1
|
Wallach I, Bernard D, Nguyen K, Ho G, Morrison A, Stecula A, Rosnik A, O’Sullivan AM, Davtyan A, Samudio B, Thomas B, Worley B, Butler B, Laggner C, Thayer D, Moharreri E, Friedland G, Truong H, van den Bedem H, Ng HL, Stafford K, Sarangapani K, Giesler K, Ngo L, Mysinger M, Ahmed M, Anthis NJ, Henriksen N, Gniewek P, Eckert S, de Oliveira S, Suterwala S, PrasadPrasad SVK, Shek S, Contreras S, Hare S, Palazzo T, O’Brien TE, Van Grack T, Williams T, Chern TR, Kenyon V, Lee AH, Cann AB, Bergman B, Anderson BM, Cox BD, Warrington JM, Sorenson JM, Goldenberg JM, Young MA, DeHaan N, Pemberton RP, Schroedl S, Abramyan TM, Gupta T, Mysore V, Presser AG, Ferrando AA, Andricopulo AD, Ghosh A, Ayachi AG, Mushtaq A, Shaqra AM, Toh AKL, Smrcka AV, Ciccia A, de Oliveira AS, Sverzhinsky A, de Sousa AM, Agoulnik AI, Kushnir A, Freiberg AN, Statsyuk AV, Gingras AR, Degterev A, Tomilov A, Vrielink A, Garaeva AA, Bryant-Friedrich A, Caflisch A, Patel AK, Rangarajan AV, Matheeussen A, Battistoni A, Caporali A, Chini A, Ilari A, Mattevi A, Foote AT, Trabocchi A, Stahl A, Herr AB, Berti A, Freywald A, Reidenbach AG, Lam A, Cuddihy AR, White A, Taglialatela A, Ojha AK, Cathcart AM, Motyl AAL, Borowska A, D’Antuono A, Hirsch AKH, Porcelli AM, Minakova A, Montanaro A, Müller A, Fiorillo A, Virtanen A, O’Donoghue AJ, Del Rio Flores A, Garmendia AE, Pineda-Lucena A, Panganiban AT, Samantha A, Chatterjee AK, Haas AL, Paparella AS, John ALS, Prince A, ElSheikh A, Apfel AM, Colomba A, O’Dea A, Diallo BN, Ribeiro BMRM, Bailey-Elkin BA, Edelman BL, Liou B, Perry B, Chua BSK, Kováts B, Englinger B, Balakrishnan B, Gong B, Agianian B, Pressly B, Salas BPM, Duggan BM, Geisbrecht BV, Dymock BW, Morten BC, Hammock BD, Mota BEF, Dickinson BC, Fraser C, Lempicki C, Novina CD, Torner C, Ballatore C, Bon C, Chapman CJ, Partch CL, Chaton CT, Huang C, Yang CY, Kahler CM, Karan C, Keller C, Dieck CL, Huimei C, Liu C, Peltier C, Mantri CK, Kemet CM, Müller CE, Weber C, Zeina CM, Muli CS, Morisseau C, Alkan C, Reglero C, Loy CA, Wilson CM, Myhr C, Arrigoni C, Paulino C, Santiago C, Luo D, Tumes DJ, Keedy DA, Lawrence DA, Chen D, Manor D, Trader DJ, Hildeman DA, Drewry DH, Dowling DJ, Hosfield DJ, Smith DM, Moreira D, Siderovski DP, Shum D, Krist DT, Riches DWH, Ferraris DM, Anderson DH, Coombe DR, Welsbie DS, Hu D, Ortiz D, Alramadhani D, Zhang D, Chaudhuri D, Slotboom DJ, Ronning DR, Lee D, Dirksen D, Shoue DA, Zochodne DW, Krishnamurthy D, Duncan D, Glubb DM, Gelardi ELM, Hsiao EC, Lynn EG, Silva EB, Aguilera E, Lenci E, Abraham ET, Lama E, Mameli E, Leung E, Christensen EM, Mason ER, Petretto E, Trakhtenberg EF, Rubin EJ, Strauss E, Thompson EW, Cione E, Lisabeth EM, Fan E, Kroon EG, Jo E, García-Cuesta EM, Glukhov E, Gavathiotis E, Yu F, Xiang F, Leng F, Wang F, Ingoglia F, van den Akker F, Borriello F, Vizeacoumar FJ, Luh F, Buckner FS, Vizeacoumar FS, Bdira FB, Svensson F, Rodriguez GM, Bognár G, Lembo G, Zhang G, Dempsey G, Eitzen G, Mayer G, Greene GL, Garcia GA, Lukacs GL, Prikler G, Parico GCG, Colotti G, De Keulenaer G, Cortopassi G, Roti G, Girolimetti G, Fiermonte G, Gasparre G, Leuzzi G, Dahal G, Michlewski G, Conn GL, Stuchbury GD, Bowman GR, Popowicz GM, Veit G, de Souza GE, Akk G, Caljon G, Alvarez G, Rucinski G, Lee G, Cildir G, Li H, Breton HE, Jafar-Nejad H, Zhou H, Moore HP, Tilford H, Yuan H, Shim H, Wulff H, Hoppe H, Chaytow H, Tam HK, Van Remmen H, Xu H, Debonsi HM, Lieberman HB, Jung H, Fan HY, Feng H, Zhou H, Kim HJ, Greig IR, Caliandro I, Corvo I, Arozarena I, Mungrue IN, Verhamme IM, Qureshi IA, Lotsaris I, Cakir I, Perry JJP, Kwiatkowski J, Boorman J, Ferreira J, Fries J, Kratz JM, Miner J, Siqueira-Neto JL, Granneman JG, Ng J, Shorter J, Voss JH, Gebauer JM, Chuah J, Mousa JJ, Maynes JT, Evans JD, Dickhout J, MacKeigan JP, Jossart JN, Zhou J, Lin J, Xu J, Wang J, Zhu J, Liao J, Xu J, Zhao J, Lin J, Lee J, Reis J, Stetefeld J, Bruning JB, Bruning JB, Coles JG, Tanner JJ, Pascal JM, So J, Pederick JL, Costoya JA, Rayman JB, Maciag JJ, Nasburg JA, Gruber JJ, Finkelstein JM, Watkins J, Rodríguez-Frade JM, Arias JAS, Lasarte JJ, Oyarzabal J, Milosavljevic J, Cools J, Lescar J, Bogomolovas J, Wang J, Kee JM, Kee JM, Liao J, Sistla JC, Abrahão JS, Sishtla K, Francisco KR, Hansen KB, Molyneaux KA, Cunningham KA, Martin KR, Gadar K, Ojo KK, Wong KS, Wentworth KL, Lai K, Lobb KA, Hopkins KM, Parang K, Machaca K, Pham K, Ghilarducci K, Sugamori KS, McManus KJ, Musta K, Faller KME, Nagamori K, Mostert KJ, Korotkov KV, Liu K, Smith KS, Sarosiek K, Rohde KH, Kim KK, Lee KH, Pusztai L, Lehtiö L, Haupt LM, Cowen LE, Byrne LJ, Su L, Wert-Lamas L, Puchades-Carrasco L, Chen L, Malkas LH, Zhuo L, Hedstrom L, Hedstrom L, Walensky LD, Antonelli L, Iommarini L, Whitesell L, Randall LM, Fathallah MD, Nagai MH, Kilkenny ML, Ben-Johny M, Lussier MP, Windisch MP, Lolicato M, Lolli ML, Vleminckx M, Caroleo MC, Macias MJ, Valli M, Barghash MM, Mellado M, Tye MA, Wilson MA, Hannink M, Ashton MR, Cerna MVC, Giorgis M, Safo MK, Maurice MS, McDowell MA, Pasquali M, Mehedi M, Serafim MSM, Soellner MB, Alteen MG, Champion MM, Skorodinsky M, O’Mara ML, Bedi M, Rizzi M, Levin M, Mowat M, Jackson MR, Paige M, Al-Yozbaki M, Giardini MA, Maksimainen MM, De Luise M, Hussain MS, Christodoulides M, Stec N, Zelinskaya N, Van Pelt N, Merrill NM, Singh N, Kootstra NA, Singh N, Gandhi NS, Chan NL, Trinh NM, Schneider NO, Matovic N, Horstmann N, Longo N, Bharambe N, Rouzbeh N, Mahmoodi N, Gumede NJ, Anastasio NC, Khalaf NB, Rabal O, Kandror O, Escaffre O, Silvennoinen O, Bishop OT, Iglesias P, Sobrado P, Chuong P, O’Connell P, Martin-Malpartida P, Mellor P, Fish PV, Moreira POL, Zhou P, Liu P, Liu P, Wu P, Agogo-Mawuli P, Jones PL, Ngoi P, Toogood P, Ip P, von Hundelshausen P, Lee PH, Rowswell-Turner RB, Balaña-Fouce R, Rocha REO, Guido RVC, Ferreira RS, Agrawal RK, Harijan RK, Ramachandran R, Verma R, Singh RK, Tiwari RK, Mazitschek R, Koppisetti RK, Dame RT, Douville RN, Austin RC, Taylor RE, Moore RG, Ebright RH, Angell RM, Yan R, Kejriwal R, Batey RA, Blelloch R, Vandenberg RJ, Hickey RJ, Kelm RJ, Lake RJ, Bradley RK, Blumenthal RM, Solano R, Gierse RM, Viola RE, McCarthy RR, Reguera RM, Uribe RV, do Monte-Neto RL, Gorgoglione R, Cullinane RT, Katyal S, Hossain S, Phadke S, Shelburne SA, Geden SE, Johannsen S, Wazir S, Legare S, Landfear SM, Radhakrishnan SK, Ammendola S, Dzhumaev S, Seo SY, Li S, Zhou S, Chu S, Chauhan S, Maruta S, Ashkar SR, Shyng SL, Conticello SG, Buroni S, Garavaglia S, White SJ, Zhu S, Tsimbalyuk S, Chadni SH, Byun SY, Park S, Xu SQ, Banerjee S, Zahler S, Espinoza S, Gustincich S, Sainas S, Celano SL, Capuzzi SJ, Waggoner SN, Poirier S, Olson SH, Marx SO, Van Doren SR, Sarilla S, Brady-Kalnay SM, Dallman S, Azeem SM, Teramoto T, Mehlman T, Swart T, Abaffy T, Akopian T, Haikarainen T, Moreda TL, Ikegami T, Teixeira TR, Jayasinghe TD, Gillingwater TH, Kampourakis T, Richardson TI, Herdendorf TJ, Kotzé TJ, O’Meara TR, Corson TW, Hermle T, Ogunwa TH, Lan T, Su T, Banjo T, O’Mara TA, Chou T, Chou TF, Baumann U, Desai UR, Pai VP, Thai VC, Tandon V, Banerji V, Robinson VL, Gunasekharan V, Namasivayam V, Segers VFM, Maranda V, Dolce V, Maltarollo VG, Scoffone VC, Woods VA, Ronchi VP, Van Hung Le V, Clayton WB, Lowther WT, Houry WA, Li W, Tang W, Zhang W, Van Voorhis WC, Donaldson WA, Hahn WC, Kerr WG, Gerwick WH, Bradshaw WJ, Foong WE, Blanchet X, Wu X, Lu X, Qi X, Xu X, Yu X, Qin X, Wang X, Yuan X, Zhang X, Zhang YJ, Hu Y, Aldhamen YA, Chen Y, Li Y, Sun Y, Zhu Y, Gupta YK, Pérez-Pertejo Y, Li Y, Tang Y, He Y, Tse-Dinh YC, Sidorova YA, Yen Y, Li Y, Frangos ZJ, Chung Z, Su Z, Wang Z, Zhang Z, Liu Z, Inde Z, Artía Z, Heifets A. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep 2024; 14:7526. [PMID: 38565852 PMCID: PMC10987645 DOI: 10.1038/s41598-024-54655-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
Collapse
|
2
|
Kihlgren A, Lammgård T, Pejner MN, Svensson F, Adolfsson AS, Lindner H. Psychometric evaluation of the Decision Support System (DSS) for municipal nurses encountering health deterioration among older adults. BMC Geriatr 2024; 24:283. [PMID: 38528517 DOI: 10.1186/s12877-024-04903-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/19/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND A valid and reliable tool is crucial for municipal registered nurses (RNs) to make quick decisions in older adults who show rapid signs of health deterioration. The aim of this study was to investigate the psychometric properties of the Decision Support System (DSS) among older adults in the municipal healthcare system. METHODS Firstly, we utilized the Rasch dichotomous model to analyze the DSS assessments (n=281) that were collected from municipal RNs working with older adults in the municipal healthcare system. We examined the properties of the DSS in terms of its unidimensionality, item fit, and separation indices. Secondly, to investigate inter-rater agreement in using the DSS, four experienced municipal RNs used the DSS to assess 60 health deterioration scenarios presented by one human patient simulators. The 60 DSS assessments were then analyzed using the ICC (2,1), percentage agreement, and Cohen κ statistics. RESULTS The sample of older adults had a mean age of 82.8 (SD 11.7). The DSS met the criteria for unidimensionality, although two items did not meet the item fit statistics when all the DSS items were analyzed together. The person separation index was 0.47, indicating a limited level of separation among the sample. The item separation index was 11.43, suggesting that the DSS has good ability to discriminate between and separate the items. At the overall DSS level, inter-rater agreements were good according to the ICC. At the individual DSS item level, the percentage agreements were 75% or above, while the Cohen κ statistics ranged from 0.46 to 1.00. CONCLUSIONS The Rasch analysis revealed that the psychometric properties of the instrument were acceptable, although further research with a larger sample size and more items is needed. The DSS has the potential to assist municipal RNs in making clinical decisions regarding health deterioration in older adults, thereby avoiding unnecessary emergency admistion and helping.
