MEDCHEM.fi

Institute of Biomedicine

University of Turku

We are an academic research group at the University of Turku, Finland. We aim to develop novel methods for computational drug discovery and utilize those methods in drug discovery, thus, Tiny Molecules and Big Discoveries.

What could be better than sitting by your computer all day and changing the world!


We focus on developing novel tools for efficient virtual screening and discovering small-molecule and macrocyclic ligands for selected target proteins. Our special interest is in the identification of first-in-class protein-protein interaction modulators. What does that mean, you ask? Scroll down to find out!


If you already scrolled down and still have no idea what we do here, look at our publications. If you are interested in what we are doing right now, look at our ongoing projects here! You can also find more details about our research topics here.

About Us

6/9/2024

Our Dynamic Duo for the summer has flown the nest—best of luck with those Master’s studies (we do not want to say goodbye, just “see you soon!”).


Their time here was a blast, filled with creative sparks and impressive research wins. Plus, thanks to them, our web pages got a makeover, and even Coolio became an Instagram sensation!


Now, if only publishing papers were as easy as becoming IG famous... Let's get to it!

News

12/8/2024

Paola’s 1st paper for her PhD was published! Congrats!

“Building shape-focused pharmacophore models for effective docking screening,” has been published online in the Journal of Cheminformatics! 🎉 You can read it here:

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00857-6


This study introduces a new computer-aided drug discovery method tested with molecular docking rescoring in mind. By focusing on shape similarity, we’ve developed a new pharmacophore modeling method that shows great promise.


Team: Paola, Olli and Pekka from UTU, and Jukka V Lehtonen from ÅAU.

24/9/2024

Aliaa’s first-author paper published! Congrats! Now, there is content for her Ph.D. thesis page titled “List of Original Publications.” Hopefully, we will see the next one very soon.

Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1" is published in Briefings in Bioinformatics (IF=6.8; JUFO=2) and is an open-access paper, available at the journal site:

https://academic.oup.com/bib/article/25/6/bbae458/7765456


Team: Aliaa, Olli and Pekka from medchem.fi, and Li-Li Li and Michael Courtney from Turku Bioscience.

19/12/2024

🎉 Exciting Funding News! 🎉

We are thrilled to announce that we've (MedChem.fi & UPlab) received a generous grant of 1.1 million Danish kroner to advance our synthesis project! 🧪✨ With this support, we're set to optimize our current hit molecules into lead compounds, pushing the boundaries of innovation and discovery. Stay tuned for more updates on our journey! 🚀

Team: Pankaj, Shelly, Tero, Kseniia, Olli, and UP-lab

14/2/2022

🎉 Exciting Funding News! 🎉

Aliaa received a two-year grant from the Finnish Cultural Foundation! Together with the DRDP graduate school funding, her funding is now secured to the end of the PhD! We could not be happier!

Olli Pentikäinen PhD, Head of MedChem.fi

Professor of Medicinal Chemistry (Institute of Biomedicine, UTu), group leader

Associate Professor (Docent) in Biochemistry (Department of Biochemistry, UTu)

CEO of Aurlide Ltd.

Pekka Postila PhD

Head of the Biophysical Unit, group leader

Associate Professor (Docent) in Cell and Molecular Biology (UJy)

Research Interests: Molecular Dynamics Simulation in Drug Discovery, Virtual Screening Technology

Pankaj Kumar Singh PhD

Head of the Synthesis Unit, group leader

Research interests: Medicinal Chemistry

Photo by Elisa Postila

@elisapostila

Tero Linnanen PhD

Senior Business Champion

Medicinal Chemistry

Kseniia Petrova-Szczasiuk MSc

Molecular Discovery, Commercialization

Senior Scientists

Santeri Puranen PhD

Consulting Scientist

Software Development

Mira Ahinko PhD

Senior Scientist

Software development

Shelly Pathania PhD

Senior Scientist

Medicinal Chemistry

Alumni (since 2024)

