Q&A: Pharmacophore modeling for potential drug discovery

Dr. Apurba K Bhattacharjee, Georgetown University

Q: What are the current approaches to screen for compounds that would fit into a given pharmacophore?
A: Pharmacophore based searching, structure similarity based searching, docking at the active site, dynamic docking and use of machine learning (AI) tools. 

Q: How to choose the 3D pharmacophore model software programs considering parameters either molecular filed or substitution pattern or a combination of both? 
A: There are various functions available in different software. You are to select them based on your specific needs. Discovery Studio (BIOVIA), COMFA (Comparative molecular field analysis (CoMFA) on the training set of active compounds has the predictive ability to test on additional compounds. There are a variety of them available commercially.

Q: How to do a 3D model when no active ligand(s) available for a known target?
A: Some experimental information of a ligand or target active site details should be available. You may hypothetically design a pharmacophore model based on complementary information from the active site of the known target. Use the hypothetical pharmacophore model as template for search of compound databases may enable you to find ligands for the target. You will even be able to identify a few compounds from the search and make a 3D model.

Q: How many compounds does one need for an effective “training set?”
A: If you use statistical methods like Catalyst (Discovery Studio) methods, you should ideally require at least 15 compounds in the training set. If you start with QM (quantum mechanical) approach to develop molecular electrostatic potential profiles, you can perform the task with lesser number known active compounds.

Q: Is it possible to provide complete molecular flexibility to the target protein?
A: Yes. Dynamic docking can be performed. You may also consider water molecules at the active site of the target.

Q: How to address a major limitation of Ligand-based pharmacophore dependence on pre-computed databases that contain a limited number of low-energy conformations per molecule?
A: Most of the procedures for generation of compound databases useful for pharmacophore based (not structure of ligand) search recommends multi-conformer generation of molecules within 0.0-20.0 kcal/mol. Catalyst, Discovery Studio (Biovia) etc already have procedures for such database generation. 

Q: In your examples you have illustrated the use of Pharmacophore in already known and validated receptors. In case if the receptors are not known or validated how does Bioinformactis/AI assist us to discover complete novel receptors and pharmacophore. 
A: Not really. Pharmacophore based procedures are most useful when the receptor structures are not known. Only a handful of active disease specific compounds (15-20) should be enough. Even less number of active compounds are also possible but will have to use QM methods for generation of molecular electrostatic potential (MEP) profiles. The MEP can be an useful guidance for pharmacophore generation even for small training set of active molecules. Approach for Bioinformatics/AI tools are useful only when you have large (really large) number active and inactive compounds in a database. 

Q: From the standpoint of pharmacophores, in your opinion, which is the least and the most favorable rule of the Linpinsky’s rules?
A: From Druglikeness point of view, Lipinsky’s rule is empirical. However, it is very useful when you have a short list of 5-10 lead compounds to promote, the rule is extremely helpful. 

Q: Specificity or Sensitivity? Which one will you prefer for pharmacophore modeling validation?
A: The goal will undoubtedly be specificity.

Q: For unknown target, what would be the average number of molecules needed to build a good pharmacophore model ? Which parameters (e.g. IC50) would be mandatory to build this model?
A: A training set of 15-20 (10 highly potent, 5 intermediately potent, and 5 inactive) molecules should be ideal training set. Any of the experimental data from IC-50, ED-50, LD-50 etc may be used to build a pharmacophore model. 

Q: Which software do you recommend for in silico ADMET property predictions?
A: I cannot recommend any single software. There are many good commercial software available now a days. Even free software are available for downloads. I have used TOPKAT from Discovery Studio many years ago.