Collapse
Affiliation(s)
- Annica Kihlgren
- School of Health Sciences, Faculty of Medicine and Health, Örebro University, 701 82, Örebro, Sweden
- Older Adults' Health and Living Condition, Örebro University, Örebro, Sweden
| | - Tomas Lammgård
- School of Health Sciences, Faculty of Medicine and Health, Örebro University, 701 82, Örebro, Sweden
| | - Margaretha Norell Pejner
- School of Health Sciences, Faculty of Medicine and Health, Örebro University, 701 82, Örebro, Sweden
- Older Adults' Health and Living Condition, Örebro University, Örebro, Sweden
- Department of Home Care, Halmstad Municipality, Halmstad, Sweden
| | - Fredrik Svensson
- School of Health Sciences, Faculty of Medicine and Health, Örebro University, 701 82, Örebro, Sweden
| | - Ann-Sofie Adolfsson
- School of Health Sciences, Faculty of Medicine and Health, Örebro University, 701 82, Örebro, Sweden
| | - Helen Lindner
- School of Health Sciences, Faculty of Medicine and Health, Örebro University, 701 82, Örebro, Sweden.
| |
Collapse
|
3
|
Atkinson BN, Willis NJ, Zhao Y, Patel C, Frew S, Costelloe K, Magno L, Svensson F, Jones EY, Fish PV. Designed switch from covalent to non-covalent inhibitors of carboxylesterase Notum activity. Eur J Med Chem 2023; 251:115132. [PMID: 36934521 PMCID: PMC10626578 DOI: 10.1016/j.ejmech.2023.115132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/14/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
N-Acyl indolines 4 are potent, non-covalent Notum inhibitors developed from a covalent virtual screening hit 2a. The lead compounds were simple to synthesise, achieved excellent potency in a biochemical Notum-OPTS assay and restored Wnt signalling in a cell-based TCF/LEF reporter assay. Multiple high resolution X-ray structures established a common binding mode of these inhibitors with the indoline bound centred in the palmiteolate pocket with key interactions being aromatic stacking and a water mediated hydrogen bond to the oxyanion hole. These N-acyl indolines 4 will be useful tools for use in vitro studies to investigate the role of Notum in disease models, especially when paired with a structurally related covalent inhibitor (e.g. 4w and 2a). Overall, this study highlights the designed switch from covalent to non-covalent Notum inhibitors and so illustrates a complementary approach for hit generation and target inhibition.
Collapse
Affiliation(s)
- Benjamin N Atkinson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Nicky J Willis
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Chandni Patel
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Sarah Frew
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Kathryn Costelloe
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Lorenza Magno
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK.
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Paul V Fish
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| |
Collapse
|
4
|
Cöster MC, Cöster A, Svensson F, Callréus M, Montgomery F. Swefoot - The Swedish national quality register for foot and ankle surgery. Foot Ankle Surg 2022; 28:1404-1410. [PMID: 35933290 DOI: 10.1016/j.fas.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Population-based register data could be used to improve our knowledge of patients surgically treated for foot and ankle disorders. The quality register Swefoot was recently created to collect surgical and patient-reported data of foot and ankle surgery. This manuscript aims to describe the development and current use of the register. METHODS The development of Swefoot started in 2014 and currently, data on 16 different diagnoses are collected in 49 units performing foot and ankle surgery. Registrations are performed by the surgeon and the patient. RESULTS Between 2014 and 2020 approximately 20,000 surgical procedures have been registered. 75.1% of the registered patients were women, 9.3% were smokers, 9.3% had a concomitant rheumatoid disease, and 18.4% a BMI larger than 30 kg/m2. CONCLUSIONS: The Swefoot is a unique national register for foot and ankle surgery. It is by now possible to present demographic, surgical, and outcome parameters based on Swefoot.
Collapse
Affiliation(s)
- Maria C Cöster
- Departments of Orthopedics and Clinical Sciences, Lund University, Skåne University Hospital Malmö, Sweden; Center of Registers Västra Götaland, Sweden; Uppsala University Hospital, Sweden; Skåne University Hospital, Sweden.
| | | | - Fredrik Svensson
- Departments of Orthopedics and Clinical Sciences, Lund University, Skåne University Hospital Malmö, Sweden; Skåne University Hospital, Sweden
| | - Mattias Callréus
- Departments of Orthopedics and Clinical Sciences, Lund University, Skåne University Hospital Malmö, Sweden; Skåne University Hospital, Sweden
| | - Fredrik Montgomery
- Departments of Orthopedics and Clinical Sciences, Lund University, Skåne University Hospital Malmö, Sweden
| |
Collapse
|
5
|
Willis N, Mahy W, Sipthorp J, Zhao Y, Woodward HL, Atkinson BN, Bayle ED, Svensson F, Frew S, Jeganathan F, Monaghan A, Benvegnù S, Jolly S, Vecchia L, Ruza RR, Kjær S, Howell S, Snijders AP, Bictash M, Salinas PC, Vincent JP, Jones EY, Whiting P, Fish PV. Design of a Potent, Selective, and Brain-Penetrant Inhibitor of Wnt-Deactivating Enzyme Notum by Optimization of a Crystallographic Fragment Hit. J Med Chem 2022; 65:7212-7230. [PMID: 35536179 PMCID: PMC9150124 DOI: 10.1021/acs.jmedchem.2c00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 12/26/2022]
Abstract
Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human diseases such as colorectal cancer and Alzheimer's disease, supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we have described the discovery and profile of 8l (ARUK3001185) as a potent, selective, and brain-penetrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identified 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases, and drug targets.
Collapse
Affiliation(s)
- Nicky
J. Willis
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - William Mahy
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - James Sipthorp
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Yuguang Zhao
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Hannah L. Woodward
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Benjamin N. Atkinson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Elliott D. Bayle
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Sarah Frew
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Fiona Jeganathan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Amy Monaghan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Stefano Benvegnù
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Sarah Jolly
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Luca Vecchia
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Reinis R. Ruza
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Svend Kjær
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Steven Howell
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | | | - Magda Bictash
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Patricia C. Salinas
- Department
of Cell and Developmental Biology, Laboratory for Molecular and Cellular
Biology, University College London, London WC1E 6BT, U.K.
| | - Jean-Paul Vincent
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - E. Yvonne Jones
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Paul Whiting
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| |
Collapse
|
6
|
Morger A, Garcia de Lomana M, Norinder U, Svensson F, Kirchmair J, Mathea M, Volkamer A. Studying and mitigating the effects of data drifts on ML model performance at the example of chemical toxicity data. Sci Rep 2022; 12:7244. [PMID: 35508546 PMCID: PMC9068909 DOI: 10.1038/s41598-022-09309-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
Machine learning models are widely applied to predict molecular properties or the biological activity of small molecules on a specific protein. Models can be integrated in a conformal prediction (CP) framework which adds a calibration step to estimate the confidence of the predictions. CP models present the advantage of ensuring a predefined error rate under the assumption that test and calibration set are exchangeable. In cases where the test data have drifted away from the descriptor space of the training data, or where assay setups have changed, this assumption might not be fulfilled and the models are not guaranteed to be valid. In this study, the performance of internally valid CP models when applied to either newer time-split data or to external data was evaluated. In detail, temporal data drifts were analysed based on twelve datasets from the ChEMBL database. In addition, discrepancies between models trained on publicly-available data and applied to proprietary data for the liver toxicity and MNT in vivo endpoints were investigated. In most cases, a drastic decrease in the validity of the models was observed when applied to the time-split or external (holdout) test sets. To overcome the decrease in model validity, a strategy for updating the calibration set with data more similar to the holdout set was investigated. Updating the calibration set generally improved the validity, restoring it completely to its expected value in many cases. The restored validity is the first requisite for applying the CP models with confidence. However, the increased validity comes at the cost of a decrease in model efficiency, as more predictions are identified as inconclusive. This study presents a strategy to recalibrate CP models to mitigate the effects of data drifts. Updating the calibration sets without having to retrain the model has proven to be a useful approach to restore the validity of most models.
Collapse
Affiliation(s)
- Andrea Morger
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Marina Garcia de Lomana
- BASF SE, 67056, Ludwigshafen, Germany
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | - Ulf Norinder
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, 751 24, Sweden
- Dept Computer and Systems Sciences, Stockholm University, Kista, 164 07, Sweden
- MTM Research Centre, School of Science and Technology, 701 82, Örebro, Sweden
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, London, WC1E 6BT, UK
| | - Johannes Kirchmair
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | | | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
| |
Collapse
|
7
|
Steadman D, Atkinson BN, Zhao Y, Willis NJ, Frew S, Monaghan A, Patel C, Armstrong E, Costelloe K, Magno L, Bictash M, Jones EY, Fish PV, Svensson F. Virtual Screening Directly Identifies New Fragment-Sized Inhibitors of Carboxylesterase Notum with Nanomolar Activity. J Med Chem 2022; 65:562-578. [PMID: 34939789 DOI: 10.1021/acs.jmedchem.1c01735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Notum is a negative regulator of Wnt signaling acting through the hydrolysis of a palmitoleoylate ester, which is required for Wnt activity. Inhibitors of Notum could be of use in diseases where dysfunctional Notum activity is an underlying cause. A docking-based virtual screen (VS) of a large commercial library was used to shortlist 952 compounds for experimental validation as inhibitors of Notum. The VS was successful with 31 compounds having an IC50 < 500 nM. A critical selection process was then applied with two clusters and two singletons (1-4d) selected for hit validation. Optimization of 4d guided by structural biology identified potent inhibitors of Notum activity that restored Wnt/β-catenin signaling in cell-based models. The [1,2,4]triazolo[4,3-b]pyradizin-3(2H)-one series 4 represent a new chemical class of Notum inhibitors and the first to be discovered by a VS campaign. These results demonstrate the value of VS with well-designed docking models based on X-ray structures.