Veera Soininen BSc

Computer-aided drug discovery, webpage
design

Post-graduate students

Aliaa Ali MSc

Molecular Dynamics

Sakari Lätti MSc

Software Development

Paola Moyano-Gómez MSc

Molecular Discovery, Virtual Screening

Principal investigators

People

Yu Zhang MSc

Machine Learning, Molecular Discovery

Graduate students

Henna-Riikka Otranen BSc

Macrocycle Discovery

Sanna Niinivehmas PhD

Academy-Industry Partnership

Drug Discovery

Sami Kurkinen PhD

Senior Scientist

Drug Discovery

Roosa Saarimaa BSc

Molecular Discovery

Novo Nordisk Foundation 1.1MDKK 2025

“Novo Nordisk Foundation granted Professor Olli Pentikäinen and Docent Ulla Pentikäinen’s research groups 150 000 euros for optimizing our hit molecules towards leads compounds.”


Novo Nordisk Foundation is an independent Danish enterprise foundation that supports scientific, humanitarian, and social causes. They support a wide range of projects and initiatives that help to promote human health and the sustainability of the planet.


SynGAP Research Fund $130k 2025-2026

“The SynGAP Research Fund announced a $130,000 grant to Associate Professor Pekka Postil for Studying the Effects of Missense Variation on SynGAP1 Trimerization, etc. Using Molecular Modelling”


SynGAP Research Fund (SRF) is a global group of families committed to accelerating the science to cure SYNGAP1 & to supporting each other.


Business Finland 700kE 2024-2025

“Business Finland granted Professor Olli Pentikäinen and Docent Ulla Pentikäinen's research groups funding of 0.7 million euros for cancer drug development. The funding will accelerate the development of treatments for various types of cancer for which no treatment methods are yet known.”


Business Finland offers funding for research, product development, and many kinds of business development needs, especially for small and medium-sized companies. Large companies and research organizations can receive funding for joint projects with smaller companies.


Novo Nordisk Foundation 6MDKK 2022-2025

“We received a grant for developing a computer platform that can identify protein-protein interactions. Understanding these interactions is important to develop drugs against diseases that cannot currently be treated, such as several types of cancer or many diseases of the nervous system. Together with our colleagues, we are at the forefront of understanding how protein-protein interactions can become targets for drugs. Our approach may potentially revolutionize the entire field of developing novel drugs for diseases that are currently hard to combat.”


Novo Nordisk Foundation is an independent Danish enterprise foundation that supports scientific, humanitarian, and social causes. They support a wide range of projects and initiatives that help to promote human health and the sustainability of the planet.


SynGAP Research Fund $100k 2023-2024

The SynGAP Research Fund 501(c)(3) announced a $100,000 grant to researchers Pekka Postila and Olli Pentikäinen from the Institute of Biomedicine and InFLAMES Flagship at the University of Turku.” Read more here.


SynGAP Research Fund (SRF) is a global group of families committed to accelerating the science to cure SYNGAP1 & to supporting each other.

Funding

Research and Publications

Below, you will hear a little about our research.

You can read more from our publications.

Panther

The one and only Panther for NIB-screening


You know Elvis is not dead but sits back in his rocking chair, a.k.a. Rocker for AUCs etc


Keep your multiconformation data - and do many other things - with SDFCONF.


Use the (brute) Force... to Optimize your Panther-models (or similar)


OVERLAP at Github

Utility tool(s) for protein-ligand modeling

Software

One of our special interests is the rational discovery of protein-protein interaction (ppi) modulators. Indeed, it is considered to be, if not impossible, highly challenging. There are very few reported successes, where the first-in-class small molecule ppi modulators would had been identified via virtual screening, from which we were the very first ones - and now we have further successes, seven in total and increasing. Note that we have not only succeeded with blockers but also with identification of binding enhancers.


Our protein-protein interaction modulator discovery begun with collagen-binding integrins. The project started from protein modeling, went to ligand identification, optimization, and tool compound production. This was one of the key factors in our learning curve towards rationalization of the process (trial and error).

