-first century as an interdisciplinary research field with the aim to accelerate target and drug discovery by making best usage of the genomic data and the data linkable to it. What started as a systematization approach within protein target families now encompasses all types of chemical compounds and gene products. A key objective of chemogenomics is the establishment, extension, analysis, and prediction of a comprehensive SAR matrix which by application will enable further systematization in drug discovery. Herein we outline future perspectives of chemogenomics including the extension to new molecular modalities, or the potential extension beyond the pharma to the agro and nutrition sectors, and the importance for environmental protection. The focus is on computational sciences with potential applications for compound library design, virtual screening, hit assessment, analysis of phenotypic screens, lead finding and optimization, and systems biology-based prediction of toxicology and translational research.
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Affiliation(s)
- Edgar Jacoby
- Janssen Research & Development, Beerse, Belgium.
| | - J B Brown
- Life Science Informatics Research Unit, Laboratory of Molecular Biosciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
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38
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Suryanarayanan V, Panwar U, Chandra I, Singh SK. De Novo Design of Ligands Using Computational Methods. Methods Mol Biol 2018; 1762:71-86. [PMID: 29594768 DOI: 10.1007/978-1-4939-7756-7_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
De novo design technique is complementary to high-throughput virtual screening and is believed to contribute in pharmaceutical development of novel drugs with desired properties at a very low cost and time-efficient manner. In this chapter, we outline the basic de novo design concepts based on computational methods with an example.
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Affiliation(s)
- Venkatesan Suryanarayanan
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ishwar Chandra
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India.
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39
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Zhang Y, Chen Y, Zhang D, Wang L, Lu T, Jiao Y. Discovery of Novel Potent VEGFR-2 Inhibitors Exerting Significant Antiproliferative Activity against Cancer Cell Lines. J Med Chem 2017; 61:140-157. [DOI: 10.1021/acs.jmedchem.7b01091] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yanmin Zhang
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yadong Chen
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Danfeng Zhang
- School
of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Lu Wang
- School
of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Tao Lu
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
- School
of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
- State
Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Yu Jiao
- School
of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
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40
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Jacoby E, Wroblowski B, Buyck C, Neefs JM, Meyer C, Cummings MD, van Vlijmen H. Protocols for the Design of Kinase-focused Compound Libraries. Mol Inform 2017; 37:e1700119. [PMID: 29116686 DOI: 10.1002/minf.201700119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 10/20/2017] [Indexed: 01/12/2023]
Abstract
Protocols for the design of kinase-focused compound libraries are presented. Kinase-focused compound libraries can be differentiated based on the design goal. Depending on whether the library should be a discovery library specific for one particular kinase, a general discovery library for multiple distinct kinase projects, or even phenotypic screening, there exists today a variety of in silico methods to design candidate compound libraries. We address the following scenarios: 1) Datamining of SAR databases and kinase focused vendor catalogues; 2) Predictions and virtual screening; 3) Structure-based design of combinatorial kinase inhibitors; 4) Design of covalent kinase inhibitors; 5) Design of macrocyclic kinase inhibitors; and 6) Design of allosteric kinase inhibitors and activators.
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Affiliation(s)
- Edgar Jacoby
- Janssen Research & Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | | | - Christophe Buyck
- Janssen Research & Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Research & Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | | | - Maxwell D Cummings
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA 19477, USA
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41
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QSAR modeling and in silico design of small-molecule inhibitors targeting the interaction between E3 ligase VHL and HIF-1α. Mol Divers 2017; 21:719-739. [PMID: 28689235 DOI: 10.1007/s11030-017-9750-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/15/2017] [Indexed: 12/19/2022]
Abstract
Protein-protein interactions (PPIs) have attracted much attention recently because of their preponderant role in most biological processes. The prevention of the interaction between E3 ligase VHL and HIF-1[Formula: see text] may improve tolerance to hypoxia and ameliorate the prognosis of many diseases. To obtain novel potent inhibitors of VHL/HIF-1[Formula: see text] interaction, a series of hydroxyproline-based inhibitors were investigated for structural optimization using a combination of QSAR modeling and molecular docking. Here, 2D- and 3D-QSAR models were developed by genetic function approximation (GFA) and comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) methods, respectively. The top-ranked models with strict validation revealed satisfactory statistical parameters (CoMFA with [Formula: see text], 0.637; [Formula: see text], 0.955; [Formula: see text], 0.944; CoMSIA with [Formula: see text], 0.649; [Formula: see text], 0.954; [Formula: see text], 0.911; GFA with [Formula: see text], 0.721; [Formula: see text], 0.801; [Formula: see text], 0.861). The selected five 2D-QSAR descriptors were in good accordance with the 3D-QSAR results, and contour maps gave the visualization of feature requirements for inhibitory activity. A new diverse molecular database was created by molecular fragment replacement and BREED techniques for subsequent virtual screening. Eventually, 31 novel hydroxyproline derivatives stood out as potential VHL/HIF-1[Formula: see text] inhibitors with favorable predictions by the CoMFA, CoMSIA and GFA models. The reliability of this protocol suggests that it could also be applied to the exploration of lead optimization of other PPI targets.