Collapse
Affiliation(s)
- David Steadman
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Benjamin N Atkinson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, OxfordOX3 7BN, U.K
| | - Nicky J Willis
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Sarah Frew
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Amy Monaghan
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Chandni Patel
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Emma Armstrong
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Kathryn Costelloe
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Lorenza Magno
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Magda Bictash
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, OxfordOX3 7BN, U.K
| | - Paul V Fish
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, LondonWC1E 6BT, U.K
| |
Collapse
|
8
|
Norinder U, Spjuth O, Svensson F. Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning. J Cheminform 2021; 13:77. [PMID: 34600569 PMCID: PMC8487527 DOI: 10.1186/s13321-021-00555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/15/2021] [Indexed: 12/05/2022] Open
Abstract
Confidence predictors can deliver predictions with the associated confidence required for decision making and can play an important role in drug discovery and toxicity predictions. In this work we investigate a recently introduced version of conformal prediction, synergy conformal prediction, focusing on the predictive performance when applied to bioactivity data. We compare the performance to other variants of conformal predictors for multiple partitioned datasets and demonstrate the utility of synergy conformal predictors for federated learning where data cannot be pooled in one location. Our results show that synergy conformal predictors based on training data randomly sampled with replacement can compete with other conformal setups, while using completely separate training sets often results in worse performance. However, in a federated setup where no method has access to all the data, synergy conformal prediction is shown to give promising results. Based on our study, we conclude that synergy conformal predictors are a valuable addition to the conformal prediction toolbox.
Collapse
Affiliation(s)
- Ulf Norinder
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden.,Department of Computer and Systems Sciences, Stockholm University, Box 7003, 164 07, Kista, Sweden.,MTM Research Centre, School of Science and Technology, Örebro University, 70182, Örebro, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden.
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
9
|
Zhao Y, Svensson F, Steadman D, Frew S, Monaghan A, Bictash M, Moreira T, Chalk R, Lu W, Fish PV, Jones EY. Structural Insights into Notum Covalent Inhibition. J Med Chem 2021; 64:11354-11363. [PMID: 34292747 PMCID: PMC8365597 DOI: 10.1021/acs.jmedchem.1c00701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Indexed: 12/28/2022]
Abstract
The carboxylesterase Notum hydrolyzes a palmitoleate moiety from Wingless/Integrated(Wnt) ligands and deactivates Wnt signaling. Notum inhibitors can restore Wnt signaling which may be of therapeutic benefit for pathologies such as osteoporosis and Alzheimer's disease. We report the identification of a novel class of covalent Notum inhibitors, 4-(indolin-1-yl)-4-oxobutanoate esters. High-resolution crystal structures of the Notum inhibitor complexes reveal a common covalent adduct formed between the nucleophile serine-232 and hydrolyzed butyric esters. The covalent interaction in solution was confirmed by mass spectrometry analysis. Inhibitory potencies vary depending on the warheads used. Mechanistically, the resulting acyl-enzyme intermediate carbonyl atom is positioned at an unfavorable angle for the approach of the active site water, which, combined with strong hydrophobic interactions with the enzyme pocket residues, hinders the intermediate from being further processed and results in covalent inhibition. These insights into Notum catalytic inhibition may guide development of more potent Notum inhibitors.
Collapse
Affiliation(s)
- Yuguang Zhao
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - David Steadman
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Sarah Frew
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Amy Monaghan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Magda Bictash
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Tiago Moreira
- Centre
for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, U.K.
| | - Rod Chalk
- Centre
for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, U.K.
| | - Weixian Lu
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - E. Yvonne Jones
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K.
| |
Collapse
|
10
|
Abstract
Predictive modeling for toxicity can help reduce risks in a range of applications and potentially serve as the basis for regulatory decisions. However, the utility of these predictions can be limited if the associated uncertainty is not adequately quantified. With recent studies showing great promise for deep learning-based models also for toxicity predictions, we investigate the combination of deep learning-based predictors with the conformal prediction framework to generate highly predictive models with well-defined uncertainties. We use a range of deep feedforward neural networks and graph neural networks in a conformal prediction setting and evaluate their performance on data from the Tox21 challenge. We also compare the results from the conformal predictors to those of the underlying machine learning models. The results indicate that highly predictive models can be obtained that result in very efficient conformal predictors even at high confidence levels. Taken together, our results highlight the utility of conformal predictors as a convenient way to deliver toxicity predictions with confidence, adding both statistical guarantees on the model performance as well as better predictions of the minority class compared to the underlying models.
Collapse
Affiliation(s)
- Jin Zhang
- Department of Drug Metabolism and Pharmacokinetics, Janssen Pharmaceutica NV, B-2340 Beerse, Belgium
| | - Ulf Norinder
- Department of Computer and Systems Sciences, Stockholm University, P.O. Box 7003, SE-164 07 Kista, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591, SE-751 24 Uppsala, Sweden.,MTM Research Centre, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
| | - Fredrik Svensson
- The Alzheimer's Research UK University College London Drug Discovery Institute, The Cruciform Building, Gower Street, London WC1E 6BT, U.K
| |
Collapse
|
11
|
Morger A, Svensson F, Arvidsson McShane S, Gauraha N, Norinder U, Spjuth O, Volkamer A. Assessing the calibration in toxicological in vitro models with conformal prediction. J Cheminform 2021; 13:35. [PMID: 33926567 PMCID: PMC8082859 DOI: 10.1186/s13321-021-00511-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/10/2021] [Indexed: 11/11/2022] Open
Abstract
Machine learning methods are widely used in drug discovery and toxicity prediction. While showing overall good performance in cross-validation studies, their predictive power (often) drops in cases where the query samples have drifted from the training data’s descriptor space. Thus, the assumption for applying machine learning algorithms, that training and test data stem from the same distribution, might not always be fulfilled. In this work, conformal prediction is used to assess the calibration of the models. Deviations from the expected error may indicate that training and test data originate from different distributions. Exemplified on the Tox21 datasets, composed of chronologically released Tox21Train, Tox21Test and Tox21Score subsets, we observed that while internally valid models could be trained using cross-validation on Tox21Train, predictions on the external Tox21Score data resulted in higher error rates than expected. To improve the prediction on the external sets, a strategy exchanging the calibration set with more recent data, such as Tox21Test, has successfully been introduced. We conclude that conformal prediction can be used to diagnose data drifts and other issues related to model calibration. The proposed improvement strategy—exchanging the calibration data only—is convenient as it does not require retraining of the underlying model.
Collapse
Affiliation(s)
- Andrea Morger
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité Universitätsmedizin, Berlin, Germany
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, London, WC1E 6BT, UK
| | - Staffan Arvidsson McShane
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 751 24, Uppsala, Sweden
| | - Niharika Gauraha
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 751 24, Uppsala, Sweden.,Division of Computational Science and Technology, KTH, 100 44, Stockholm, Sweden
| | - Ulf Norinder
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 751 24, Uppsala, Sweden.,Dept. Computer and Systems Sciences, Stockholm University, Box 7003, 164 07, Kista, Sweden.,MTM Research Centre, School of Science and Technology, Örebro University, 70 182, Örebro, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 751 24, Uppsala, Sweden
| | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité Universitätsmedizin, Berlin, Germany.
| |
Collapse
|
12
|
Bayle E, Svensson F, Atkinson BN, Steadman D, Willis NJ, Woodward HL, Whiting P, Vincent JP, Fish PV. Carboxylesterase Notum Is a Druggable Target to Modulate Wnt Signaling. J Med Chem 2021; 64:4289-4311. [PMID: 33783220 PMCID: PMC8172013 DOI: 10.1021/acs.jmedchem.0c01974] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Indexed: 12/12/2022]
Abstract
Regulation of the Wnt signaling pathway is critically important for a number of cellular processes in both development and adult mammalian biology. This Perspective will provide a summary of current and emerging therapeutic opportunities in modulating Wnt signaling, especially through inhibition of Notum carboxylesterase activity. Notum was recently shown to act as a negative regulator of Wnt signaling through the removal of an essential palmitoleate group. Inhibition of Notum activity may represent a new approach to treat disease where aberrant Notum activity has been identified as the underlying cause. Reliable screening technologies are available to identify inhibitors of Notum, and structural studies are accelerating the discovery of new inhibitors. A selection of these hits have been optimized to give fit-for-purpose small molecule inhibitors of Notum. Three noteworthy examples are LP-922056 (26), ABC99 (27), and ARUK3001185 (28), which are complementary chemical tools for exploring the role of Notum in Wnt signaling.
Collapse
Affiliation(s)
- Elliott
D. Bayle
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Benjamin N. Atkinson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - David Steadman
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Nicky J. Willis
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Hannah L. Woodward
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Paul Whiting
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Jean-Paul Vincent
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| |
Collapse
|
13
|
Mattsson L, Sörenson E, Capo E, Farnelid HM, Hirwa M, Olofsson M, Svensson F, Lindehoff E, Legrand C. Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System. Front Bioeng Biotechnol 2021; 9:651895. [PMID: 33968914 PMCID: PMC8100445 DOI: 10.3389/fbioe.2021.651895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/23/2021] [Indexed: 01/22/2023] Open
Abstract
Functionally uniform monocultures have remained the paradigm in microalgal cultivation despite the apparent challenges to avoid invasions by other microorganisms. A mixed microbial consortium approach has the potential to optimize and maintain biomass production despite of seasonal changes and to be more resilient toward contaminations. Here we present a 3-year outdoor production of mixed consortia of locally adapted microalgae and bacteria in cold temperate latitude. Microalgal consortia were cultivated in flat panel photobioreactors using brackish Baltic Sea water and CO2 from a cement factory (Degerhamn, Cementa AB, Heidelberg Cement Group) as a sustainable CO2 source. To evaluate the ability of the microbial consortia to maintain stable biomass production while exposed to seasonal changes in both light and temperature, we tracked changes in the microbial community using molecular methods (16S and 18S rDNA amplicon sequencing) and monitored the biomass production and quality (lipid, protein, and carbohydrate content) over 3 years. Despite changes in environmental conditions, the mixed consortia maintained stable biomass production by alternating between two different predominant green microalgae (Monoraphidium and Mychonastes) with complementary tolerance to temperature. The bacterial population was few taxa co-occured over time and the composition did not have any connection to the shifts in microalgal taxa. We propose that a locally adapted and mixed microalgal consortia, with complementary traits, can be useful for optimizing yield of commercial scale microalgal cultivation.