Protein-Protein Interaction Modulators

Macrocycle Discovery and Synthesis

Rational discovery of drug like or slightly beyond the Ro5 ligands to modulate selected drug discovery targets

How about finding a new type of ligands to treat diseases? Although we work a lot with the discovery of small molecules, the traditional small molecules are often too small or unspecific to become approved drugs, and the development and production of biologicals are too expensive. Then, the solution could be macrocycles. We develop macrocycles consisting of 3-5 amino acids cyclized with various strategies. Our discovery is guided by the target protein structures (and models of them) with an accurate prediction of pharmacokinetic properties - especially the cellular permeability.

We develop novel methods for the rational macrocycle discovery, and utilize these methods to identify novel type of function modulators for various drug discovery targets.


You can find more information from our current research projects (WEE1, KRAS, TNFa, EGFR, etc.).

Here is a look at our ONGOING PROJECTS.

Identifying Novel WEE1 Inhibitors

A wee1 bit of information: Project Introduction

The WEE1 kinase is a critical cell cycle regulator, playing a pivotal role in the G2 checkpoint to prevent cells with DNA damage from entering mitosis. Targeting WEE1 has emerged as a promising strategy in cancer therapy, as its inhibition can enhance the efficacy of DNA-damaging agents and induce synthetic lethality in tumors with specific genetic backgrounds. This project, which is at the forefront of innovation, seeks to identify and characterize novel WEE1 inhibitors that can be developed into potent therapeutic agents. Through high-throughput screening, computational modeling, and biochemical assays, we aim to discover compounds that effectively inhibit WEE1 activity. The successful identification and optimization of these novel inhibitors could revolutionize cancer treatment by providing new options for combination therapies and overcoming resistance to existing treatments.

This project is a collaborative project between MEDCHEM.fi, UP-lab, and Aurlide Ltd.

Cancer cell dies
due to DNA
damage

WEE1

G2 checkpoint

G1

S

G2

M

WEE1

G2 checkpoint

DNA-damage

Cell cycle arrest

G1

S

G2

M

DNA-damage

Cell cycle continues with DNA damage

With WEE1 inhibitor

Cancer cell continues to live

Normal

Project Introduction

Epidermal Growth Factor Receptor (EGFR) mutations are frequently implicated in various cancers, with specific mutations leading to resistance against first- and second-generation EGFR inhibitors. The triple-mutant EGFR, particularly the T790M/C797S/L858R mutations, poses a significant challenge due to its enhanced oncogenic potential and resistance to conventional therapies. This project aims to rationally design and develop macrocyclic compounds that can effectively inhibit this triple-mutant EGFR variant. Utilizing a combination of structure-based drug design, molecular dynamics simulations, and high-throughput screening, we seek to identify macrocyclic inhibitors that can overcome the steric and kinetic challenges presented by these mutations. Our goal is to produce highly selective and potent inhibitors, offering a new therapeutic avenue for patients with resistant EGFR-mutant cancers.


This project is a collaborative project between MEDCHEM.fi and UP-lab.

Rational Development of Macrocyclic
Compounds to Inhibit Triple-Mutant EGFR

EGFR mutations

1st and 2nd
generation
EGFR inhibitors

Cancer continues to
grow due to
resistance caused by
EGFR mutations

Cancer can be treated with
new therapies targeting
specific EGFR mutations

EGFR mutations

We develop small molecule modulators, targeted to two mutant forms of KRAS. If you are interested in collaborating with us, obtaining funding, and developing new treatments, contact us. Here is a reminder about the importance of these mutants...


Cancer drug discovery is a complex and dynamic field that involves the identification and development of drugs specifically designed to target and treat cancer. One of the crucial steps in this process is understanding the genetic alterations that drive cancer development and progression. Mutations in genes called oncogenes, such as KRAS, play a significant role in many types of cancer.


KRAS is one of the most frequently mutated oncogenes, and mutations in the KRAS gene are particularly common in several cancer types, including lung, pancreatic, and colorectal cancers. Two prevalent KRAS mutations are the KRAS G12V and G12D mutations. These mutations involve a single amino acid change (glycine to valine in G12V and glycine to aspartic acid in G12D) within the KRAS protein.