Q: Can you please provide a list of general references about the methodology

  • O.A. Gunner. In Pharmacophore, perception, development, and use in drug design. Ed. University International Line (IUL Biotechnology Series), San Diego, pp. 17, 2000.
  • A.R. Leach, V.J. Gillet, R.A. Lewis, R. Taylor. Three-dimensional pharmacophore methods in drug discovery. J. Med. Chem., 53, 539, 2010.
  • A.K. Bhattacharjee, J. A. Geyer, C.L. Woodard, A.K. Kathcart, D.A. Nichols, S.T. Prigge, Z. Li, B.T. Mott, and N.C. Waters. A Three Dimensional In Silico Pharmacophore Model for Inhibition of Plasmodium Falciparum Cyclin Dependent Kinases and Discovery of Different Classes of Novel Pfmrk Specific Inhibitors. J. Med. Chem., 2004, 47, 5418-5426.
  • A.K. Bhattacharjee. In silico 3D pharmacophores for aiding discovery of the Pfmrk (Plasmodium Cyclin-dependent protein kinases) specific inhibitors for therapeutic treatment of malaria. Expert Opinion on Drug Discovery 2007, 2(8):1115-1127.
  • A. K. Bhattacharjee, K. Kuča, K. Musilek, R.K. Gordon. In Silico Pharmacophore Model for Tabun-inhibited Acetylcholinesterase (AChE) Reactivators: a Study of their Stereoelectronic Properties. Chem. Res. Toxicol. 2010, 23, 26-36.
  • A.K. Bhattacharjee, E. Marek, H.T. Le, R.K. Gordon. Discovery of non-oxime reactivators using an in silico pharmacophore model of oxime reactivators of OP-inhibited acetylcholinesterase. European J. Med. Chem, 2012, 49 229-238; 2015, 90, 209-220.

Q: How to find out trend/correlation between biological activity and physicochemical (ADME-Tox) properties of the molecules using 3D modeling?
A: Again you would require experimental data (or reliable in silico ADME-Tox) for a set of at least 15 compounds to create a training set to find out the correlation and trend .

Q: How do you anticipate/address active or potentially genotoxic metabolites?
A: You need to know the metabolites. In order to know the metabolites, you will have to have the knowledge of mechanism of action of the active compounds. Please remember when pharmacophores are generated, metabolites are not considered

Q: How often (percentage wise) does an in silico ‘hit’ translate to biological activity?
A: If iterative processes of refining the pharmacophore, search for databases and in vitro testing are carried out, the chance of a very reliable pharmacophore model could be achieved. 

Q: Given that good antitumor drugs are usually not having a good water solubility, one question here is that through this computer drug discovery technology, we may rule out some good candidates that have good antitumor activity for example but due to its poor water solubility (but this can be improved by formulation), such compounds may be ruled out without further consideration.
A: Yes, you are very correct. That is why a computational chemist should be always in consultation with a medicinal chemist before promoting a lead compound.

Q: Where this database come from?
A: There are many commercial compound databases, such as Maybridge, ChemNavigator, Zinc etc. I have used our own in-house database (WRAIR) of about three hundred thousand compounds.

Q: Can we use electrostatic surface potential predicted from QM method to study ligand-protein interactions? If yes how interpret the results?
A: Absolutely. Molecular electrostatic potential (MEP) profile is the interaction pharmacophore of a compound. You can even calculate MEP in water or other solvents using the dielectric values of solvents.

Q: How people get exposure to Nerve agents these days?
A: Mostly from pesticides and certain kind of insect repellents commonly used crop protections.

Q: Are there any studies on how often in silico screening finds real hits? I have seen a few examples where it worked, but I have seen many more that haven’t. Gives hits that are not active when tested?
A: You see experimental testing is absolutely necessary. Many cases are there in literature where it failed. However, iterative refining of models with testing usually produce good results. Remember in silico approach is another tool only like x-ray crystallography, nmr, spectroscopy etc. 

Q: If a compound has a clogP of 6 or 7, but satisfies all other criteria, should it be excluded right away?
A: It should be tried for in vitro testing before discarding it. Lipinsky’s rule is an empirical rule only not hundred percent guaranteed.

 

David Preston
David Preston

Chairman

David Preston has had 38 years of healthcare experience with publicly – Traded and Private companies in the fields of Pharmaceutical’s, Animal Health and Biotechnology as a Board Member. The last 30 years of his experience has been in China, Taiwan and Hong Kong building successful high growth businesses. David Has been Chairman and CEO for Greater China for Sanofi and Boehringer – Ingelheim as well as the Janssen Corporation since 1991 in China. During this time he build high Growth businesses in China through diversified strategies in Innovative Pharmaceuticals, branded Generics, Biotechnology, and Animal Healthcare.


