an expert in fragment-based and covalent drug discovery.

Chief Scientific Officer of Arvinas

Johannes holds a Ph.D. in quantum & molecular mechanics

data science expert

global Head for Data Science at Johnson & Johnson Medical Devices Technology

Vice President of Oncology Research at AstraZeneca

DANIEL K. NOMURA, Ph.D.

Journal of the American Chemical Society. 2018, 140, 8069-8073.

From the molecules in the candidate pool find the one that has the maximum value for its minimum distance to molecules in the picked set (hence the MaxMin name), calculating and recording the distances as required. This molecule is the most distant one to those already picked so is transferred to the picked set.

This furyl amide series was of particular interest due to its starting potency, modular nature, structural properties and absence of reactive functionality found within typical covalent modifiers.

30-min pre-incubation of inhibitors and BTK

In situations where Greek letters are unavailable (for example, on some computer displays), they may be replaced by upper case Roman letters (a = A, p = B, 7 = G, d = D, E = E, 4 = Z, 17 = H).

their structure formed by interrelated dimeric polypeptide chains

Generally the intensity of the detected STD-NMR signal depends not only on the efficiency of the receptor-to-ligand saturation transfer but also on the number of ligand molecules in solution that received saturation from the receptor. Because ligand exchange is in place during the saturation time, long saturation times (up to 3 seconds)8 or high ligand excess (10 to 100 fold), allow transfer of saturation from one receptor molecule to much more than one molecule of ligand.

Normally, for a determinate system the ligand-to-protein ratio and the saturation time have to be selected according to the expected KD

only the signals of the hydrogens that are in closecontact to the protein (e5 Å) and receive magnetization transfer

This value is about 10 times higher than thevalue reported in literature for this system

Thecovalentinhibitordisplayeda5-foldincreasein cellularactivitycomparedto the reversiblecounterpart

To stabilizethe readilyreversiblealdimineadduct,anortho-boronicacidgroupwas included

5MKS

Theirreversiblecovalentinhibitor29displayedsuperiorcellularactivitycomparedtoits reversiblecounterpart

N-a-acetyl-lysine

however, there was noevidence of covalent bonding to the protein.

owever, neither of these two new compounds appeared to form a covalent bond with Cys481 in our crystal structures

the typical concentrations of protein and ligand are 2.0–20μM and0.2–2.0 mM, respectively, the ranges of which may depend on solubility of the chemical compounds inwater or available amounts of both interacting partners

NOE-Based Methods

Ligand-based NMR approaches have limitations with respect to the exchange rate between thetarget protein and ligand compound

the presence of large excess of ligand, the satu-ration of free ligands in solution gets amplified because the relaxation of small molecules is slower than the saturation transfer.

This is in agreementwiththe lackof slowlyexchangingpolarresiduesin the CTBbindingpocket

use of solventsuppression

aromaticproteinspectralregions

theseproton

Anothersourceof minordifferencesinepitopemapsisthesolven

incethefrequenciesof irradiationcan be chosen,we can selectwhattypesof proteinprotonswill be “directlyirradiated”,so thatthe differenceswill highlightpartsof the ligandcontactingthosetypesof proteinresiduesin the boundstate

x 64

WhichDSTD values should be considered significantwill depend on the sizes of the STD factors for the protein-ligand system under study

Y525, which is known to have a very fast kinetics of exchange

the 3D structure of the protein can be used to predict the chemical shifts using existing software

protonated residues within 4 Å

100%D2O

SaturationtransferNMRwasapioneeringtechniquedevelopedin1979

wereobtainedbycollecting128scans

nfact,thereisanincreaseofsensitivitywiththesizeofproteinduetoamoreefficientinter-andintramolecularsaturationtransfer

Usinghigherfieldspectrometerswillmakethemethodevenmoreefficientsincesensitivityandspindiffusionincreasewithfieldstrength

wheatgermagglutinin

thedegreeofsaturationofligandsdependsonthesizeoftheprotein,theoffset,andthedurationoftheon-resonanceirradiation,thedissociationrateconstantkoff,andtheexcessofligand

highturnoverratesresultinalargereffectathigherligand-to-proteinratios.SlowdissociationrateswillyieldsmallerSTDNMRsignalsand,thus,reducesensitivity