Targeting the KRAS G12V and G12D mutations is of great interest in cancer drug discovery for several reasons that are described next.


This project is a collaborative project between MEDCHEM.fi and UP-lab.

KRAS

Prevalence

KRAS mutations, including G12V and G12D, are found in a significant proportion of cancer patients, making them attractive targets for therapeutic interventions. The frequency of KRAS mutations underscores the potential impact of developing drugs that specifically inhibit these mutations.


Oncogenicity

The G12V and G12D mutations in KRAS are known to confer increased oncogenic potential, leading to uncontrolled cell growth, proliferation, and survival. Consequently, targeting these specific mutations could disrupt the signaling pathways that drive cancer development, leading to improved treatment outcomes.


Lack of effective therapies

Despite the importance of KRAS mutations in cancer, developing effective drugs that directly target KRAS has been challenging. Traditional approaches to targeting proteins with small molecules have not been successful in inhibiting KRAS mutations. However, recent advancements have shown promise in developing targeted therapies against KRAS G12V and G12D mutations, making it an active area of research.


Therapeutic opportunities

The identification of specific vulnerabilities associated with KRAS G12V and G12D mutations opens up new therapeutic opportunities. Scientists are exploring various strategies, such as inhibiting KRAS downstream effectors or exploiting synthetic lethal interactions, to develop drugs that can selectively target cancer cells harboring these mutations while sparing normal cells.


The development of targeted therapies against KRAS mutations, including G12V and G12D, is an ongoing area of research and holds great potential for improving cancer treatment outcomes. Scientists and pharmaceutical companies are investing significant efforts in unraveling the complex biology of KRAS mutations and designing innovative therapeutic approaches to address the challenges associated with targeting these mutations.

TNFα

We develop macrocycle modulators, targeted to the tumor necrosis factor alpha (TNFα). Macrocycles could present a promising avenue in drug discovery for targeting TNFα due to several advantageous properties:


  1. Enhanced Binding Specificity: Macrocycles offer a larger and more complex structure compared to traditional small molecules, allowing for increased specificity in binding to the target protein, such as TNFα. This specificity reduces the likelihood of off-target effects, potentially leading to safer and more effective treatments.
  2. Ability to Engage Challenging Binding Sites: TNFα often features challenging binding sites that are difficult to target with traditional small molecules due to their size and complexity. Macrocycles, with their larger size and flexible structure, can more readily engage with these challenging binding sites, potentially enabling more effective inhibition of TNFα activity.
  3. Improved Pharmacokinetic Properties: Macrocycles typically exhibit improved pharmacokinetic properties compared to small molecules, such as enhanced stability and longer half-lives. These properties can lead to improved drug efficacy and reduced dosing frequency, enhancing patient compliance and treatment outcomes.
  4. Potential for Oral Availability: While many biological drugs targeting TNFα require intravenous administration, macrocycles hold the potential for oral availability. This route of administration is generally preferred by patients and can improve treatment adherence and convenience.
  5. Cost-Efficient Discovery Methods: Despite the computational challenges associated with macrocycle discovery, advances in technology and computational methods have made the process more feasible and cost-efficient. With the development of innovative computational platforms, the discovery of macrocycle ligands targeting TNFα can be streamlined, potentially accelerating the drug development process.


In summary, macrocycle ligands offer a promising solution for TNFα targeting in drug discovery due to their enhanced binding specificity, ability to engage challenging binding sites, improved pharmacokinetic properties, potential for oral availability, and cost-efficient discovery methods. These attributes make macrocycles an attractive option for developing novel therapeutics against TNFα and other challenging drug targets.


This project is a collaborative project between MEDCHEM.fi, UP-lab, and Aurlide Ltd.