Key highlights in this period included building of the first Western Multinational Biotechnology C.M.O. facility as well as obtaining the first Test C.M.O.[ MAH] license. Establishment of a number of High tech Vaccine Plants, and R and D facilities in in the field of Animal Health. Signing and development of numerous JV’s as well as Wholly owned  Subsidiaries, Mergers and Acquisitions across Pharmaceutical’s, Animal Health, and Biotechnology industries.

 

David’s achievement’s in the Healthcare industry and it Growth and development in China is widely recognized By the Chinese Government and the City of Shanghai. In 2013 he was awarded the Silver Magnolia followed in 2015 the Gold Magnolia award. This was then followed by being awarded in 2017 the Honorary Citizen of Shanghai by 40th People’s Municipal Congress of Shanghai. David Holds a Business Science Degree .

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Filippo
Filippo de Vecchi

Director, Advent Partner

Filippo de Vecchi joined Advent in February 2000. He started in the Advent São Paulo office, then moved to Milan in 2002, in 2012 set up the Advent office in Shanghai and in 2016 set up the Hong Kong office. Before joining Advent, he was a senior consultant with Value Partners, in São Paulo and Milan, focusing on strategy and organization in the automotive, energy, cable and media sectors. He began his career at Wasserstein Perella & Co., working as an analyst in the Mergers and Acquisitions department in London and New York. Filippo holds an undergraduate degree cum laude in Economics, with a major in Business Administration, from the LUISS University and an MBA from Columbia Business School, where he currently serves as a member of the Board of Overseers.

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Andrew Li
Andrew Li

Director, Advent Partner

Andrew Li joined Advent in 2012. He previously worked at Warburg Pincus, HSBC PE, Solera Capital and Credit Suisse where he focused on the retail and consumer, healthcare, industrial, and energy sectors. Andrew has worked in finance and private equity throughout the U.S. and China since 1999. Andrew holds a BA from Middlebury College and an MBA from Harvard Business School.

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Michael Miltenberger
Michael Miltenberger

Director, Advent Partner

Michael Miltenberger joined Advent in 2011 as an associate on the healthcare team. Following business school, he rejoined Advent’s Boston office, focusing on healthcare investments. Prior to Advent, Michael was a consultant at McKinsey & Company in their Washington DC office, serving a range of healthcare and private equity clients. Michael earned a BA, cum laude, from Harvard College and an MBA from Harvard Business School, graduating with High Distinction as a Baker Scholar and a Harvey Fellow.

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Masood
Masood Tayebi, PhD

Director, Operating Partner

Dr. Masood Tayebi is the Founder of BioDuro. He currently serves as CEO of a nationwide real estate portfolio and is a Partner and Chief Executive Officer of the Bridgewest Group. Prior to BioDuro, Dr. Tayebi was Co-Founder and Chairman of Wireless Facilities, Inc. (NASDAQ: WFI), a global leader in telecommunications outsourcing.

Achievements
  • Co-Founder of Wireless Facilities, Inc.
  • Co-Founder of BioAtla, LLC
  • Recipient of the Ernst and Young 2000 Entrepreneur of the Year award in San Diego

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Kewen Jin
Kewen Jin, PhD

Director, Operating Partner

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Amit patel
Amit Patel

Director, Operating Partner

Amit Patel has twenty years of healthcare industry experience with publicly-traded, private equity-backed, and start-up companies in the capacity of executive, board member, advisor, and investor.  He is currently Executive Chairman of Azurity Pharmaceuticals (a NovaQuest Capital Management portfolio company) and a board member at BioDuro (Advent International portfolio company), Tergus Pharma (Great Point Partners portfolio company) and Calyptus Pharma.  Recently, Amit was SVP & President of Dosage Form Solutions at Capsugel, a KKR portfolio company (purchased from Pfizer in 2011 and sold to Lonza in 2017).