Collapse
Affiliation(s)
- Lina Mattsson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eva Sörenson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eric Capo
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Hanna Maria Farnelid
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Maurice Hirwa
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.,Axis Communications, Lund, Sweden
| | | | - Fredrik Svensson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Elin Lindehoff
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| |
Collapse
|
14
|
Magno L, Bunney TD, Mead E, Svensson F, Bictash MN. TREM2/PLCγ2 signalling in immune cells: function, structural insight, and potential therapeutic modulation. Mol Neurodegener 2021; 16:22. [PMID: 33823896 PMCID: PMC8022522 DOI: 10.1186/s13024-021-00436-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/24/2021] [Indexed: 01/21/2023] Open
Abstract
The central role of the resident innate immune cells of the brain (microglia) in neurodegeneration has become clear over the past few years largely through genome-wide association studies (GWAS), and has rapidly become an active area of research. However, a mechanistic understanding (gene to function) has lagged behind. That is now beginning to change, as exemplified by a number of recent exciting and important reports that provide insight into the function of two key gene products – TREM2 (Triggering Receptor Expressed On Myeloid Cells 2) and PLCγ2 (Phospholipase C gamma2) – in microglia, and their role in neurodegenerative disorders. In this review we explore and discuss these recent advances and the opportunities that they may provide for the development of new therapies.
Collapse
Affiliation(s)
- Lorenza Magno
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK.
| | - Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Emma Mead
- Alzheimer's Research UK Oxford Drug Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, OX3 7FZ, UK
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Magda N Bictash
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| |
Collapse
|
15
|
Norinder U, Spjuth O, Svensson F. Correction to “Using Predicted Bioactivity Profiles to Improve Predictive Modeling”. J Chem Inf Model 2020; 60:6722. [DOI: 10.1021/acs.jcim.0c01327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
16
|
Smit IA, Afzal AM, Allen CHG, Svensson F, Hanser T, Bender A. Systematic Analysis of Protein Targets Associated with Adverse Events of Drugs from Clinical Trials and Postmarketing Reports. Chem Res Toxicol 2020; 34:365-384. [PMID: 33351593 DOI: 10.1021/acs.chemrestox.0c00294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Adverse drug reactions (ADRs) are undesired effects of medicines that can harm patients and are a significant source of attrition in drug development. ADRs are anticipated by routinely screening drugs against secondary pharmacology protein panels. However, there is still a lack of quantitative information on the links between these off-target proteins and the reporting of ADRs in humans. Here, we present a systematic analysis of associations between measured and predicted in vitro bioactivities of drugs and adverse events (AEs) in humans from two sources of data: the Side Effect Resource, derived from clinical trials, and the Food and Drug Administration Adverse Event Reporting System, derived from postmarketing surveillance. The ratio of a drug's therapeutic unbound plasma concentration over the drug's in vitro potency against a given protein was used to select proteins most likely to be relevant to in vivo effects. In examining individual target bioactivities as predictors of AEs, we found a trade-off between the positive predictive value and the fraction of drugs with AEs that can be detected. However, considering sets of multiple targets for the same AE can help identify a greater fraction of AE-associated drugs. Of the 45 targets with statistically significant associations to AEs, 30 are included on existing safety target panels. The remaining 15 targets include 9 carbonic anhydrases, of which CA5B is significantly associated with cholestatic jaundice. We include the full quantitative data on associations between measured and predicted in vitro bioactivities and AEs in humans in this work, which can be used to make a more informed selection of safety profiling targets.
Collapse
Affiliation(s)
- Ines A Smit
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Avid M Afzal
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chad H G Allen
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Fredrik Svensson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Thierry Hanser
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, United Kingdom
| | - Andreas Bender
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
17
|
Mahy W, Willis NJ, Zhao Y, Woodward HL, Svensson F, Sipthorp J, Vecchia L, Ruza RR, Hillier J, Kjær S, Frew S, Monaghan A, Bictash M, Salinas PC, Whiting P, Vincent JP, Jones EY, Fish PV. 5-Phenyl-1,3,4-oxadiazol-2(3 H)-ones Are Potent Inhibitors of Notum Carboxylesterase Activity Identified by the Optimization of a Crystallographic Fragment Screening Hit. J Med Chem 2020; 63:12942-12956. [PMID: 33124429 DOI: 10.1021/acs.jmedchem.0c01391] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Carboxylesterase Notum is a negative regulator of the Wnt signaling pathway. There is an emerging understanding of the role Notum plays in disease, supporting the need to discover new small-molecule inhibitors. A crystallographic X-ray fragment screen was performed, which identified fragment hit 1,2,3-triazole 7 as an attractive starting point for a structure-based drug design hit-to-lead program. Optimization of 7 identified oxadiazol-2-one 23dd as a preferred example with properties consistent with drug-like chemical space. Screening 23dd in a cell-based TCF/LEF reporter gene assay restored the activation of Wnt signaling in the presence of Notum. Mouse pharmacokinetic studies with oral administration of 23dd demonstrated good plasma exposure and partial blood-brain barrier penetration. Significant progress was made in developing fragment hit 7 into lead 23dd (>600-fold increase in activity), making it suitable as a new chemical tool for exploring the role of Notum-mediated regulation of Wnt signaling.
Collapse
Affiliation(s)
- William Mahy
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
| | - Nicky J Willis
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, U.K
| | - Hannah L Woodward
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
- The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K
| | - James Sipthorp
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
- The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, U.K
| | - Reinis R Ruza
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, U.K
| | - James Hillier
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, U.K
| | - Svend Kjær
- The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K
| | - Sarah Frew
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
| | - Amy Monaghan
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
| | - Magda Bictash
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
| | - Patricia C Salinas
- Department of Cell and Developmental Biology, Laboratory for Molecular and Cellular Biology, University College London, London WC1E 6BT, U.K
| | - Paul Whiting
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
| | - Jean-Paul Vincent
- The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, U.K
| | - Paul V Fish
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K
- The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K
| |
Collapse
|
18
|
Mahy W, Patel M, Steadman D, Woodward HL, Atkinson BN, Svensson F, Willis NJ, Flint A, Papatheodorou D, Zhao Y, Vecchia L, Ruza RR, Hillier J, Frew S, Monaghan A, Costa A, Bictash M, Walter MW, Jones EY, Fish PV. Screening of a Custom-Designed Acid Fragment Library Identifies 1-Phenylpyrroles and 1-Phenylpyrrolidines as Inhibitors of Notum Carboxylesterase Activity. J Med Chem 2020; 63:9464-9483. [PMID: 32787107 DOI: 10.1021/acs.jmedchem.0c00660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Wnt family of proteins are secreted signaling proteins that play key roles in regulating cellular functions. Recently, carboxylesterase Notum was shown to act as a negative regulator of Wnt signaling by mediating the removal of an essential palmitoleate. Here we disclose two new chemical scaffolds that inhibit Notum enzymatic activity. Our approach was to create a fragment library of 250 acids for screening against Notum in a biochemical assay followed by structure determination by X-ray crystallography. Twenty fragments were identified as hits for Notum inhibition, and 14 of these fragments were shown to bind in the palmitoleate pocket of Notum. Optimization of 1-phenylpyrrole 20, guided by structure-based drug design, identified 20z as the most potent compound from this series. Similarly, the optimization of 1-phenylpyrrolidine 8 gave acid 26. This work demonstrates that inhibition of Notum activity can be achieved by small, drug-like molecules possessing favorable in vitro ADME profiles.
Collapse
Affiliation(s)
- William Mahy
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Mikesh Patel
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - David Steadman
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Hannah L Woodward
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Benjamin N Atkinson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
- The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, United Kingdom
| | - Nicky J Willis
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Alister Flint
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Dimitra Papatheodorou
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, Bloomsbury, London WC1N 1AX, United Kingdom
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Reinis R Ruza
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - James Hillier
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Sarah Frew
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Amy Monaghan
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Artur Costa
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Magda Bictash
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Magnus W Walter
- Eli Lilly, Erl Wood Manor, Windlesham, Surrey GU20 6PH, United Kingdom
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Paul V Fish
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
- The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, United Kingdom
| |
Collapse
|
19
|
Abstract
Iterative screening is a process in which screening is done in batches, with each batch filled by using machine learning to select the most promising compounds from the library based on the previous results. We believe iterative screening is poised to enhance the screening process by improving hit finding while at the same time reducing the number of compounds screened. In addition, we see this process as a key enabler of next-generation high-throughput screening (HTS), which uses more complex assays that better describe the biology but demand more resource per screened compound. To demonstrate the utility of these methods, we retrospectively analyze HTS data from PubChem with a focus on machine learning–based screening strategies that can be readily implemented in practice. Our results show that over a variety of HTS experimental paradigms, an iterative screening setup that screens a total of 35% of the screening collection over as few as three iterations has a median return rate of approximately 70% of the active compounds. Increasing the portion of the library screened to 50% yields median returns of approximately 80% of actives. Using six iterations increases these return rates to 78% and 90%, respectively. The best results were achieved with machine learning models that can be run on a standard desktop. By demonstrating that the utility of iterative screening holds true even with a small number of iterations, and without requiring significant computational resources, we provide a roadmap for the practical implementation of these techniques in hit finding.
Collapse
Affiliation(s)
- Gabriel H S Dreiman
- The Alzheimer's Research UK University College London Drug Discovery Institute, London, UK.,Department of Computer Science, University College London, London, UK
| | - Magda Bictash
- The Alzheimer's Research UK University College London Drug Discovery Institute, London, UK
| | - Paul V Fish
- The Alzheimer's Research UK University College London Drug Discovery Institute, London, UK
| | - Lewis Griffin
- Department of Computer Science, University College London, London, UK
| | - Fredrik Svensson
- The Alzheimer's Research UK University College London Drug Discovery Institute, London, UK
| |
Collapse
|
20
|
Alghamdi AH, Munday JC, Campagnaro GD, Gurvic D, Svensson F, Okpara CE, Kumar A, Quintana J, Martin Abril ME, Milić P, Watson L, Paape D, Settimo L, Dimitriou A, Wielinska J, Smart G, Anderson LF, Woodley CM, Kelly SPY, Ibrahim HM, Hulpia F, Al-Salabi MI, Eze AA, Sprenger T, Teka IA, Gudin S, Weyand S, Field M, Dardonville C, Tidwell RR, Carrington M, O'Neill P, Boykin DW, Zachariae U, De Koning HP. Positively selected modifications in the pore of TbAQP2 allow pentamidine to enter Trypanosoma brucei. eLife 2020; 9:56416. [PMID: 32762841 PMCID: PMC7473772 DOI: 10.7554/elife.56416] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/06/2020] [Indexed: 11/25/2022] Open
Abstract
Mutations in the Trypanosoma brucei aquaporin AQP2 are associated with resistance to pentamidine and melarsoprol. We show that TbAQP2 but not TbAQP3 was positively selected for increased pore size from a common ancestor aquaporin. We demonstrate that TbAQP2’s unique architecture permits pentamidine permeation through its central pore and show how specific mutations in highly conserved motifs affect drug permeation. Introduction of key TbAQP2 amino acids into TbAQP3 renders the latter permeable to pentamidine. Molecular dynamics demonstrates that permeation by dicationic pentamidine is energetically favourable in TbAQP2, driven by the membrane potential, although aquaporins are normally strictly impermeable for ionic species. We also identify the structural determinants that make pentamidine a permeant although most other diamidine drugs are excluded. Our results have wide-ranging implications for optimising antitrypanosomal drugs and averting cross-resistance. Moreover, these new insights in aquaporin permeation may allow the pharmacological exploitation of other members of this ubiquitous gene family. African sleeping sickness is a potentially deadly illness caused by the parasite Trypanosoma brucei. The disease is treatable, but many of the current treatments are old and are becoming increasingly ineffective. For instance, resistance is growing against pentamidine, a drug used in the early stages in the disease, as well as against melarsoprol, which is deployed when the infection has progressed to the brain. Usually, cases resistant to pentamidine are also resistant to melarsoprol, but it is still unclear why, as the drugs are chemically unrelated. Studies have shown that changes in a water channel called aquaglyceroporin 2 (TbAQP2) contribute to drug resistance in African sleeping sickness; this suggests that it plays a role in allowing drugs to kill the parasite. This molecular ‘drain pipe’ extends through the surface of T. brucei, and should allow only water and a molecule called glycerol in and out of the cell. In particular, the channel should be too narrow to allow pentamidine or melarsoprol to pass through. One possibility is that, in T. brucei, the TbAQP2 channel is abnormally wide compared to other members of its family. Alternatively, pentamidine and melarsoprol may only bind to TbAQP2, and then ‘hitch a ride’ when the protein is taken into the parasite as part of the natural cycle of surface protein replacement. Alghamdi et al. aimed to tease out these hypotheses. Computer models of the structure of the protein were paired with engineered changes in the key areas of the channel to show that, in T. brucei, TbAQP2 provides a much broader gateway into the cell than observed for similar proteins. In addition, genetic analysis showed that this version of TbAQP2 has been actively selected for during the evolution process of T. brucei. This suggests that the parasite somehow benefits from this wider aquaglyceroporin variant. This is a new resistance mechanism, and it is possible that aquaglyceroporins are also larger than expected in other infectious microbes. The work by Alghamdi et al. therefore provides insight into how other germs may become resistant to drugs.