Project Description


Project Title: Rational Design and Development of Macrocyclic Compounds to Inhibit α2β1 Integrin-Collagen Interaction


Project Overview: This project aims to design and develop novel macrocyclic compounds that effectively inhibit the α2β1 integrin-collagen interaction. Building on our previous success with the small molecule inhibitor BTT-3033, we seek to leverage the unique properties of macrocycles to enhance selectivity, potency, and pharmacokinetic profiles. We aim to create new therapeutic agents for preventing and treating thrombotic diseases by targeting this interaction.


Background: The α2β1 integrin plays a crucial role in platelet adhesion and aggregation by mediating the binding of platelets to collagen in the vascular subendothelium. Dysregulation of this interaction contributes to pathological thrombosis, leading to conditions such as myocardial infarction, stroke, and deep vein thrombosis. While BTT-3033 has demonstrated efficacy in inhibiting this interaction, developing macrocyclic compounds offers several advantages, including improved binding affinity, enhanced specificity, and better pharmacokinetic properties.


Objectives:

  • Design Macrocyclic Inhibitors: Utilize structure-based drug design and computational modeling to create a library of macrocyclic compounds targeting the α2β1 integrin-collagen interaction.
  • Synthesize and Screen Compounds: Synthesize the designed macrocycles and perform high-throughput screening to identify candidates with high binding affinity and inhibitory activity.
  • Optimize Lead Compounds: Optimize the lead macrocycles through iterative synthesis and biological testing cycles for improved pharmacokinetic properties, selectivity, and potency.
  • Evaluate in Preclinical Models: Assess the efficacy and safety of optimized macrocyclic inhibitors in relevant preclinical thrombosis models.
  • Prepare for Clinical Development: Advance the most promising candidates towards clinical development by conducting necessary preclinical studies and regulatory assessments.


Methodology:

  1. Structure-Based Drug Design:
    • Utilize the crystal structure of α2β1 integrin and its binding interface with collagen to design macrocyclic scaffolds to disrupt this interaction.
    • Perform molecular dynamics simulations and docking studies to predict binding affinity and selectivity.
  2. Synthesis and Screening:
    • Employ solid-phase peptide synthesis and other macrocyclization techniques to create a diverse library of macrocyclic compounds.
    • Use high-throughput screening assays to evaluate the inhibitory activity of synthesized macrocycles on α2β1 integrin-collagen binding.
  3. Lead Optimization:
    • Conduct structure-activity relationship (SAR) studies to refine the lead compounds.
    • Optimize pharmacokinetic properties through modifications to improve stability, bioavailability, and half-life.
  4. Preclinical Evaluation:
    • Test the optimized macrocyclic inhibitors in in vitro assays for platelet adhesion, aggregation, and activation.
    • Evaluate lead compounds' efficacy in animal arterial and venous thrombosis models.
    • Assess the safety profile through toxicological studies.
  5. Regulatory and Clinical Preparation:
    • Prepare regulatory documentation and engage with regulatory agencies to outline the clinical development pathway.
    • Plan and initiate preclinical studies to support an Investigational New Drug (IND) application.


Expected Outcomes:

  • Identification of potent and selective macrocyclic inhibitors of the α2β1 integrin-collagen interaction.
  • Preclinical validation of lead macrocyclic compounds with demonstrated efficacy in thrombosis models.
  • Advancement of at least one lead macrocyclic inhibitor towards clinical development for preventing and treating thrombotic diseases.


Significance: Developing macrocyclic compounds targeting the α2β1 integrin-collagen interaction represents a novel and promising approach in anti-thrombotic therapy. Macrocycles offer the potential for superior drug-like properties, including enhanced selectivity and pharmacokinetics, which could translate into more effective and safer therapeutic options for patients at risk of thrombotic events. This project aims to expand our therapeutic arsenal and improve clinical outcomes in the management of thrombotic diseases.


Development of Macrocyclic Compounds
Targeting α2β1 Integrin-Collagen Interaction

@elisapostila

Photo by Elisa Postila

Follow us

@medchemfiutu

Institute of Biomedicine

University of Turku

Finland

Contact us

olli@medchem.fi