<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2019-05-08</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001662774</issuerCik>
        <issuerName>Cortexyme, Inc.</issuerName>
        <issuerTradingSymbol>CRTX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001771657</rptOwnerCik>
            <rptOwnerName>Takeda Ventures, Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>435 TASSO STREET, SUITE 300</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>PALO ALTO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94301</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001395064</rptOwnerCik>
            <rptOwnerName>TAKEDA PHARMACEUTICAL CO LTD</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1-1, NIHONBASHI-HONCHO 2-CHOME</rptOwnerStreet1>
            <rptOwnerStreet2>CHUO-KU</rptOwnerStreet2>
            <rptOwnerCity>TOKYO</rptOwnerCity>
            <rptOwnerState>M0</rptOwnerState>
            <rptOwnerZipCode>103-8668</rptOwnerZipCode>
            <rptOwnerStateDescription>JAPAN</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001688140</rptOwnerCik>
            <rptOwnerName>Takeda Pharmaceuticals International AG</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>THURGAUERSTRASSE 130</rptOwnerStreet1>
            <rptOwnerStreet2>8152 GLATTPARK-OPFIKON</rptOwnerStreet2>
            <rptOwnerCity>ZURICH</rptOwnerCity>
            <rptOwnerState>2M</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>GERMANY</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001716229</rptOwnerCik>
            <rptOwnerName>Takeda Pharmaceuticals U.S.A., Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE TAKEDA PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>DEERFIELD</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60015</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Reedemable Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2360071</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Reedemable Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>319731</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The Series A Redeemable Convertible Preferred Stock is convertible into the issuer's common stock on a one-for-one basis and has no expiration date. It will automatically convert into common stock upon the closing of the issuer's initial public offering.</footnote>
        <footnote id="F2">These shares are owned directly by Takeda Ventures, Inc. Takeda Ventures, Inc. is a wholly-owned direct subsidiary of Takeda Pharmaceuticals U.S.A., Inc. (&quot;Takeda USA&quot;). Takeda Pharmaceuticals International AG owns 41.91% of Takeda USA, and Takeda Pharmaceutical Company Limited owns 58.09% of Takeda USA.  Takeda Pharmaceuticals International AG is a wholly-owned direct subsidiary of Takeda Pharmaceutical Company Limited.</footnote>
        <footnote id="F3">The Series B Redeemable Convertible Preferred Stock is convertible into the issuer's common stock on a one-for-one basis and has no expiration date. It will automatically convert into common stock upon the closing of the issuer's initial public offering.</footnote>
    </footnotes>

    <remarks>Exhibit 24.1: Power of Attorney - Takeda Ventures, Inc.
Exhibit 24.2: Power of Attorney - Takeda Pharmaceutical Company Limited
Exhibit 24.3: Power of Attorney - Takeda Pharmaceuticals International AG
Exhibit 24.4: Power of Attorney - Takeda Pharmaceuticals U.S.A., Inc.</remarks>

    <ownerSignature>
        <signatureName>/s/ Christopher Lowe, as Attorney-in-Fact for Takeda Ventures, Inc.</signatureName>
        <signatureDate>2019-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Christopher Lowe, as Attorney-in-Fact for Takeda Pharmaceutical Company Limited</signatureName>
        <signatureDate>2019-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Christopher Lowe, as Attorney-in-Fact for Takeda Pharmaceuticals International AG</signatureName>
        <signatureDate>2019-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Christopher Lowe, as Attorney-in-Fact for Takeda Pharmaceuticals U.S.A, Inc.</signatureName>
        <signatureDate>2019-05-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