Prior to Capsugel, he worked at Dr. Reddy’s Laboratories, Inc. as EVP & Head of North America, and SVP & Head of Global Corporate Development & Strategic Planning. Earlier, Amit was VP of Corporate Development at CTIS, Inc., and Co-founder & CEO of MedOnTime, Inc. (acquired by CTIS).  He started his career as a strategy consultant with Marakon Associates. Amit holds an M.B.A. degree from Harvard Business School, a B.S. degree in Economics from the Wharton School of Business, University of Pennsylvania, and a B.A.S. degree in Systems Engineering from the Moore School of Engineering, University of Pennsylvania

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Haijun photo - 2.4.21 black and white
Haijun Dong

Chief Executive Officer

Dr. Haijun Dong currently serves as global CEO of BioDuro-Sundia. He previously was CEO for over 5 years at PharmaBlock Sciences Inc., a public company listed in the Shenzhen Stock Exchange (300725.SZ). The positions he held prior to PharmaBlock includes, among others, Senior Scientist at Boehringer Ingelheim Pharmaceuticals in Ridgefield, Connecticut; Senior Principal Scientist at Roche in Nutley, New Jersey; Head of DMPK and Drug Safety at Roche China R&D Company in Shanghai; Chief Operating Officer of Eli Lilly China R&D Center in Shanghai.

Dr. Dong received his PhD in organic chemistry from the University of Washington in Seattle, Washington, and MBA from China Europe International Business School in Shanghai. 

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Jeffery
Jeffery Blazevich

Chief Financial Officer

Jeff brings over 30 years of professional experience working for publicly traded, venture-backed, and private equity companies in the technology, health care and medical device industries. Prior to joining BioDuro, Jeff was the CFO for Zest Dental Solutions, a private-equity-owned manufacturer of a diverse portfolio of dental products.  From 2008 to 2013, he served as Senior Vice President and Corporate Controller for DJO Global, formerly a Blackstone-owned manufacturer of orthopedic products.

Jeff is a Certified Public Accountant and started his career at Ernst & Young LLP after receiving his bachelor’s degree in Accounting from the University of San Diego.

Achievements

 

  • Jeff held CFO positions at Vativ Technologies Inc. Staccato Communications, and Applied Micro Circuits Corporation, a publicly listed semiconductor company.

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TJ
TJ Deng, PhD

President, Discovery

Dr TJ Deng joined BioDuro in the initial stages of the company and helped BioDuro grow to an industry leading discovery services organization. He established and managed several scientific departments, including DMPK, before transitioning to a leader of the business and operations functions. Prior to joining BioDuro, Dr. Deng spent six years at PPD, in positions with increasing responsibilities from scientist to scientific manager.

Achievements

 

 

  • Developed the extractable/leachable capabilities at PPD
  • 18 years industry experience

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Kent
Kent M. Payne, PhD

President, Global CMC Solutions

Kent is distinguished as a business operator and leader in areas of sales, commercial manufacturing and product development. He has extensive executive experience in M&A as well as successfully running, start up, growth and turn around businesses. This includes both Fortune 500 and Private Equity environments. He combines strong business leadership, successful P&L track record, and technical background to strategically lead and grow enterprise value across Biotechnology and Pharmaceutical market segments. He has successfully led the geographic expansion of businesses into Europe, Asia, South America in addition to the United States.

He also currently serves as a board member for Goodwin Biotechnologies (a biological contract manufacturer), and board advisor for Vitruvias Therapeutics (a specialty generic pharmaceutical business)

Achievements

  • CEO Socorro Pharmaceuticals, a generic pharmaceutical company
  • President Americas, Qualicaps Inc.
  • Principal Consultant and Partner at CoreFactor LLC, providing executive strategic, licensing and operational advisory services to clients.
  • Vice President/General Manager Catalent Pharma Solutions, Inc. (a Blackstone Group company formed in 2007, formerly part of Cardinal Health)
  • Progressive leadership responsibility at: Novartis, Monsanto and G.D. Searle.
    Prior Board Positions:
  • Board Advisor, Corporate Strategy Office, Life Science Institute Inc. (a wholly-owned subsidiary of Mitsubishi Chemical Holdings.
  • Board member for Technophar, Inc.; Qualicaps, Inc.
  • Non-executive Chair and Board Member PDS Biotechnology (PDS

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Tommy
Tommy Broudy, PhD

Executive Vice President, Marketing

Tommy Broudy joined BioDuro as Executive Vice President, Translational Sciences in 2018 following the acquisition of Molecular Response, a patient-derived tumor modeling company he cofounded in 2010. Tommy is now leading BioDuro’s translational oncology group, with focus on in vivo and in vitro oncology testing services that help more efficiently translate novel anti-cancer medicines into the clinic. Tommy previously served as General Manager of Crown Bioscience San Diego, where he led the US preclinical operation. Prior to that, Tommy served as Director at AltheaDx, working closely with the Business Development and R&D teams to establish gene expression-based companion diagnostics for oncology therapeutics. He also spent six years at Affymetrix, where he managed the company’s pharmacogenomic and toxicogenomic solutions in support of pharmaceutical R&D.