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42
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Podlewska S, Czarnecki WM, Kafel R, Bojarski AJ. Creating the New from the Old: Combinatorial Libraries Generation with Machine-Learning-Based Compound Structure Optimization. J Chem Inf Model 2017; 57:133-147. [DOI: 10.1021/acs.jcim.6b00426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sabina Podlewska
- Department of Medicinal
Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland
| | - Wojciech M. Czarnecki
- Faculty
of Mathematics and Computer Science, Jagiellonian University, 30-348 Kraków, Poland
| | - Rafał Kafel
- Department of Medicinal
Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland
| | - Andrzej J. Bojarski
- Department of Medicinal
Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland
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43
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Quo vadis G protein-coupled receptor ligands? A tool for analysis of the emergence of new groups of compounds over time. Bioorg Med Chem Lett 2016; 27:626-631. [PMID: 27993519 DOI: 10.1016/j.bmcl.2016.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/24/2022]
Abstract
Exponential growth in the number of compounds with experimentally verified activity towards particular target has led to the emergence of various databases gathering data on biological activity. In this study, the ligands of family A of the G Protein-Coupled Receptors that are collected in the ChEMBL database were examined, and special attention was given to serotonin receptors. Sets of compounds were examined in terms of their appearance over time, they were mapped to the chemical space of drugs deposited in DrugBank, and the emergence of structurally new clusters of compounds was indicated. In addition, a tool for detailed analysis of the obtained visualizations was prepared and made available online at http://chem.gmum.net/vischem, which enables the investigation of chemical structures while referring to particular data points depicted in the figures and changes in compounds datasets over time.
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44
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Computer-aided drug discovery research at a global contract research organization. J Comput Aided Mol Des 2016; 31:309-318. [DOI: 10.1007/s10822-016-9991-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/26/2016] [Indexed: 10/20/2022]
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45
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Lauck F, Rarey M. FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption. J Chem Inf Model 2016; 56:1641-53. [DOI: 10.1021/acs.jcim.6b00117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Florian Lauck
- ZBH - Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
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46
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Abstract
Cyclin-dependent kinases (CDKs) are core components of the cell cycle machinery that govern the transition between phases during cell cycle progression. Abnormalities in CDKs activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. One of the main bottlenecks hampering the development of drugs for kinase is the difficulty to attain selectivity. A huge variety of small molecules have been reported as CDK inhibitors, as potential anticancer agents, but none of these has been approved for commercial use. Computer-based molecular design supports drug discovery by suggesting novel new chemotypes and compound modifications for lead candidate optimization. One of the methods known as de novo ligand design technique has emerged as a complementary approach to high-throughput screening. Several automated de novo software programs have been written, which automatically design novel structures to perfectly fit in known binding site. The de novo design supports drug discovery assignments by generating novel pharmaceutically active agents with desired properties in a cost as well as time efficient approach. This chapter describes procedure and an overview of computer-based molecular de novo design methods on a conceptual level with successful examples of CDKs inhibitors.
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47
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Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Körner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M. A Real-World Perspective on Molecular Design. J Med Chem 2016; 59:4087-102. [PMID: 26878596 DOI: 10.1021/acs.jmedchem.5b01875] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.
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Affiliation(s)
- Bernd Kuhn
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Wolfgang Guba
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jérôme Hert
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - David Banner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Caterina Bissantz
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Simona Ceccarelli
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Wolfgang Haap
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Matthias Körner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andreas Kuglstatter
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Christian Lerner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Patrizio Mattei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Werner Neidhart
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Emmanuel Pinard
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tanja Schulz-Gasch
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Thomas Woltering
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Martin Stahl
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
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48
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Abstract
Computational medicinal chemistry offers viable strategies for finding, characterizing, and optimizing innovative pharmacologically active compounds. Technological advances in both computer hardware and software as well as biological chemistry have enabled a renaissance of computer-assisted "de novo" design of molecules with desired pharmacological properties. Here, we present our current perspective on the concept of automated molecule generation by highlighting chemocentric methods that may capture druglike chemical space, consider ligand promiscuity for hit and lead finding, and provide fresh ideas for the rational design of customized screening of compound libraries.
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Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.,inSili.com LLC , Segantinisteig 3, 8049 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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49
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Li Y, Zhao Z, Liu Z, Su M, Wang R. AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. J Chem Inf Model 2016; 56:435-53. [DOI: 10.1021/acs.jcim.5b00691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yan Li
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhixiong Zhao
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhihai Liu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Minyi Su
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Renxiao Wang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, People’s Republic of China
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50
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Grove LE, Vajda S, Kozakov D. Computational Methods to Support Fragment-based Drug Discovery. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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