The on-resonance frequency needs to be optimized for each protein

excess concentration of ligand

Off‐ratescreening

Thermalmeltmethodsunreliable

nn8

Substitution Count [Query]

restrictingligandconformationalflexibilityacceleratedthebinding

seriesofagonistsoftheA2Aadenosinereceptor

narrowpassageway

diffusion-limitedon-rate(kon109M1s1)

As shown in Appendix B, for the specific case of AMP, we could have reducedthe computational cost grossly by one order of magnitude

For the purpose of comparing the features of the conformational ensemble extracted from ourMD simulations (plain and replica-exchange) to the structures generated by conformer generators(vide infra), we performed a symmetric root mean square displacement-based cluster analysis using thehierarchical agglomerative algorithm

AMBERTOOLS14[59] adopting GAFFparameters [42] for the molecule and the TIP3P model of water

GAUSSIAN09

performs slightly better than some widely-used conformer generation tools when considering boththe abilities to generate high-diversity conformational ensembles and to reproduce experimentally theavailable structures

(i) consistent with that obtained from REMD simulations

there is a negligible impact of these differences on zwitterionicAMP dynamics as sampled alongμs-long MD simulations using both sets of charges

PD3.1)

The selection process from 1000 (seeSupplement Data File S1) to thefinal list of 16 compounds

he enrichment process from thefirst BUDEdocking reduced the number of conformers from 160 millionto 100 000

Timings for Open3DALIGN validation suites

(0.02 s conformation-1)

themixed and atom-based superposition algorithms are thosegiving rise to the most consistent and well-ordered align-ments,

0.6mgof recombinant AR, SRC-3 and p300 proteins were incubated with 200 ng of ARE DNA in the presence of 1mM R1881

AR interacts with SRC-3 through its N-terminal domain (NTD)

AR Recruits SRC-3 and p300 Mainly through Its NTD

Preclinical studies of a p300 inhib-itor also reveal efficacy in patient-derived prostate tumor ex-plants (Butler et al., 2019) and the growth of castration-resistantprostate cancer (Jin et al., 2017)

The rela-tively large-sized AR NTDs, however, wrap around the LBDs,blocking the access of SRC-3 to the LBD. Consequently,SRC-3 is solely recruited by the AR NTD, and p300 recruitmentis stabilized by contacting two AR NTDs

in the presence of 1mM R1881

Based on the structure (Figure 3C), we did not observe thatSRC-3 directly contacts the AR LBDs. The interaction betweenSRC-3 and the AR NTD is clearly observed in our structuraldata

both NTDs also connect toeach other to contribute to AR dimerization

The combination of the anti-body locations, crystal structure docking, and the observed DNA

different conformation of the β-helix region creates a hydrophobic cavity that is absent in tau filaments from the brains of patients with Alzheimer’s disease

astigmatism

additional density—which is not present in the Alzheimer fold—is surrounded by the density of the tau protein chain within the ordered cor

a predominant helical filament type in all three case

FROG2

nscm

Low-MODe (LMOD) optimization methods

LMOD

parm

strip

Coordinates (COORDS) Data Set Commands

cluster

cluster

nscm

ntwr

ntt

tempi

temp0

ntr

ntc

taup

igb

ig

irest

imin

rms | rmsd

Atom Mask Selection Syntax

icrosecond time scale molecular dynamics

Solvent-balance method of computing binding enthalpies.

11

KI-MS2-002

The F2X-Entry Screen is a subset of the F2X-Universal Library

However, for compound libraries witheven smaller compounds (about five to seven non-hydrogenatoms) higher hit rates were reported

the PanDDA approachincreased the hit yield significantl

Of these, 10 hits (10 binding events) were observed onAar2, 11 hits (12 binding events) on RNaseH, and 1 hit (one bind-ing event) at the functional interface of the two proteins

FragMAXapp

numerous commercial libraries are availableon the market, a large subset of them being reviewed in detail

All of the fragment hits in this case were identified through visual inspection of the electron density maps

Soaking each of the compounds at 100 mM yielded 8 structures, 5 of which bound in the active site.

crystallography has become the most popular technique for FBLD

cryoprotectant

1,103-membered F2X-Universal Library

ry presentation of the libraries al-lows CFS campaigns to be carried out with or without the co-solvent DMSO present.

200 μmol/L potential hit compound or 200 μmol/L potential hit compound in the presence of 5 μmol/L protein.