Collapse
Affiliation(s)
- Ali H Alghamdi
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Jane C Munday
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | | | - Dominik Gurvic
- Computational Biology Centre for Translational and Interdisciplinary Research, University of Dundee, Dundee, United Kingdom
| | - Fredrik Svensson
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cambridge, United Kingdom
| | - Chinyere E Okpara
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom
| | - Arvind Kumar
- Chemistry Department, Georgia State University, Atlanta, United States
| | - Juan Quintana
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | | | - Patrik Milić
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Laura Watson
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Daniel Paape
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Luca Settimo
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Anna Dimitriou
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Joanna Wielinska
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Graeme Smart
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Laura F Anderson
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | | | - Siu Pui Ying Kelly
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Hasan Ms Ibrahim
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry, University of Ghent, Ghent, Belgium
| | - Mohammed I Al-Salabi
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Anthonius A Eze
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Teresa Sprenger
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ibrahim A Teka
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Simon Gudin
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mark Field
- School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | - Richard R Tidwell
- Department of Pathology and Lab Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Paul O'Neill
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom
| | - David W Boykin
- Chemistry Department, Georgia State University, Atlanta, United States
| | - Ulrich Zachariae
- Computational Biology Centre for Translational and Interdisciplinary Research, University of Dundee, Dundee, United Kingdom
| | - Harry P De Koning
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
21
|
Abstract
Predictive modeling is a cornerstone in early drug development. Using information for multiple domains or across prediction tasks has the potential to improve the performance of predictive modeling. However, aggregating data often leads to incomplete data matrices that might be limiting for modeling. In line with previous studies, we show that by generating predicted bioactivity profiles, and using these as additional features, prediction accuracy of biological endpoints can be improved. Using conformal prediction, a type of confidence predictor, we present a robust framework for the calculation of these profiles and the evaluation of their impact. We report on the outcomes from several approaches to generate the predicted profiles on 16 datasets in cytotoxicity and bioactivity and show that efficiency is improved the most when including the p-values from conformal prediction as bioactivity profiles.
Collapse
Affiliation(s)
- Ulf Norinder
- Department of Computer and Systems Sciences, Stockholm University, Box 7003, SE-164 07 Kista, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-75124 Uppsala, Sweden.,MTM Research Centre, School of Science and Technology, Örebro University, SE-70182 Örebro, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-75124 Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Box 591, SE-75124 Uppsala, Sweden
| | - Fredrik Svensson
- The Alzheimer's Research UK University College London Drug Discovery Institute, The Cruciform Building, Gower Street, WC1E 6BT London, U.K
| |
Collapse
|
22
|
Affiliation(s)
- Henriëtte Willems
- The ALBORADA Drug Discovery Institute, University of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K
| | - Stephane De Cesco
- Alzheimer’s Research UK Oxford Drug Discovery Institute, University of Oxford, NDM Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Fredrik Svensson
- Alzheimer’s Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London WC1E 6BT, U.K
| |
Collapse
|
23
|
Atkinson BN, Steadman D, Mahy W, Zhao Y, Sipthorp J, Bayle ED, Svensson F, Papageorgiou G, Jeganathan F, Frew S, Monaghan A, Bictash M, Jones EY, Fish PV. Scaffold-hopping identifies furano[2,3-d]pyrimidine amides as potent Notum inhibitors. Bioorg Med Chem Lett 2020; 30:126751. [PMID: 31862412 PMCID: PMC6961116 DOI: 10.1016/j.bmcl.2019.126751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 11/26/2022]
Abstract
The carboxylesterase Notum is a key negative regulator of the Wnt signaling pathway by mediating the depalmitoleoylation of Wnt proteins. Our objective was to discover potent small molecule inhibitors of Notum suitable for exploring the regulation of Wnt signaling in the central nervous system. Scaffold-hopping from thienopyrimidine acids 1 and 2, supported by X-ray structure determination, identified 3-methylimidazolin-4-one amides 20-24 as potent inhibitors of Notum with activity across three orthogonal assay formats (biochemical, extra-cellular, occupancy). A preferred example 24 demonstrated good stability in mouse microsomes and plasma, and cell permeability in the MDCK-MDR1 assay albeit with modest P-gp mediated efflux. Pharmacokinetic studies with 24 were performed in vivo in mouse with single oral administration of 24 showing good plasma exposure and reasonable CNS penetration. We propose that 24 is a new chemical tool suitable for cellular studies to explore the fundamental biology of Notum.
Collapse
Affiliation(s)
- Benjamin N Atkinson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK
| | - David Steadman
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK
| | - William Mahy
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
| | - James Sipthorp
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK
| | - Elliott D Bayle
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK
| | - George Papageorgiou
- The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK
| | - Fiona Jeganathan
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK
| | - Sarah Frew
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK
| | - Amy Monaghan
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK
| | - Magda Bictash
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Paul V Fish
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK.
| |
Collapse
|
24
|
Safitri D, Harris M, Potter H, Yan Yeung H, Winfield I, Kopanitsa L, Svensson F, Rahman T, Harper MT, Bailey D, Ladds G. Elevated intracellular cAMP concentration mediates growth suppression in glioma cells. Biochem Pharmacol 2020; 174:113823. [PMID: 31987856 DOI: 10.1016/j.bcp.2020.113823] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
Supressed levels of intracellular cAMP have been associated with malignancy. Thus, elevating cAMP through activation of adenylyl cyclase (AC) or by inhibition of phosphodiesterase (PDE) may be therapeutically beneficial. Here, we demonstrate that elevated cAMP levels suppress growth in C6 cells (a model of glioma) through treatment with forskolin, an AC activator, or a range of small molecule PDE inhibitors with differing selectivity profiles. Forskolin suppressed cell growth in a PKA-dependent manner by inducing a G2/M phase cell cycle arrest. In contrast, trequinsin (a non-selective PDE2/3/7 inhibitor), not only inhibited cell growth via PKA, but also stimulated (independent of PKA) caspase-3/-7 and induced an aneuploidy phenotype. Interestingly, a cocktail of individual PDE 2,3,7 inhibitors suppressed cell growth in a manner analogous to forskolin but not trequinsin. Finally, we demonstrate that concomitant targeting of both AC and PDEs synergistically elevated intracellular cAMP levels thereby potentiating their antiproliferative actions.
Collapse
Affiliation(s)
- Dewi Safitri
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom; Pharmacology and Clinical Pharmacy Research Group, School of Pharmacy, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Harriet Potter
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Ho Yan Yeung
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Ian Winfield
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Liliya Kopanitsa
- IOTA Pharmaceuticals Ltd, Cambridge University Biomedical Innovation Hub, Clifford Allbutt Building, Hills Road, Cambridge CB2 0AH, United Kingdom
| | - Fredrik Svensson
- IOTA Pharmaceuticals Ltd, Cambridge University Biomedical Innovation Hub, Clifford Allbutt Building, Hills Road, Cambridge CB2 0AH, United Kingdom
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Matthew T Harper
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - David Bailey
- IOTA Pharmaceuticals Ltd, Cambridge University Biomedical Innovation Hub, Clifford Allbutt Building, Hills Road, Cambridge CB2 0AH, United Kingdom
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom.
| |
Collapse
|
25
|
Svensson F, Norinder U. Conformal Prediction for Ecotoxicology and Implications for Regulatory Decision-Making. Methods in Pharmacology and Toxicology 2020. [DOI: 10.1007/978-1-0716-0150-1_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
26
|
Svensson F, Westerman B, Würdinger T, Bailey D. GBM Drug Bank-a new resource for glioblastoma drug discovery and informatics research. Neuro Oncol 2019; 20:1680-1681. [PMID: 30137543 DOI: 10.1093/neuonc/noy122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Bart Westerman
- VU Medical Center, Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Thomas Würdinger
- VU Medical Center, Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | |
Collapse
|
27
|
Zhang J, Mucs D, Norinder U, Svensson F. LightGBM: An Effective and Scalable Algorithm for Prediction of Chemical Toxicity-Application to the Tox21 and Mutagenicity Data Sets. J Chem Inf Model 2019; 59:4150-4158. [PMID: 31560206 DOI: 10.1021/acs.jcim.9b00633] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Machine learning algorithms have attained widespread use in assessing the potential toxicities of pharmaceuticals and industrial chemicals because of their faster speed and lower cost compared to experimental bioassays. Gradient boosting is an effective algorithm that often achieves high predictivity, but historically the relative long computational time limited its applications in predicting large compound libraries or developing in silico predictive models that require frequent retraining. LightGBM, a recent improvement of the gradient boosting algorithm, inherited its high predictivity but resolved its scalability and long computational time by adopting a leaf-wise tree growth strategy and introducing novel techniques. In this study, we compared the predictive performance and the computational time of LightGBM to deep neural networks, random forests, support vector machines, and XGBoost. All algorithms were rigorously evaluated on publicly available Tox21 and mutagenicity data sets using a Bayesian optimization integrated nested 10-fold cross-validation scheme that performs hyperparameter optimization while examining model generalizability and transferability to new data. The evaluation results demonstrated that LightGBM is an effective and highly scalable algorithm offering the best predictive performance while consuming significantly shorter computational time than the other investigated algorithms across all Tox21 and mutagenicity data sets. We recommend LightGBM for applications of in silico safety assessment and also other areas of cheminformatics to fulfill the ever-growing demand for accurate and rapid prediction of various toxicity or activity related end points of large compound libraries present in the pharmaceutical and chemical industry.