Achievements

 

  • Earned his PhD at Rockefeller University in the Laboratory of Bacterial Pathogenesis and Immunology
  • Held postdoctoral appointments at Rockefeller and Stanford University studying host/microbial genomics

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Roy
Roy Xu

Chief Strategy Officer

Roy has over 25 years of healthcare industry experience.  He started his career as an orthopedic surgeon.  Roy joined Eli Lilly as a sales rep in 1997.  Since then he has had various roles in market research, business intelligence, BU head, strategy, regional general management, business development etc., both at Eli Lilly and Boehringer Ingelheim (BI).  Roy also spent more than two years in Germany where he was BI’s Director of Corporate Business and Enabling Strategy.

Roy obtained a bachelor’s degree in Clinical Medicine at Zhejiang Traditional Chinese Medicine University, and an MBA from Zhejiang University.

Achievements

 

  • 25 years of healthcare industry experience including Eli Lily and Boehringer Ingelheim. 
  • Former Director of Corporate Business & Enabling Strategy at oehringer Ingelheim in Germany.

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San Diego/圣地亚哥

BioDuro- San Diego Facility

Our San Diego site is our corporate headquarters. The facility is home to BioDuro’s drug product development technologies and has 9 GMP clean rooms. Development and manufacturing operations are conducted for projects up to Phase III clinical trials.

Size: 44,000 sq. ft.
Featured capabilites: Tableting, Coating, Hot Melt Extrusion, Spray Dried Dispersion

11011 Torreyana Rd.
San Diego
CA 92121
United States

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Beijing/北京

BioDuro Beijing
Operating since 2006, our Beijing site is home to BioDuro’s first wet chemistry operations. With 300 regular fume hoods and 18 scale-up chemistry hoods the Beijing facility houses most of BioDuro’s chemistry operations, while also hosting labs for biology and monoclonal antibody discovery.

Size: 100,000 sq. ft. 
Featured capabilities: Radioactivity Lab, Monoclonal Antibody Discovery, Medicinal Chemistry

No. 29 Life Science Park Road
Changping District Beijing,
102206
P.R. China

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Shanghai-Waigaoqiao/上海-外高桥

BioDuro- Shanghai Facility

Established in 2012, BioDuro’s Shanghai facility has been growing with its departments. The cutting edge facility contains labs for ADME, bioanalysis, in vitro assays and translational research. The site includes a 18,000 sq. ft vivarium and 20,000 sq. ft of office space.

Size: 92,000 sq. ft.
Featured capabilities: Scale-up Chemistry, Discovery Biology, DMPK, In Vivo Pharmacology

No. 233 North Fu Te Road
Waigaoqiao Free Trade Zone
Shanghai, 200131
P.R. China

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Cathy
Cathy Yen

Director, Operating Partner

Cathy joined the Board of Directors of BioDuro-Sundia in 2020, with the Advent-led acquisition of Sundia and creation of BioDuro-Sundia. Prior to that, she was Chairman of the Board at Sundia Meditech Group, where she was the key architect of Sundia’s strategic vision and growth. Under her leadership, Sundia solidified its position as one of the leading pre-clinical CROs in China.

Prior to Sundia, Cathy had a distinguished career as a seasoned venture capitalist, having led numerous investments in high-growth companies in Asia. Cathy served as a Partner of AsiaVest Partners, TCW/YFY Ltd., a global venture capital firm, for over a decade, Vice President at Global Financial Services, Vice President at Crimson Ventures/Chinatrust Bank and Senior Manager at Fortune Capital. She brings over 20 years of experience in corporate finance, accounting, strategic planning and private equity investments.

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Wuxi/无锡

Wuxi - BioDuro

Established in 2019, BioDuro-Sundia’s fully integrated discovery facility located at the heart of Jiangsu Wuxi Life Science & Technology Industrial Park with plans of growing staff to 1000+ scientists

Size: 300,000 sq. ft.
Featured capabilities:
Discovery Chemistry & Biologics, Biology, DMPK, Pharmacology, CMC Services

no.1699,Huishan avenue

Huishan Economic 

Development Zone,Wuxi

P.R. China

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Hebei/河北

Hebei - Sundia
Established in 2011, this pilot plant this handles mg to kg scale up

Size: 45,208 sq. ft.