00 μmol/L of the compound mixture

DMSO-d6 stock solu-tions with a group compound concentration of 10 mmol/L were prepared and used for screening

Chemdiv and Enamine,

During the fragment hit-to-lead process, we typically synthesize 50–100 compounds to increase the binding affinity from millimolar to nanomolar, and we routinely generate multiple lead series for each target

emphasizing X-ray crystallography.

the most potent fragment is often not the best starting point for hit-to-lead chemistry.

Although better cross-validation would provide increased confidence in fragment hits, there is a danger that this may also result in the systematic selection of more potent hits,

great importance should be placed on accurately characterizing the solubility of a fragment library

observe a correlation of 30–40% using these two techniques.

use ligand-observed NMR

Another area of active debate centres on the lack of correlation of fragment hits obtained using different detection techniques

that current fragment libraries are largely composed of ‘flat structures’

our results support the view that less complex molecules give a higher hit rat

cryoprotectant

but subsequent trials failed to show any acti

UT-34 induced the regression of enzalutamide-resistant tumors at doses when the AR is degraded

T-34 caused the degradation of the full-length AR, but not the tau-5-deleted AR

SDS-PAGE disrupts noncovalent interactions and is used to determine covalent binding.

chloroform extracts of ten marine sponges werescreened for their antimicrobial activit

more than5000 different compounds have been isolated fromabout 500 species of sponges

Since then well over 14,000 dif-ferent natural products from marine organismshave been described

Dynamic properties of PPAR-γ

Our laboratory recently reported the structure of the intact PPARγ-RXRα heterodimer bound to its idealized DNA site, with coactivator peptides and ligands of both receptors

he studies using the LNCaP xenograft tumor model show that JJ-450 can suppress AR functionin vivo

inhibiting both full-length AR andAR splice variants lacking LBD.

with (
)-JJ-450 beingapproximately 9-fold more potent than (þ)-JJ-450 in the luciferasePSA-reporter assay (24)

Enzalutamide is an inhibitor of androgen-receptor signaling that exerts its activity by binding avidly to the ligand-binding domain of the androgen receptor, competing with and displacing the natural ligands of this receptor (testosterone and dihydrotestosterone)

A 2 fold molar excess of peptide was added to the protein prior to crystallization (RGAFQNLFQSV).

he discoveryof five distinct pockets in these complexes expands the possibilities fortargeting HIF protein activities with drug-like molecules for thera-peutic purposes.

A proposed mechanism by which 0X3 binding candestabilize the HIF-2a–ARNT heterodimer.

. This mech-anistic hypothesis suggests perturbation of a few amino acidresidues within the PAS-B domain is sufficient to disrupt a largeprotein:protein interface leading to complete blockage of HIF2a-driven gene transcription

6TX6, 6TX4, 6TX7, 6TX8, 6TX5 and 6TX9). (

ragment 1

site-identification by ligand competitive saturation (SILCS)

MiniFrags

IkBaphosphopeptide (IPP)

when using miniconda, you can’t move the Amber install folder fromits original location

10.2 inclusive

ecommended choice isgaff2

gamma_ln

OPCwater model in combination with the ff99SB was found to improve, significantly, accuracy of atomistic simulationsof IDPs

ff19SB

wt1mg_min_water

ecommended choice isgaff2

nrt1 deletion

DPI

ramifications

Protein:lipid~3:1

sapiens

Over 60 Drug Discovery Webinars

4 missing angle parameters

Ideally you should really test these parameters (by comparing to ab initio calculations for example) to ensure they are reasonable

parmchk

C, N, O, S, P, H, F, Cl, Br and I

GAFF

the commented Python scripts optFromSmiles.py, optLigandInProtein.py and torsionalScan.py which serve as examplesof simple and constrained MMFF minimizations

ositionalCartesian restraint

The possibility of adding these restrainingpotentials to the force field expression has also beenadded to the existing RDKit UFF implementation

relax ligand-receptor complexeswithout causing major alterations of their originalgeometry, or to perform a torsional scan on a selecteddihedral while relaxing the rest of the molecule.

SARS-CoV PLpro

MONN contains a pairwise interaction prediction module, which can capture the non-covalent interactions between atoms of a compound and residues of a protein with extra supervision from the labels extracted from available high-quality 3D compound-protein complex structures

Arv7

AutoDock Vina ignores the user-supplied partial charges

available

theMMFFMolProperties

MMFFGetMoleculeForceField(),