Collapse
Affiliation(s)
- Jin Zhang
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | - Daniel Mucs
- Swetox, Unit of Toxicology Sciences , Karolinska Institutet , Forskargatan 20 , SE-151 36 Södertälje , Sweden
| | - Ulf Norinder
- Swetox, Unit of Toxicology Sciences , Karolinska Institutet , Forskargatan 20 , SE-151 36 Södertälje , Sweden.,Department of Computer and Systems Sciences , Stockholm University , Box 7003, SE-164 07 Kista , Sweden
| | - Fredrik Svensson
- The Alzheimer's Research UK University College London Drug Discovery Institute , The Cruciform Building, Gower Street , London WC1E 6BT , U.K.,The Francis Crick Institute , 1 Midland Road , London NW1 1AT , U.K
| |
Collapse
|
28
|
Mahmoud SY, Svensson F, Zoufir A, Módos D, Afzal AM, Bender A. Understanding Conditional Associations between ToxCast in Vitro Readouts and the Hepatotoxicity of Compounds Using Rule-Based Methods. Chem Res Toxicol 2019; 33:137-153. [DOI: 10.1021/acs.chemrestox.8b00382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Samar Y. Mahmoud
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Fredrik Svensson
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Azedine Zoufir
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Dezső Módos
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Avid M. Afzal
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| |
Collapse
|
29
|
Svensson F, Felson DT, Turkiewicz A, Guermazi A, Roemer FW, Neuman P, Englund M. Scrutinizing the cut-off for "pathological" meniscal body extrusion on knee MRI. Eur Radiol 2019; 29:2616-2623. [PMID: 30631922 PMCID: PMC6443617 DOI: 10.1007/s00330-018-5914-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 10/24/2018] [Accepted: 11/23/2018] [Indexed: 01/25/2023]
Abstract
OBJECTIVES Medial meniscal body extrusion ≥ 3 mm on MRI is often considered "pathologic." The aims of this study were to (1) assess the adequacy of 3 mm as cut-off for "pathological" extrusion and (2) find an optimal cut-off for meniscal extrusion cross-sectionally associated with radiographic knee osteoarthritis, bone marrow lesions (BMLs), and cartilage damage. METHODS Nine hundred fifty-eight persons, aged 50-90 years from Framingham, MA, USA, had readable 1.5 T MRI scans of the right knee for meniscal body extrusion (measured in mm). BMLs and cartilage damage were read using the whole organ magnetic resonance imaging score (WORMS). Knee X-rays were read according to the Kellgren and Lawrence (KL) scale. We evaluated the performance of the 3-mm cut-off with respect to the three outcomes and estimated a new cut-off maximizing the sum of sensitivity and specificity. RESULTS The study persons had mean age of 62.2 years, 57.0% were women and the mean body mass index was 28.5 kg/m2. Knees with radiographic osteoarthritis, BMLs, and cartilage damage had overall more meniscal extrusion than knees without. The 3-mm cut-off had moderate sensitivity and low specificity for all three outcomes (sensitivity between 0.68 [95% CI 0.63-0.73] and 0.81 [0.73-0.87], specificity between 0.49 [0.45-0.52] and 0.54 [0.49-0.58]). Using 4 mm maximized the sum of sensitivity and specificity and improved the percentage of correctly classified subjects (from between 54 and 61% to between 64 and 79%). CONCLUSIONS The 4-mm cut-off may be used as an alternative cut-off for denoting pathological meniscal extrusion. KEY POINTS • Medial meniscal body extrusion is strongly associated with osteoarthritis. • The 3-mm cut-off for medial meniscal body extrusion has high sensitivity but low specificity with respect to bone marrow lesions, cartilage damage, and radiographic osteoarthritis. • The 4-mm cut-off maximizes the sensitivity and specificity with respect to all three osteoarthritis features.
Collapse
Affiliation(s)
- F Svensson
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopedics, Clinical Epidemiology Unit, Lund University, Lund, Sweden.
| | - D T Felson
- Clinical Epidemiology Research & Training Unit, Boston University School of Medicine, Boston, MA, USA
| | - A Turkiewicz
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopedics, Clinical Epidemiology Unit, Lund University, Lund, Sweden
| | - A Guermazi
- Department of Radiology, Boston University School of Medicine, Boston, MA, USA
| | - F W Roemer
- Department of Radiology, Boston University School of Medicine, Boston, MA, USA
- Department of Radiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - P Neuman
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopedics, Clinical Epidemiology Unit, Lund University, Lund, Sweden
| | - M Englund
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopedics, Clinical Epidemiology Unit, Lund University, Lund, Sweden
- Clinical Epidemiology Research & Training Unit, Boston University School of Medicine, Boston, MA, USA
| |
Collapse
|
30
|
Abstract
Multitask prediction of bioactivities is often faced with challenges relating to the sparsity of data and imbalance between different labels. We propose class conditional (Mondrian) conformal predictors using underlying Macau models as a novel approach for large scale bioactivity prediction. This approach handles both high degrees of missing data and label imbalances while still producing high quality predictive models. When applied to ten assay end points from PubChem, the models generated valid models with an efficiency of 74.0-80.1% at the 80% confidence level with similar performance both for the minority and majority class. Also when deleting progressively larger portions of the available data (0-80%) the performance of the models remained robust with only minor deterioration (reduction in efficiency between 5 and 10%). Compared to using Macau without conformal prediction the method presented here significantly improves the performance on imbalanced data sets.
Collapse
Affiliation(s)
- Ulf Norinder
- Swetox, Unit of Toxicology Sciences , Karolinska Institutet , Forskargatan 20 , SE-151 36 Södertälje , Sweden.,Department of Computer and Systems Sciences , Stockholm University , Box 7003 , SE-164 07 Kista , Sweden
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , U.K.,The Francis Crick Institute , 1 Midland Road , London , NW1 1AT , U.K
| |
Collapse
|
31
|
Svensson F, Felson DT, Zhang F, Guermazi A, Roemer FW, Niu J, Aliabadi P, Neogi T, Englund M. Meniscal body extrusion and cartilage coverage in middle-aged and elderly without radiographic knee osteoarthritis. Eur Radiol 2019; 29:1848-1854. [PMID: 30280250 PMCID: PMC6420611 DOI: 10.1007/s00330-018-5741-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/20/2017] [Accepted: 10/18/2017] [Indexed: 01/27/2023]
Abstract
OBJECTIVES To determine meniscal extrusion and cartilage coverage on magnetic resonance (MR) images and factors associated with these parameters in knees of middle-aged and elderly persons free from radiographic tibiofemoral osteoarthritis (OA). METHODS Seven hundred eighteen persons, free of radiographic tibiofemoral OA, aged 50-90 years from Framingham, MA, USA, were included. We measured meniscal extrusion on 1.5 T MRI of both knees to evaluate both medial and lateral meniscal body extrusion and cartilage coverage. We also determined meniscal morphology and structural integrity. The multivariable association with age, body mass index (BMI), and ipsilateral meniscal damage was also evaluated. RESULTS The mean meniscal body extrusion medially was 2.7 mm and laterally 1.8 mm. The tibial cartilage coverage was about 30% of ipsilateral cartilage surface (both compartments). The presence of ipsilateral meniscal damage was associated with more extrusion in only the medial compartment, 1.0 mm in men and 0.6 mm in women, and less cartilage coverage proportion, -5.5% in men and -4.6% in women. CONCLUSIONS Mean medial meniscal body extrusion in middle-aged or older persons without radiographic tibiofemoral OA approximates the commonly used cutoff (3 mm) to denote pathological extrusion. Medial meniscal damage is a factor associated with medial meniscal body extrusion and less cartilage coverage. KEY POINTS • Medial meniscal extrusion in middle-aged/older persons without OA is around 3 mm. • Lateral meniscal extrusion in middle-aged/older persons without OA is around 2 mm. • Meniscal damage is associated with medial meniscal extrusion and less cartilage coverage.
Collapse
Affiliation(s)
- Fredrik Svensson
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopedics, Clinical Epidemiology Unit, Lund University, Lund, Sweden.
| | - David T Felson
- Clinical Epidemiology Research & Training Unit, Boston University School of Medicine, Boston, MA, USA
| | - Fan Zhang
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopedics, Clinical Epidemiology Unit, Lund University, Lund, Sweden
| | - Ali Guermazi
- Department of Radiology, Boston University School of Medicine, Boston, MA, USA
| | - Frank W Roemer
- Clinical Epidemiology Research & Training Unit, Boston University School of Medicine, Boston, MA, USA
- Department of Radiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Jingbo Niu
- Clinical Epidemiology Research & Training Unit, Boston University School of Medicine, Boston, MA, USA
| | - Piran Aliabadi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tuhina Neogi
- Clinical Epidemiology Research & Training Unit, Boston University School of Medicine, Boston, MA, USA
| | - Martin Englund
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopedics, Clinical Epidemiology Unit, Lund University, Lund, Sweden
- Clinical Epidemiology Research & Training Unit, Boston University School of Medicine, Boston, MA, USA
| |
Collapse
|
32
|
Zanders ED, Svensson F, Bailey DS. Therapy for glioblastoma: is it working? Drug Discov Today 2019; 24:1193-1201. [PMID: 30878561 DOI: 10.1016/j.drudis.2019.03.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/06/2019] [Accepted: 03/08/2019] [Indexed: 12/21/2022]
Abstract
Glioblastoma (GBM) remains one of the most intransigent of cancers, with a median overall survival of only 15 months after diagnosis. Drug treatments have largely proven ineffective; it is thought that this is related to the heterogeneous nature and plasticity of GBM-initiating stem cell lineages. Although many combination drug therapies are being positioned to address tumour heterogeneity, the most promising therapeutic approaches for GBM to date appear to be those targeting GBM by vaccination or antibody- and cell-based immunotherapy. We review the most recent clinical trials for GBM and discuss the role of adaptive clinical trials in developing personalised treatment strategies to address intra- and inter-tumoral heterogeneity.
Collapse
Affiliation(s)
- Edward D Zanders
- IOTA Pharmaceuticals Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 0WS, UK
| | - Fredrik Svensson
- IOTA Pharmaceuticals Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 0WS, UK
| | - David S Bailey
- IOTA Pharmaceuticals Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 0WS, UK.
| |
Collapse
|
33
|
Broman E, Li L, Fridlund J, Svensson F, Legrand C, Dopson M. Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure. Microb Ecol 2019; 77:288-303. [PMID: 30019110 PMCID: PMC6394492 DOI: 10.1007/s00248-018-1229-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2- + NO3- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO2- + NO3- was observed in the overlying benthic water in all amended and control incubations. The combination of NO2- + NO3- diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.
Collapse
Affiliation(s)
- Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden.
| | - Lingni Li
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| | - Jimmy Fridlund
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| | - Fredrik Svensson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| |
Collapse
|
34
|
Svensson F, Zoufir A, Mahmoud S, Afzal AM, Smit I, Giblin KA, Clements PJ, Mettetal JT, Pointon A, Harvey JS, Greene N, Williams RV, Bender A. Information-Derived Mechanistic Hypotheses for Structural Cardiotoxicity. Chem Res Toxicol 2018; 31:1119-1127. [PMID: 30350600 DOI: 10.1021/acs.chemrestox.8b00159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adverse events resulting from drug therapy can be a cause of drug withdrawal, reduced and or restricted clinical use, as well as a major economic burden for society. To increase the safety of new drugs, there is a need to better understand the mechanisms causing the adverse events. One way to derive new mechanistic hypotheses is by linking data on drug adverse events with the drugs' biological targets. In this study, we have used data mining techniques and mutual information statistical approaches to find associations between reported adverse events collected from the FDA Adverse Event Reporting System and assay outcomes from ToxCast, with the aim to generate mechanistic hypotheses related to structural cardiotoxicity (morphological damage to cardiomyocytes and/or loss of viability). Our workflow identified 22 adverse event-assay outcome associations. From these associations, 10 implicated targets could be substantiated with evidence from previous studies reported in the literature. For two of the identified targets, we also describe a more detailed mechanism, forming putative adverse outcome pathways associated with structural cardiotoxicity. Our study also highlights the difficulties deriving these type of associations from the very limited amount of data available.