Featured capabilities: SFFS Chemistry: mg to kg scale up
(150 hood)

238 Changjiang Road

Shijiazhuang,

Hebei province
P.R. China

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Taiwan/台湾

Taiwan - Sundia (1)
Our site in Taiwan supports Discovery Biology and Chemistry

Size: 3,352sq.ft.
Featured capabilities: Chemistry;Biology

7F, No. 107, Sec. 4

Ren Ai Road,

Da-an District,

Taipei, Taiwan

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Bengbu/蚌埠

Bengbu - Sundia
Scheduled to open in fall of 2020, this site is designed to handle API manufacturing and additional expertise in intermediates, GMP starting material upto IND enabling sttudies

Size: 43,056 sq. ft.
Featured capabilities: Intermediates, GMP starting materials, API manufacturing

Mohekou Industrial Park,

Huaishang District, Bengbu, 

Anhui province
P.R. China

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Shanghai-Changli/上海-长利园区

Shanghai-changli - Sundia-min (1)
Our Shanghai-Changli site supports FTE cheimistry and advanced Discovery Chemistry processes.

Size: 71,844 sq. ft.
Featured capabilities: Chiral Analytical Lab, Analytical and Purification Lab, NMR Lab, Synthetic Lab, Parallel Synthesis Lab, Flash Chromatography Lab..(380 hoods)

法拉第路251号8号楼;

Building 8, 251 Faladi Road,

Zhangjiang Hi-Tech Park,

Shanghai,China
P.R. China

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Shanghai-Halei/上海哈雷园区

Shanghai-halei - Sundia
Opened recently in 2018, BioDuro-Sundia’s Shanghai-Halei contains facilities that supports both Discovery and CMC parts of the drug development & manufacturing process. Facilities include amorphous dispersion techniques like SDD & Discovery Biology.

Size: 31,043 sq. ft.

Featured capabilities: Formulation : Preformulation, Wet Granulation, Compression, Tablet Coating, Fluid Bed Room, Spray Dryer, Hot Melt Extrusion, Dry Granulation Biology: Kinase selectivity, Cellular Assay, Compound Screen, Immune oncology service

哈雷路917弄1号;

Building 1, 917 Halei Road,

Zhangjiang Hi-Tech Park,

Shanghai,China

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Shanghai-Kelun/上海-克伦

Shanghai-kelun - Sundia-min (1)
Established in 2008, our Shangahi-Kelun site is desgined to handle advanced process and analytical chemistry including process GMP and non-GMP kilo lab

Size: 98,503 sq. ft.

Featured capabilities: general chemistry; Process: GMP & non-GMP kilo lab, Process analytical, Column Purification , Flow Chemistry. Analytical: 22 HPLC/UPLC. 8 Stability Chambers . DMPK: animal PK, Bioanlysis Metabolite ID, In Vitro Studies, In- Life studies

Building 8, 388 Jialilue Road,
Zhangjiang Hi-Tech Park,

Shanghai China, 201203

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Jim-Li
Jim Li PhD

President, Global CMC Solutions (China)

Dr. Li has led a distinguished career in the pharmaceutical industry, having spent over 18 years at various companies including Henkel, Wyeth, Pfizer and Wuxi Apptec in the area of process research and medicinal chemistry. During his career, he was involved in numerous drug discovery programs such as COPD, asthma, Rheumatoid/osteoarthritis, and diabetes. Dr. Li has co-authored more than 60 research articles and patents.

Dr. Li received his Ph.D in Organic Chemistry from University of Central Lancashire UK followed by a Postdoctoral fellow at the University of Chicago with Dr. Philip Eaton.

Achievements

  • Earned his PhD at University of Central Lancashire UK 
  • Held postdoctoral appointments at University of Chicago with Dr Philip Eaton
  • Dr. Jim Li was chief executive officer of Sundia. In this role, Dr. Li was responsible for the oversight of all business divisions across the organization as well as formulating and driving key strategies for diversifying and growing the company. Dr. Li also leads the company’s executive committee, helping to drive Sundia’s overall global strategy.

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