Collapse
Affiliation(s)
- Fredrik Svensson
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Azedine Zoufir
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Samar Mahmoud
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Avid M Afzal
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Ines Smit
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Kathryn A Giblin
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Peter J Clements
- GlaxoSmithKline R&D Ltd , Park Road , Ware, Hertfordshire SG12 0DP , United Kingdom
| | - Jerome T Mettetal
- Drug Safety and Metabolism , AstraZeneca , 35 Gatehouse Drive , Waltham , Massachusetts 02451 , United States
| | - Amy Pointon
- Safety and ADME Translational Sciences , AstraZeneca , Cambridge Science Park, Milton Road , Cambridge CB4 0WG , United Kingdom
| | - James S Harvey
- GlaxoSmithKline R&D Ltd , Park Road , Ware, Hertfordshire SG12 0DP , United Kingdom
| | - Nigel Greene
- Predictive Compound Safety and ADME , AstraZeneca , 35 Gatehouse Drive , Waltham , Massachusetts 02451 , United States
| | - Richard V Williams
- Lhasa Limited , Granary Wharf House, 2 Canal Wharf , Leeds LS11 5PS , United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| |
Collapse
|
35
|
Abdul KU, Houweling M, Svensson F, Narayan RS, Cornelissen FMG, Küçükosmanoglu A, Metzakopian E, Watts C, Bailey D, Wurdinger T, Westerman BA. WINDOW consortium: A path towards increased therapy efficacy against glioblastoma. Drug Resist Updat 2018; 40:17-24. [PMID: 30439622 DOI: 10.1016/j.drup.2018.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/19/2018] [Accepted: 10/27/2018] [Indexed: 02/04/2023]
Abstract
Glioblastoma is the most common and malignant form of brain cancer, for which the standard treatment is maximal surgical resection, radiotherapy and chemotherapy. Despite these interventions, mean overall survival remains less than 15 months, during which extensive tumor infiltration throughout the brain occurs. The resulting metastasized cells in the brain are characterized by chemotherapy resistance and extensive intratumoral heterogeneity. An orthogonal approach attacking both intracellular resistance mechanisms as well as intercellular heterogeneity is necessary to halt tumor progression. For this reason, we established the WINDOW Consortium (Window for Improvement for Newly Diagnosed patients by Overcoming disease Worsening), in which we are establishing a strategy for rational selection and development of effective therapies against glioblastoma. Here, we overview the many challenges posed in treating glioblastoma, including selection of drug combinations that prevent therapy resistance, the need for drugs that have improved blood brain barrier penetration and strategies to counter heterogeneous cell populations within patients. Together, this forms the backbone of our strategy to attack glioblastoma.
Collapse
Affiliation(s)
- Kulsoom U Abdul
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, Netherlands
| | - Megan Houweling
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, Netherlands
| | - Fredrik Svensson
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cowley Road, Cambridge, CB4 0WS, United Kingdom
| | - Ravi S Narayan
- Department of Radiation Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, Netherlands
| | - Fleur M G Cornelissen
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, Netherlands
| | - Asli Küçükosmanoglu
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, Netherlands
| | | | - Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - David Bailey
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cowley Road, Cambridge, CB4 0WS, United Kingdom
| | - Tom Wurdinger
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, Netherlands
| | - Bart A Westerman
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, Netherlands.
| |
Collapse
|
36
|
Mervin LH, Bulusu KC, Kalash L, Afzal AM, Svensson F, Firth MA, Barrett I, Engkvist O, Bender A. Orthologue chemical space and its influence on target prediction. Bioinformatics 2018; 34:72-79. [PMID: 28961699 PMCID: PMC5870859 DOI: 10.1093/bioinformatics/btx525] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 08/25/2017] [Indexed: 01/05/2023] Open
Abstract
Motivation In silico approaches often fail to utilize bioactivity data available for orthologous targets due to insufficient evidence highlighting the benefit for such an approach. Deeper investigation into orthologue chemical space and its influence toward expanding compound and target coverage is necessary to improve the confidence in this practice. Results Here we present analysis of the orthologue chemical space in ChEMBL and PubChem and its impact on target prediction. We highlight the number of conflicting bioactivities between human and orthologues is low and annotations are overall compatible. Chemical space analysis shows orthologues are chemically dissimilar to human with high intra-group similarity, suggesting they could effectively extend the chemical space modelled. Based on these observations, we show the benefit of orthologue inclusion in terms of novel target coverage. We also benchmarked predictive models using a time-series split and also using bioactivities from Chemistry Connect and HTS data available at AstraZeneca, showing that orthologue bioactivity inclusion statistically improved performance. Availability and implementation Orthologue-based bioactivity prediction and the compound training set are available at www.github.com/lhm30/PIDGINv2. Contact ab454@cam.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Lewis H Mervin
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Krishna C Bulusu
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
- Oncology Innovative Medicines and Early Development, AstraZeneca, Cambridge, UK
| | - Leen Kalash
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Avid M Afzal
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Fredrik Svensson
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Mike A Firth
- Discovery Sciences, AstraZeneca R&D, Cambridge Science Park, Cambridge, UK
| | - Ian Barrett
- Discovery Sciences, AstraZeneca R&D, Cambridge Science Park, Cambridge, UK
| | - Ola Engkvist
- Discovery Sciences, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
- To whom correspondence should be addressed.
| |
Collapse
|
37
|
Affiliation(s)
- Matthew Harris
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Fredrik Svensson
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cambridge CB4 0WS, UK
| | - Liliya Kopanitsa
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cambridge CB4 0WS, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - David Bailey
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cambridge CB4 0WS, UK
| |
Collapse
|
38
|
Svensson F, Aniceto N, Norinder U, Cortes-Ciriano I, Spjuth O, Carlsson L, Bender A. Conformal Regression for Quantitative Structure–Activity Relationship Modeling—Quantifying Prediction Uncertainty. J Chem Inf Model 2018; 58:1132-1140. [DOI: 10.1021/acs.jcim.8b00054] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Fredrik Svensson
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- IOTA Pharmaceuticals, St Johns Innovation Centre, Cowley Road, Cambridge CB4 0WS, U.K
| | - Natalia Aniceto
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Ulf Norinder
- Swetox, Unit of Toxicology Sciences, Karolinska Institutet, Forskargatan 20, SE-151 36 Södertälje, Sweden
- Department of Computer and Systems Sciences, Stockholm University, Box 7003, SE-164 07 Kista, Sweden
| | - Isidro Cortes-Ciriano
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-75124, Uppsala Sweden
| | - Lars Carlsson
- Quantitative Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, SE-43183, Mölndal, Sweden
- Department of Computer Science, Royal Holloway, University of London, Egham Hill, Surrey, U.K
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| |
Collapse
|
39
|
Affiliation(s)
- Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
- Department of Chemistry, Center for Molecular Informatics, Cambridge, UK
| | - Fredrik Svensson
- Department of Chemistry, Center for Molecular Informatics, Cambridge, UK
- IOTA Pharmaceuticals, St John’s Innovation Centre, Cambridge, UK
| | - Azedine Zoufir
- Department of Chemistry, Center for Molecular Informatics, Cambridge, UK
| | - Andreas Bender
- Department of Chemistry, Center for Molecular Informatics, Cambridge, UK
| |
Collapse
|
40
|
Abstract
Iterative screening has emerged as a promising approach to increase the efficiency of screening campaigns compared to traditional high throughput approaches. By learning from a subset of the compound library, inferences on what compounds to screen next can be made by predictive models, resulting in more efficient screening. One way to evaluate screening is to consider the cost of screening compared to the gain associated with finding an active compound. In this work, we introduce a conformal predictor coupled with a gain-cost function with the aim to maximise gain in iterative screening. Using this setup we were able to show that by evaluating the predictions on the training data, very accurate predictions on what settings will produce the highest gain on the test data can be made. We evaluate the approach on 12 bioactivity datasets from PubChem training the models using 20% of the data. Depending on the settings of the gain-cost function, the settings generating the maximum gain were accurately identified in 8-10 out of the 12 datasets. Broadly, our approach can predict what strategy generates the highest gain based on the results of the cost-gain evaluation: to screen the compounds predicted to be active, to screen all the remaining data, or not to screen any additional compounds. When the algorithm indicates that the predicted active compounds should be screened, our approach also indicates what confidence level to apply in order to maximize gain. Hence, our approach facilitates decision-making and allocation of the resources where they deliver the most value by indicating in advance the likely outcome of a screening campaign.
Collapse
Affiliation(s)
- Fredrik Svensson
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- IOTA Pharmaceuticals, St Johns Innovation Centre, Cowley Road, Cambridge, CB4 0WS UK
| | - Avid M. Afzal
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Ulf Norinder
- Unit of Toxicology Sciences, Karolinska Institutet, Swetox, Forskargatan 20, 151 36 Södertälje, Sweden
- Department of Computer and Systems Sciences, Stockholm University, Box 7003, 164 07 Kista, Sweden
| | - Andreas Bender
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| |
Collapse
|
41
|
Kalash L, Val C, Azuaje J, Loza MI, Svensson F, Zoufir A, Mervin L, Ladds G, Brea J, Glen R, Sotelo E, Bender A. Computer-aided design of multi-target ligands at A 1R, A 2AR and PDE10A, key proteins in neurodegenerative diseases. J Cheminform 2017; 9:67. [PMID: 29290010 PMCID: PMC5748027 DOI: 10.1186/s13321-017-0249-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/01/2017] [Indexed: 01/30/2023] Open
Abstract
Compounds designed to display polypharmacology may have utility in treating complex diseases, where activity at multiple targets is required to produce a clinical effect. In particular, suitable compounds may be useful in treating neurodegenerative diseases by promoting neuronal survival in a synergistic manner via their multi-target activity at the adenosine A1 and A2A receptors (A1R and A2AR) and phosphodiesterase 10A (PDE10A), which modulate intracellular cAMP levels. Hence, in this work we describe a computational method for the design of synthetically feasible ligands that bind to A1 and A2A receptors and inhibit phosphodiesterase 10A (PDE10A), involving a retrosynthetic approach employing in silico target prediction and docking, which may be generally applicable to multi-target compound design at several target classes. This approach has identified 2-aminopyridine-3-carbonitriles as the first multi-target ligands at A1R, A2AR and PDE10A, by showing agreement between the ligand and structure based predictions at these targets. The series were synthesized via an efficient one-pot scheme and validated pharmacologically as A1R/A2AR-PDE10A ligands, with IC50 values of 2.4-10.0 μM at PDE10A and Ki values of 34-294 nM at A1R and/or A2AR. Furthermore, selectivity profiling of the synthesized 2-amino-pyridin-3-carbonitriles against other subtypes of both protein families showed that the multi-target ligand 8 exhibited a minimum of twofold selectivity over all tested off-targets. In addition, both compounds 8 and 16 exhibited the desired multi-target profile, which could be considered for further functional efficacy assessment, analog modification for the improvement of selectivity towards A1R, A2AR and PDE10A collectively, and evaluation of their potential synergy in modulating cAMP levels.
Collapse
Affiliation(s)
- Leen Kalash
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
| | - Cristina Val
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jhonny Azuaje
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María I. Loza
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Fredrik Svensson
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cowley Road, Cambridge, CB40WS UK
| | - Azedine Zoufir
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
| | - Lewis Mervin
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- Discovery Sciences, AstraZeneca R&D, Cambridge Science Park, Cambridge, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB21QJ UK
| | - José Brea
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Robert Glen
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Eddy Sotelo
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Andreas Bender
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
| |
Collapse
|
42
|
Affiliation(s)
- Fredrik Svensson
- IOTA Pharmaceuticals, St Johns
Innovation Centre, Cowley Road, Cambridge CB4 0WS, U.K
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Andreas Bender
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David Bailey
- IOTA Pharmaceuticals, St Johns
Innovation Centre, Cowley Road, Cambridge CB4 0WS, U.K
| |
Collapse
|
43
|
Svensson F, Norinder U, Bender A. Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. J Chem Inf Model 2017; 57:439-444. [DOI: 10.1021/acs.jcim.6b00532] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fredrik Svensson
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ulf Norinder
- Swetox,
Karolinska Institutet, Unit of Toxicology Sciences, Forskargatan
20, SE-151 36 Södertälje, Sweden
- Department
of Computer and Systems Sciences, Stockholm University, Box 7003, SE-164
07 Kista, Sweden
| | - Andreas Bender
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
44
|
Svensson F, Norinder U, Bender A. Modelling compound cytotoxicity using conformal prediction and PubChem HTS data. Toxicol Res (Camb) 2017; 6:73-80. [PMID: 30090478 PMCID: PMC6061930 DOI: 10.1039/c6tx00252h] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/28/2016] [Indexed: 12/28/2022] Open
Abstract
The assessment of compound cytotoxicity is an important part of the drug discovery process. Accurate predictions of cytotoxicity have the potential to expedite decision making and save considerable time and effort. In this work we apply class conditional conformal prediction to model the cytotoxicity of compounds based on 16 high throughput cytotoxicity assays from PubChem. The data span 16 cell lines and comprise more than 440 000 unique compounds. The data sets are heavily imbalanced with only 0.8% of the tested compounds being cytotoxic. We trained one classification model for each cell line and validated the performance with respect to validity and accuracy. The generated models deliver high quality predictions for both toxic and non-toxic compounds despite the imbalance between the two classes. On external data collected from the same assay provider as one of the investigated cell lines the model had a sensitivity of 74% and a specificity of 65% at the 80% confidence level among the compounds assigned to a single class. Compared to previous approaches for large scale cytotoxicity modelling, this represents a balanced performance in the prediction of the toxic and non-toxic classes. The conformal prediction framework also allows the modeller to control the error frequency of the predictions, allowing predictions of cytotoxicity outcomes with confidence.
Collapse
Affiliation(s)
- Fredrik Svensson
- Centre for Molecular Informatics , Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Ulf Norinder
- Swedish Toxicology Sciences Research Center , SE-151 36 Södertälje , Sweden
- Dept. Computer and Systems Sciences , Stockholm Univ. , Box 7003 , SE-164 07 Kista , Sweden
| | - Andreas Bender
- Centre for Molecular Informatics , Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| |
Collapse
|
45
|
Kihlgren A, Svensson F, Lövbrand C, Gifford M, Adolfsson A. A Decision support system (DSS) for municipal nurses encountering health deterioration among older people. BMC Nurs 2016; 15:63. [PMID: 27833455 PMCID: PMC5101660 DOI: 10.1186/s12912-016-0184-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/28/2016] [Indexed: 11/22/2022] Open
Abstract
Background This study is part of a larger project called ViSam and includes testing of a decision support system developed and adapted for older people on the basis of M (R) ETTS (Rapid Emergency Triage and Treatment System). The system is designed to allow municipal nurses to determine the optimal level of care for older people whose health has deteriorated. This new system will allow more structured assessment, the patient should receive optimal care and improved data transmission to the next caregiver. Methods This study has an explanatory approach, commencing with quantitative data collection phase followed by qualitative data arising from focus group discussions over the RNs professional experience using the Decision Support system. Focus group discussions were performed to complement the quantitative data to get a more holistic view of the decision support system. Results Using elements of the decision support system (vital parameters for saturation, pain and affected general health) together with the nurses' decision showed that 94 % of the older persons referred to hospital were ultimately hospitalized. Nurses felt that they worked more systematically, communicated more effectively with others and felt more professional when using the decision support system. Conclusions The results of this study showed that, with the help of a decision support system, the correct patients are sent to the Emergency Department from municipal home care. Unnecessary referrals of older patients that might lead to poorer health, decreased well-being and confusion can thus be avoided. Using the decision support system means that healthcare co-workers (nurses, ambulance/emergency department/district doctor/SOS alarm) begin to communicate more optimally. There is increased understanding leading to the risk of misinterpretation being reduced and the relationship between healthcare co-workers is improved. However, the decision support system requires more extensive testing in order to enhance the evidence base relating to the vital parameters among older people and the use of the decision support system.
Collapse
Affiliation(s)
- Annica Kihlgren
- Faculty of Medicine and Health, School of Health Örebro University, SE-701 82 Örebro, Sweden
| | | | - Conny Lövbrand
- Ambulance Department, Örebro University Hospital, Örebro, Sweden ; Faculty of Medicine and Health, School of Health Örebro University, SE-701 82 Örebro, Sweden
| | - Mervyn Gifford
- Faculty of Medicine and Health, School of Health Örebro University, SE-701 82 Örebro, Sweden
| | - Annsofie Adolfsson
- Faculty of Medicine and Health, School of Health Örebro University, SE-701 82 Örebro, Sweden ; The Centre of Women's Health, Faculty of Health Science, Buskerud Vestfold University College, Kongsberg, Norway
| |
Collapse
|
46
|
Palmiero G, Imbalzano E, Van Zalen JJ, Svensson F, Lagerstrand KM, Hamdanchi A, Kim KJ, Ascione L, Carlomagno G, Sordelli C, Ferro A, Ascione R, Severino S, Caso P, Vatrano M, Mandraffino G, Dalbeni A, Carerj S, D'angelo M, Ceravolo R, Ciconte VA, Saitta A, Zito C, Badiani S, Ewer J, Patel NR, Lloyd GW, Bech-Hanssen O, Polte CL, Johnsson ÅA, Lagerstrand KM, Svensson F, Polte CL, Johnsson ÅA, Gao SA, Bech-Hanssen O, Asadi Y, Otto S, Hoyme M, Jung C, Lauten A, Doenst T, Figulla HR, Poerner TC, Goebel B, Park JB, Kim HK, Yoon YE, Lee SP, Kim YJ, Cho GY, Sohn DW, Kim KH, Ahn H. Rapid Fire Abstract session: novelties in valves regurgitation831Significant functional mitral regurgitation impairs left atrial function in patients with heart failure due to left ventricular systolic dysfunction832Arterial stiffness and mitral regurgitation: an intriguing pathophysiological link833Progression rate of mild and moderate aortic regurgitation in a physiologist led valve clinic834The blood flow complexity affect the reliability of aortic regurgitation assessment by phase-contrast magnetic resonance imaging835Two-dimensional phase-contrast magnetic resonance imaging can describe the complexity of flow in ascending aorta in patients with aortic regurgitation836A cross-sectional study of endocardial lead-related tricuspid regurgitation: towards proposing a new practical 2D/3D echocardiographic approach for better risk stratification837Prognostic value of cardiac magnetic resonance for preoperative assessment of patients with severe functional tricuspid regurgitation. Eur Heart J Cardiovasc Imaging 2015. [DOI: 10.1093/ehjci/jev267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
47
|
Svensson F, Engen K, Lundbäck T, Larhed M, Sköld C. Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates. J Chem Inf Model 2015; 55:1984-93. [DOI: 10.1021/acs.jcim.5b00359] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Fredrik Svensson
- Organic
Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University, P.O.
Box 574, SE-751 23 Uppsala, Sweden
| | - Karin Engen
- Organic
Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University, P.O.
Box 574, SE-751 23 Uppsala, Sweden
| | - Thomas Lundbäck
- Chemical
Biology Consortium Sweden, Science for Life Laboratory, Division of
Translational Medicine and Chemical Biology, Department of Medical
Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen
23A, SE-171 65 Solna, Sweden
| | - Mats Larhed
- Science
for Life Laboratory, Department of Medicinal Chemistry, BMC, Uppsala University, P.O.
Box 574, SE-751 23 Uppsala, Sweden
| | - Christian Sköld
- Organic
Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University, P.O.
Box 574, SE-751 23 Uppsala, Sweden
| |
Collapse
|
48
|
Lindh M, Svensson F, Schaal W, Zhang J, Sköld C, Brandt P, Karlén A. Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data. J Chem Inf Model 2015; 55:343-53. [DOI: 10.1021/ci5005465] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Martin Lindh
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Fredrik Svensson
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Wesley Schaal
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Jin Zhang
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Christian Sköld
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Peter Brandt
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Anders Karlén
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| |
Collapse
|
49
|
Belfrage AK, Gising J, Svensson F, Åkerblom E, Sköld C, Sandström A. Efficient and Selective Palladium-Catalysed C-3 Urea Couplings to 3,5-Dichloro-2(1H)-pyrazinones. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
50
|
Borhade SR, Rosenström U, Sävmarker J, Lundbäck T, Jenmalm-Jensen A, Sigmundsson K, Axelsson H, Svensson F, Konda V, Sköld C, Larhed M, Hallberg M. Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Arylsulfonamides. ChemistryOpen 2014; 3:256-63. [PMID: 25558444 PMCID: PMC4280825 DOI: 10.1002/open.201402027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Indexed: 01/07/2023] Open
Abstract
The inhibition of insulin-regulated aminopeptidase (IRAP, EC 3.4.11.3) by angiotenesin IV is known to improve memory and learning in rats. Screening 10 500 low-molecular-weight compounds in an enzyme inhibition assay with IRAP from Chinese Hamster Ovary (CHO) cells provided an arylsulfonamide (N-(3-(1H-tetrazol-5-yl)phenyl)-4-bromo-5-chlorothiophene-2-sulfonamide), comprising a tetrazole in the meta position of the aromatic ring, as a hit. Analogues of this hit were synthesized, and their inhibitory capacities were determined. A small structure–activity relationship study revealed that the sulfonamide function and the tetrazole ring are crucial for IRAP inhibition. The inhibitors exhibited a moderate inhibitory potency with an IC50=1.1±0.5 μm for the best inhibitor in the series. Further optimization of this new class of IRAP inhibitors is required to make them attractive as research tools and as potential cognitive enhancers.
Collapse
Affiliation(s)
- Sanjay R Borhade
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University P.O. Box 574, 751 23 Uppsala (Sweden)
| | - Ulrika Rosenström
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University P.O. Box 574, 751 23 Uppsala (Sweden)
| | - Jonas Sävmarker
- Beijer Laboratory, Department of Medicinal Chemistry, BMC, Uppsala University P.O. Box 574, 751 23 Uppsala (Sweden)
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm 171 77 (Sweden)
| | - Annika Jenmalm-Jensen
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm 171 77 (Sweden)
| | - Kristmundur Sigmundsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm 171 77 (Sweden)
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm 171 77 (Sweden)
| | - Fredrik Svensson
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University P.O. Box 574, 751 23 Uppsala (Sweden)
| | - Vivek Konda
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University P.O. Box 574, 751 23 Uppsala (Sweden)
| | - Christian Sköld
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University P.O. Box 574, 751 23 Uppsala (Sweden)
| | - Mats Larhed
- Department of Medicinal Chemistry, Science for Life Laboratory, BMC, Uppsala University P.O. Box 574, 751 23 Uppsala (Sweden)
| | - Mathias Hallberg
- Beijer Laboratory, Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence, BMC, Uppsala University P.O. Box 591, 751 24 Uppsala (Sweden) E-mail:
| |
Collapse
|